Criteria

• Population from Atlantic Canada (NB, NS, PEI, NL)

• Human genetic data (Whole exome sequencing, whole genome sequencing, panels, individual mutations, other genetic data)

• Case studies (less than 25 people total receiving genetic testing)

• Individual family units

• Small samples sizes (less than 25 people), unless the small sample size is representative of all cases of a condition in a province.

• Non-human genetic data (ex. from animals, viruses, bacteria, etc.)

McKee-Muir, Dyack, Taillon, et al. (2023)¹

IWK REB and Horizon Health Network REB. Waiver of full patient consent was obtained.

30 patients born from 2000–2020 with SMA due to positive SMN1 from the IWK Clinical Genomics Laboratory database and MMGS. (patients from NS, NB, and PEI)

DNA: Not specified.

Additional data from health records at IWK, NS SHARE, and Horizon Health Network (NB).

Performed to detect the homozygous deletion of SMN1 gene exons 7 and 8.

DNA: MMGS clinical database

Heath records: Nova Scotia Secure Health Access Record (SHARE), and Horizon Health Network

No statement on data storage or availability.

Jordan Sheriko, Department of Pediatrics, Dalhousie University, Halifax

jordan.sheriko@iwk.nshealth.ca

Sweeney, Cui, DeClercq, et al. (2017)²

Participants were recruited between 2009 and 2015 with REB approvals in place for all 4 Atlantic provinces. Participants provided consent to be followed over a 30-year period and use of their data by Canadian and international researchers, and a research platform was designed specifically for this purpose.

Harmonized dataset for Atlantic PATH includes 34,000+ participants aged 30 to 69 (expanded to 74 after 2017).

• Questionnaires (demographic, comorbidities, cancer history, lifestyle habits, etc.).

• Physical measures (e.g., BMI, waist, hip)

• Biosamples (blood, urine, saliva and toenail)s. ≥ 1 sample provided by 91% of participants (venous blood provided by 84%).

Once processed, plasma, buffy coat, red blood cells, serum, saliva and urine were transferred to 2-ml cryovials and stored in −80°C freezers. Toenail samples were collected in Ziplock bags and stored in cabinets at room temperature

*Genotyped data are currently available for 1000 participants.

Can be linked to health data from administrative health databases:

• Cancer Registries

• Physician Billing

• Hospital Discharge Abstracts

• Vital Statistics (death)

• Hospital-based and community-based ambulatory care, including emergency rooms.

Application for data process is found here: Data Access Process – Atlantic PATH

Levesque, Wood, Carter, et al. (2023)³

Ethics approval from the Nova Scotia Health Research Ethics Board (1026033).

*Consent not noted.

Nova Scotians diagnosed with endometrial cancer between 2017 and 2020. Tumour IHC staining was performed in 444 patients. 98 Received germline testing, 9 with germline tested had Lynch syndrome mutation

DNA sample (germline testing): Not stated

Tumor biopsy and staining

Also: Age, body mass index, tumour mismatch repair protein immuno­histochemistry results, personal and family histories (from patient charts and Tupper gynecologic database (internal database)

Specific genetic tests and level of availability of data to researchers not stated. Germline testing results, and personal and family histories of Lynch-associated malignant disease for all eligible patients were extracted from medical genetics records by an endometrial cancer, MMGS genetic counsellor.

Data used in this study are available in an unidentified, coded format from the first author on reasonable request: Marianne.levesque@dal.ca.

Dr. Katharina Kieser

Dalhousie University; Maritime Medical Genetics Service, IWK Health Centre; Division of Gynaecologic Oncology, Department of Obstetrics and Gynaecology, Dalhousie University, Halifax, NS

kkieser@dal.ca

Allen, Schollenberg, Aberg, and Brock (2025)⁴

IWK Health Research Ethics Board approval obtained May 21, 2019 (File #1024606), with annual renewal approval. IWK Health REB approved the Waiver of Consent due to impracticability.

Retrospective cohort (derived from the IWK Health Clinical Genomics Laboratory Information System) of 593 fetuses that had genetic testing performed due to structural anomalies identified by ultrasound in the Maritime Provinces from 2014 to 2022.

DNA Samples: chorionic villus sampling, amniocentesis, fetal blood, and products of conception Data combined with maternal health records review, EMR chart reviewed when appropriate.

First tier testing included rapid aneuploidy detection (RAD) and CMA, with subsequent sequence-based testing reserved for those cases meeting the selected testing criteria.

Results of genetic testing, including RAD, karyotype, microarray (done in-house at IWK Health CGL), and gene sequencing (Single genes and small gene panels performed at the IWK CGL, larger gene panels and exomes performed and reported by referral laboratories.)

For each eligible prenatal, cord, and newborn sample, an electronic health records chart review identified specific ultrasound findings, findings from other imaging modalities, involvement with medical genetic specialties, postnatal findings, and clinical outcomes including gestational age at delivery and pregnancy complications placental insufficiency, as well as newborn examination and autopsy findings.

Dr. Victoria Allen

Department of Obstetrics and Gynaecology

Dalhousie University and IWK Health, Halifax, Canada

victoria.allen@dal.ca

Dr. Victoria Allen

Department of Obstetrics and Gynaecology

Dalhousie University and IWK Health, Halifax, Canada

victoria.allen@dal.ca

Guernsey, Matsuoka, Jiang, et al., (2011)⁵

*Letter

Approval for the research study was obtained from the IWK Health Centre and CHU Ste-Justine research ethics boards. Informed consent was obtained for all participants in the study.

5 individuals with Meier-Gorlin syndrome:

1 Maritime-Acadian, 2 Quebec and 2 Louisiana-Acadian families (individuals 1652, 1768, 1882, 1899 and 1627)

314 local Maritime control chromosomes, which (include a substantial proportion of Acadians).

DNA Sample: blood samples

Also, anthropometric measurements

High density genome-wide SNP genotyping using Illumina Human 610K panel of approximately 600,000 markers, used PLINK to search for shared haplotypes among subsets of the genotyped individuals

Case and control samples sequenced at McGill University and Genome Quebec Centre for Innovation. Sequence traces analyzed using Mutation Surveyor.

Illumina used to sequence data.

Data from this study deposited in the RefSeq database under the following accession codes: human ORC4 mRNA, NM_002552; human ORC4 protein, NP_ 002543; human ORC1 mRNA, NM_004153.3; human ORC1 protein, NP_004144.2; human CDT1 mRNA, NM_030928.3; human CDT1 protein, NP_112190.2.

Mark E Samuels

mark.e.samuels@umontreal.ca

Kokorovic, Thomas, Serrano-Lomelin et al., (2020)⁶

No research ethics approval listed.

*Secondary data sources, no patient consent.

75 patients/family members who were evaluated for hereditary RCC syndrome and received genetic testing from January 2006 until December 2017 (collected retrospectively) received genetic testing

Clinical, pathological, and genetic analysis data.

Panel for genetic testing including FH, FLCN, MET, PTEN, SDHB, SDHC, SDHD, TMEM127, and VHL genes. Genetic testing was performed by the Clinical Genomic Laboratory, IWK, Halifax; Leeds Genetics Laboratory (Molecular Genetics), St. James’ University Hospital, Leeds, UK, or Blueprint Genetics, Helsinki, Finland.

*Level of detail with genetic results available to researchers unclear

*No statement on data availability.

Dr. Ricardo A. Rendon

Queen Elizabeth II Health Sciences Centre, Halifax, NS, Canada; rrendon@dal.ca

Walsh (2001)⁷

Ly, Walsh, and Pasternak (2012)⁸

Fleming, Ly, Pasternak et al. (2014)⁹

Carter, Gaston, Huang, et al. (2018)¹⁰

DeCoste, Carter, Pasternak, et al. (2021)¹¹

DeCoste, Walsh, Gaston, et al., (2022)¹²

study approved by the Capital Health Research Ethics Board, Halifax, Nova

Scotia.

(REB #1021594)

*No mention of participant consent to study or secondary use.

Total of 142 study cases submitted through the Pathology Department of the Victoria General Hospital/Queen Elizabeth II Health Sciences Centre in Halifax, identified through a search of laboratory computer records and review of a previously published case series of MCCs. All cases diagnosed between 1989 and 2020. Only those with available paraffin-embedded tissue samples included.

42 primary MCCs,13 MCC metastases, 57 non-MCC cutaneous lesions, 15 pulmonary neuroendocrine carcinomas and 15 GI NETs were included.

Clinical information was obtained from pathology requisition forms, requesting physicians, and pathology reports.

Thirteen MCC metastases were examined. Ten of these metastases were derived from 8 primary PMCC and 2 primary CMCC tumours already included in the study.

No genetic testing conducted. IHC was performed on paraffin-embedded archival tissue to detect positivity for CK20 and CM2B4⁷

For 83 cases in 2014, new slides were cut from archived paraffin-embedded tissue blocks and stained with p63 as per the manufacturer's instructions (Clone BC4A4 [Biocare Medical, Concord, CA), CC1 antigen retrieval and iView Kit detection method [Ventana])⁹

46 cases, 21 pure Merkel cell polyomavirus (MCPyV)+, 10 pure MCPyV−, and 15 combined MCPyV− MCCs. DNA (80 ng) from each sample was probed with SNP-containing oligonucleotides targeting interrogation sites of 40 base pairs. Genome-wide CNA studies were performed for from 28 MCCs (9 MCPyV+, 9 MCPyV−, and 10 combined tumours). DNA from all 46 cases was analyzed by NGS using a custom set of primers for 8 tumour suppressor genes and 1 oncogene previously shown to have inactivating and activating mutations in MCC, (TP53, RB1, APC, NOTCH1, NOTCH2, MLL2, MLL3, BRCA1,and PIK3CA)¹⁰

NGS of 51 cases were selected primary cutaneous Merkel cell carcinomas (21 MCPyV +, 13 pure MCPyV− and 17 combined MCPyV−) derived from the Maritime region of Canada (1993 to 2020).extracted DNA was analyzed via the Illumina TSO500 hybrid capture DNA panel, performed on an Illumina NextSeq550 instrument (San Diego, CA), in accordance with the manufacturer's instructions. The panel analyzes 523 cancer-related genes for small mutations, a subset of genes for copy number gains, as well as global parameters of tumour mutation burden (TMB) and microsatellite instability (MSI) Cases with median exon coverage < 100x (unique reads employed for all thresholds) were excluded from analysis^11,12

*These cases were obtained through medical points of contact and patients required information on tests performed, therefore these are likely likable to administrative data.

DNA was extracted using QIAamp DNA FFPE (Qiagen Inc, Valencia, CA) or MagNA Pure Compact (Roche, Basel, Switzerland) commercial kits and quantitated using the Qubit dsDNA BR kit (Thermo Fisher Scientific Inc, Grand Island, NY). Affymetrix (Santa Clara, CA), conducted genome-wide CNA studies using the OncoScanFFPE gene chip probe array,

Next-generation DNA sequencing data were processed using an in-house bioinformatics analysis pipeline conducted on an Illumina MiSeq gene sequencer (San Diego, CA). Processed using Picard and the Genome Analysis Toolkit following community-developed best practices. Copy number aberration data from each sample were analyzed using Nexus Copy Number version 9.0 (BioDiscovery, El Segundo, CA).¹⁰

Data were first analyzed using Illumina's TSO500 LocalApp workflow for alignment and variant calling of mutations 33 cases (9 MCPyV+, 10 pure MCPyV− and 14 combined MCPyV−) were sent to Mayo Clinic Laboratories (Rochester, MN) for Rb immuno­histochemical (IHC) staining, which was performed in accordance with their institutional protocols.

The datasets used and/or analyzed during the current study are available from the corresponding author on reasonable request. ^11,12

Dr. Sylvia Pasternak

Dalhousie University

Department of Pathology Halifax, Nova Scotia,

sylvia.pasternak@nshealth.ca

Noreen M.G. Walsh, MD, Division of Anatomical Pathology, Queen Elizabeth II Health Sciences Centre, Halifax, NS Canada

Dr. Ryan C. DeCoste

Department of Pathology and Laboratory Medicine, QEII Health Sciences Centre), Halifax, NS, ryan.decoste@dal.ca

Li, Wang, Lee et al., (2021)¹³

Patients with exfoliation syndrome were enrolled following informed consent. Both studies approved by the REB of the NSHA (protocols 1011873 and 1020512).

Multiple cohorts from multiple countries included

403 cases, 392 controls included from NS (Supplemental materials)

Reference controls were obtained from the DNA diagnostic laboratory serving the same population.

All participants were of self-reported European ancestry.

Venous blood samples

Eye testing results

NS participants underwent whole exome Sequencing during first validation stage

Whole-exome sequencing and targeted sequencing (targeting the CYP39A1 [Refseq NM_016593] coding sequence) libraries were prepared using hybridization capture kits (Roche-Nimblegen SeqCap)

Cases and controls sequenced together using 2 × 151 base-pair, paired-end reads on Illumina instruments.

Raw DNA sequence reads from the Illumina HiSeq 4000 and Novaseq 6000 instruments were aligned to the hg19 genome build. Variant detection was performed using exons and 50 base-pair regions flanking the exons.

DNA sequence reads were mapped using Burrows-Wheeler Aligner software (version 0.7.16a-r1181). Variant calling was performed using the Genome Analysis Tool Kit (version 3.7) and the Picard (v

*No statement of data availability

*unclear if data can be linked to administrative data

Chiea Chuen Khor, MD, Ph.D., Genome Institute of Singapore, 60 Biopolis St, 02-01 Genome Bldg, Singapore 138672 (khorcc@gis.a-star.edu.sg

Aung, Ozaki, Lee et al., (2017)¹⁴

For Canada, individuals with Exfoliation syndrome were enrolled following informed consent from within the Nova Scotia Health Authority (NSHA), Nova Scotia (protocols 1011873 and 1020512)

World-wide GWAS partnership study (Canada): 341 cases and 247 controls

Canada Replication:136 cases, 747 controls

All participants were of self-reported European ancestry

DNA samples obtained from ocular tissues

Deep sequencing was performed on a total of 5,570 XFS cases and 6,279 controls from 9 countries (excluding Canada (NS)).

A genome-wide association study (GWAS) of Exfoliation syndrome cases and controls from 24 countries (including Canada) followed by replication in 18 countries (including Canada) identified 7 genome-wide significant loci.

Genome-wide genotyping was undertaken using the Illumina OmniExpress BeadChip.

All 9,035 XFS cases and 17,008 controls for the GWAS discovery stage genotyped using Illumina OmniExpress array.

In the replication stage, direct genotyping using the Sequenom Mass-Array and Applied Biosystems Taqman genotyping platforms was carried out for cases and controls from Nova Scotia (Supplemental materials).

Tin Aung

Dept of Ophthalmology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore

aung.tin@singhealth.com.sg

Francesca Pasutto

Institute of Human Genetics, Friedrich-Alexander-Universität, Erlangen-Nürnberg, Erlangen, Germany

Francesca.Pasutto@uk-erlangen.de

Janey L. Wiggs

Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts, US

Janey_Wiggs@meei.harvard.edu

Chiea Chuen Khor

Genome Institute of Singapore, Singapore

khorcc@gis.a-star.edu.sg

Cutler, Knopf, Campbell, et al., (2021)¹⁵

Conducted under ethical approval by the Nova Scotia Health Authority (NSHA) Research Ethics Board (1021520 and 1021397), and patients provided written informed consent for research.

77 patient samples (from 76 patients) bone marrow was collected from patients with plasma cell dyscrasias at the Victoria General Hospital (Halifax, NS, Canada)

Patient bone marrow samples laboratory data, including albumin, Beta₂-microglobulin, lactate dehydrogenase, bone marrow plasma cell burden, serum M-protein quantity, immunoglobulin heavy and light chain type and quantity, serum free light chain ratio, and FISH data, coinciding with the time of bone marrow acquisition, were collected from the NSHA laboratory information system. Patient clinical data, including age, sex, diagnosis at time of bone marrow acquisition, therapies received, follow-up period, stage, and time of events, were also collected from the NSHA hospital information system.

A custom panel to target exons of these 26 genes was designed using Illumina DesignStudio (Illumina, San Diego, CA).genes that were mutated in > 1% of the population of patients were included (25 genes) in published WES and WGS studies as well as MYC.

MM-specific targeted-sequencing approach using a custom-designed 26-gene panel, the DMG26, that is applicable in a standard clinical molecular laboratory and demonstrates that the DMG26 captures prognostically relevant genomic abnormalities that are distinct from those captured by FISH.

Genomic data generated during this study are available on request, with access managed by the Dalhousie Pathology Biobank. All programming scripts used in this work are available at GitLab, last accessed November 25, 2020).

DNA library preparations for the DMG26 panel were performed per Illumina TruSeq and AmpliSeq for Illumina custom panel reference guides.

Libraries were sequenced in 2 runs on an Illumina MiSeq at a mean depth of approximately 1000 times. FastQ files were analyzed using an in-house bioinformatic pipeline

Data is linkable to administrative health data

Daniel Gaston, Ph.D.,

5788 University Ave., Halifax, NS, Canada.

dan. gaston@nshealth.ca

Robitaille, MacDonald, Kaykas, et al., (2002)¹⁶

IWK Health Centre Research Ethics Board and the Oakland University Institutional Review Board of Human Subjects Investigation Committee approved these studies. Informed consent obtained.

81 subjects: 27 people with FEVR from NS and 54 of their family members without FEVR

DNA from blood samples

Determined genotypes of 8 family members using 6 DNA markers (D11S1887, D11S896, D11S4082, D11S1780, D11S873 and D11S1311) from the EVR1 locus.

Performed Linkage analysis after collection of samples from additional family members with 4 Genethon (D11S1887, D11S4082, D11S1780, D11S1311) and 2 Marshfield markers (D11S896, D11S873). Examined an additional 11 Genethon, 7 CHLC and 9 novel CA-repeat markers (33 total)(fine mapping).

Haplotype construction using 33 polymorphic markers revealed 5 proximal and 4 distal recombination’s (5 were affected, 4 unaffected).

Analyzed the coding regions of FZD4 and FLJ22104 for mutations 3 family members (2 affected, 1 unaffected) by sequencing PCR amplified fragments.

Used PCR–RFLP analysis and fluorescence capillary electrophoresis to screen the remainder of the family and a control population for presence of mutations observed in the affected individuals. Detected both the M493_W494del and L501fsX533 mutations.

Genotyping using marker sequences from the Genome Database on an Applied Biosystems Prism 3100 Genetic Analyzer running GeneMapper software (Applied Biosystems), and we verified mendelian inheritance of alleles using the PedCheck program performed two-point linkage analysis using the MLINK program version 4.1p from the FASTLINK software package, and multipoint linkage analysis using VITESSE version 1.0 and SIMWALK version 2.8, assuming a disease allele frequency of 0.000

Designed intronic primer pairs for each exon in FZD4 and FLJ22104 using the Primer3 program.

Used an Applied Biosystems Prism 3100 Genetic Analyzer to detect M493_W494del and L501fsX533 mutations.

Dr. Michael R. Hayden

Xenon Genetics, Inc.,

Burnaby, BC

mrh@cmmt.ubc.ca

Ells, Guernsey, Wallace et al., (2010)¹⁷

Approvals obtained from IWK Health Center, Calgary Health

Region (Alberta Children’s Hospital site), and the St

Joseph Health Care London. Consent obtained according to the Canadian Tri-Council guidelines.

104 premature infants recruited both prospectively and retrospectively between March 1, 2003 and April 30, 2008, 71 with severe ROP, 33 mild to no ROP.

173 random Canadian samples

*Number from NS not stated

Tissue samples (blood or buccal swabs)

Direct automated sequencing of the 2 coding exons of the FZD4 gene. Mutation detection was performed both manually and using Mutation Surveyor

Primers can be requested from the corresponding author.

*No other statements of data availability.

Johane Robitaille

Eye Care Team, IWK Health

Center, University Ave.

Halifax, Nova Scotia

Canada. E-mail: jrobitai@dal.ca

Robitaille, Gillett, 

LeBlanc et al., (2014)¹⁸

Approved by IWK REB. Written informed consent obtained from participant

72 probands recruited from April 1998-September 2013. Unclear how many from Halifax.

DNA extracted from blood or saliva samples

Collected clinical data retrospectively.

WES conducted.

Also direct automated Sanger sequencing of 2 coding exons of the FZD4 gene, the 23 coding exons of the LRP5 gene, and 22 coding exons of the KIF11 gene.

WES conducted at McGill University and Genome Quebec Innovation Centre. DNA sequenced with 100 base pair paired-end reads (HiSeq 2000 sequencer; Illumina). Genomic variants called using Genome Analysis Toolkit pipeline and annotated with ANNOVAR.

Specific exons sequenced using Sanger sequencing performed with ABI PRISM 3100 Genetic Analyzer and mutation calling was done by Mutation Surveyor, version 3.97)

Dr. Johane M. Robitaille

University Avenue, PO Box 9700, Halifax, NS, jrobitai@dal.ca.

van der Ende, Bedard, Wallace, et al., (2025)¹⁹

Approved by the REB of the IWK Health Centre. Consent obtained in accordance with Declaration of Helsinki.

Patients with retinal features compatible with FEVR, affected relatives, and 1st-degree relatives were recruited between 1998 and 2024. Excluded people with retinopathy of prematurity. 94 people (76 had WES, 18 had Sanger sequencing data.)

DNA was extracted from peripheral blood or saliva samples

Also: results from eye examinations and IV fluorescein angiography and fundus photography (if available). Ethnicity provided at discretion of referring physician.

Sanger sequencing was used to identify rare variants in known genes, and this method alone identified a molecular diagnosis for 18 probands. 76, including 2 diagnosed with Sanger sequencing in prior publications.

A virtual FEVR gene panel was used in those 76 probands to identify variants in FZD4, LRP5, TSPAN12, NDP, ZNF408, CTNNB1, KIF11, ATOH7, ILK, JAG1, TGFBR2, RCBTB1, DOCK6, ARHGAP31 (, NOTCH1, CTNNA1, CTNND1, DLG1, COL9A1, LRP6, TUBGCP4, TUBGCP6, PLK4, CDK19, and LAMA1.

At minimum, the Gene, Nucleotide Change, Amino Acid Change, Variant Type, REVEL, CADD, SpliceAI, gnomAD, Sex, ACMG ranking, SVI evidence were collected.

WES completed using Illumina NextSeq 550.

Genomic variants called using the Genome Analysis Toolkit and Picard.

Variants were annotated with Annovar and compared against dbSNP, 1000 Genomes project, and the genome aggregation dataset version 4.

No statement of data availability.

Data likely linkable to administrative health data as patents recruited through health care system.

Dr. Johane M. Robitaille

University Avenue, PO Box 9700, Halifax, NS, jrobitai@dal.ca.

Christopher R. McMaster, Department of Pharmacology, Dalhousie University Halifax, NS, christopher.mcmaster@dal.ca

Sinha, Gaston, Manders, et al., (2018)²⁰

Approved by our institutional research ethics board.

All colonic tumours (269?) with a previous diagnosis of MANEC, high-grade NEC, and adenocarcinoma with neuroendocrine differentiation were retrieved from the archives of the Department of Pathology, QE II Health Sciences Center, between July 2000 and July 2015.

269 colorectal adenocarcinomas used as controls

Tumor samples. Samples de­identified, and tissue cores obtained from an area containing at least 80% viable tumour cells.

Immuno­histochemistry (IHC) of tumour sections

Sought to identify unique chromosomal alterations of MANEC and NEC by comparing their genome-wide CNAs to those of 269 conventional adenocarcinomas characterized the genome-wide copy number aberrations of 14 MANECs and 5 neuroendocrine carcinomas using the OncoScan FFPE (Affymetrix, Santa Clara, CA) assay.

Genomic Identification of Significant Targets in Cancers algorithm identified 7 peaks that drive the tumorgenesis of MANEC.

Genomic Identification of Significant Targets in Cancer (GISTIC) analysis was used to distinguish significant chromosomal aberrations from random background.

CNA data generated for colonic MANEC and NEC were compared colorectal adenocarcinomas.

For statistical comparison of copy number alternations between MANEC and adenocarcinoma, false discovery rate–corrected Ps were then obtained using the Benjamini-Hochberg procedure.

MSI kit from Promega (Madison, WI): The presence of the BRAF V600 mutation was detected using a SNaPshot-based assay that can detect the V600E, V600K, V600M, V600R, and V600D mutations

comparison colorectal adenocarcinomas investigated and analyzed by the OncoScan FFPE assay and Nexus copy number software the OncoScan FFPE assay from Affymetrix (Santa Clara, CA) was performed on 19 samples.

Raw data analyzed using Nexus Copy Number 7.5 Discovery Edition software (BioDiscovery, El Segundo, CA).

Dr. Weei-Yuarn Huang

Division of Anatomical Pathology, Queen Elizabeth II Health Sciences Centre and Dalhousie University, Halifax, Nova Scotia, Canada B3H 1V8. huangw@nshealth.ca

Hou, Heilbronner, Degenhard, et al. (2016)²¹

Stone, Nunes, Akiyama, et al. (2021)²²

O’Connell, Lee, Koromina, et al. (2025)²³

Written informed consent was obtained from all participants. Ethical and regulatory approvals were obtained at each site that contributed anonymized data and DNA to the analysis.

GWAS of lithium response in 2563 patients with DSM III or DSM-IV diagnosis of a bipolar spectrum disorder, collected by 22 participating sites from the International Consortium on Lithium Genetics. Patients required to have taken lithium for ≥ 6 months with no additional mood stabilizer (2008 and 2013). One site was Halifax. They conducted GWAS in 2 parts: Halifax: 353 total, GWAS 1: 241, GWAS 2: 112

Whole blood samples.

assessment methods: semi-structured clinical interviews (clinical), medical records, registries and questionnaire data (community) and self-reported surveys)

largest-ever set of genomic data from BD patients treated with lithium for maintenance therapy over a duration of at least 1 year, from 14 international site members of the Consortium on Lithium Genetics (ConLiGen) and 79 cohorts.

A total of 3193 participants were genotyped; 2563 remained after quality control (1162 in GWAS 1 and 1401 in GWAS 2). Data from common single nucleotide polymorphisms (SNPs) were tested for association with categorical and continuous ratings of lithium response. Lithium response was measured using a well established scale (Alda scale). Identified 337 linkage disequilibrium-independent genome-wide significant variants that map to 298 loci

Samples were genotyped at the National Institute of Mental Health (Bethesda, MD, US), Life and Brain Center at the University of Bonn (Bonn, Germany), or Broad Institute (Cambridge, MA, US) using either Affymetrix or Illumina SNP arrays

Halifax: 241 individuals genotyped with an SNP array from Illumina Omni1-Quad in GWAS1 and 112 individuals genotyped with Illumina OmniExpress 1·1 in GWAS 2 (supplementary materials). After basic quality control and linkage disequilibrium (LD) pruning, about 40K directly genotyped SNPs shared across all SNP arrays were used for the relatedness testing by PLINK.

Thomas G Schulze, Institute of Psychiatric Phenomics and Genomics (IPPG), Medical Center of the University of Munich, Munich, Germany

thomas.schulze@med.uni-muenchen.de

McAusland, Burton, Bagnell, (2024)²⁴

*Study protocol* Not yet conducted

Eligible youth will complete the consent form and may opt-in to long-term storage of their DNA sample. In some cases parental consent will be obtained with youth assenting to participate.

The goal is to recruit 13,000 youth aged 10 to 19 of which 50% are expected to endorse symptoms of anxiety that indicate the presence of an anxiety disorder. The GAYA study with local sites in Calgary, Halifax (IWK Health Centre community), Hamilton, and Vancouver. Clinical recruitment approach and online recruitment (Social media content and visuals)

An OG-600 Oragene saliva DNA sample kit or choose to have an OCR-100 ORA collect DNA sample kit mailed to their home with a pre-paid return envelope. Also, participants will be asked to complete the Screen for Child Anxiety Related Emotional Disorders (SCARED), the Short Mood and Feeling Questionnaire (SMFQ), the CPSS-SR-5, the Behavioural Inhibition and Behavioural Activation System (BIS/BAS) scales. Also 5 optional surveys.

Genetic Architecture of Youth Anxiety (GAYA):

De-identified research IDs will link data and saliva samples. The linked IDs will be logged in REDCap to document and track the handling of biologic samples.

DNA extraction from saliva is performed at each individual site following best practice and according to the manufacturers’ protocols. Subsequent genotyping will be performed in 3 batches. All individuals will be genotyped.

genotyped (using DNA from the saliva samples) with Illumina’s Global Screening Array v3.0 (GSA).

For genotyping calling Illumina’s GenomeStudio will be used. Spit for Science genotyping will be done locally using the same Illumina array and their genetic data are sent to the Halifax site once the participant has completed the questionnaires and/or app portion of the study.

Dr. Laina McAusland

Department of Psychiatry, University of Calgary, Calgary, AB, Canada

Kmochová, Kidd, Orr, et al. (2024)²⁵

Approved by Nova Scotia Health REB

5 families found to have autosomal dominant medullary amyloidosis due to 2 different pathogenic APOA4 variants. From sites in United States, Czech Republic, and Nova Scotia, Canada (at least 32 people from 1 family)

Whole blood or whole saliva

Whole exome of whole genome sequencing underwent whole genome sequencing with identification of a chr11:116692578 G>C (hg19) variant encoding the missense mutation p.L66V of the ApoA4 protein.

Sanger Sequencing

Dr. Anthony Bleyer

Wakefeild School of Medicine

Winston-Salem, North Carolina

ableyer@wakehealth.edu

Ouellette, Richard, and Maïcas, (2004)²⁶

REB approval not specified.

Consent for both surgical procedures and SLN analysis was obtained from all patients.

53 consecutive patients (42 patients retained for analysis) with breast CA (cases) and 25 patients with melanoma (controls) at CHU Dumont from 1999 to 2002.

SLN biopsy

RNA and DNA from samples assessed for genes coding for MGB1 and MGB2 using PT-PCR testing.

Not specified.

Not specified.

Dr. Rodney Ouellette, MD Ph.D.

Dr Georges-L. Dumont Hospital

University of Moncton

Gauvin, Allain, Bouhamdani, Williams, et al. (2025)²⁷

Approved by the Vitalité Health Network REB (#101703). No consent due to retrospective design

445 participants from NB (Acadian and French Canadian, European descent (non-French or Acadian), South-American, Native American, African or Asian origins) tested for hereditary breast C gene from 2019 to 2022

Not specified.

Data on other health information collected from patient charts.

Multi-gene panel testing (268), or targeted predictive testing for a known familial variant (39) for genes known to be associated with breast CA.

Genetic testing performed by Fulgent Genetics or GeneDx.

Paired-end sequencing with Illumina sequencers.

Data is available upon request.

Eric Allain

eric.allain@vitalitenb.ca

Mouna Ben Amor

mouna.benamor@vitalitenb.ca

Northrup, Maybank, Carson, et al. (2020)²⁸

Approved by the Horizon Health Network REB

178 (156 from Saint John, 22 other locations) randomly selected specimens from patients with Myeloid Neoplasms submitted for the NGS Ion AmpliSeq Myeloid Panel (2017) or the Oncomine Myeloid Panel (Thermo Fisher)(2018)

43 bone marrow aspirates and 136 peripheral blood samples

NGS of a genetic panel of genes related to hematologic malignancies

Additionally, karyotyping done in 75 cases

Library preparation performed using Ion AmpliSeq Myeloid Panel (145 samples) or Oncomine Myeloid Panel (33 samples) at the Saint John Regional Hospital.

Victoria Northrup, MSc,

Dalhousie Medicine NB, Saint John, Canada; and Departments of Laboratory Medicine and Research Services, Saint John Regional Hospital, Saint John, Canada.

Robichaud, Allain, Belbraouet et al. (2022)²⁹

Vitalité Health Network REB

Consent obtained from all subjects for DNA collection and project participation

60 from Southeast NB (all at least 1 Acadian grandparent born in the region)

*Plans to expand to more areas of NB

DNA samples collected using the Oracollect DNA buccal swab from DNA Genotek inc.

DNA from oral swabs was extracted by Fulgent Genetics.

WES of 312 autosomal recessive and 30 X-linked diseases connected with French ancestry

NGS libraries generated using modified KAPA DNA Library.

Prepared DNA libraries sequenced using a HiSeqX or NovaSeq 6000 from Illumina inc. (San Diego, CA, US).

Data restricted due to higher risk of re-identification from genetic information

Dr. Mouna Ben Amor

Department of Medical Genetics, Vitalité Health Network, Dr. Georges L.-Dumont University Hospital Centre, Moncton

mouna.benamor@vitalitenb.ca

Roy, Wajnberg, Ouellette, et al. (2023)³⁰

Approval obtained from Vitalité Health Network REB consent obtained from patients

16 PDAC patients and 13 non-affected individuals

Plasma samples

Assessed utility of the Vn96 synthetic peptide for the isolation of extracellular vesicles from human plasma and the subsequent detection of small RNA biomarkers of PDAC by NGS analysis.

Tumoral Biobank at CHU Dumont and the Ontario Pancreas CA Study at Mount Sinai Hospital (Toronto, ON).

No statements of data availability.

Stephen M. Lewis

Atlantic Cancer Research Institute, Moncton, NB, Canada

Beatrice Hunter Cancer Research Institute, Halifax, NS, Canada

Department of Chemistry and Biochemistry, Université de Moncton, Moncton, NB, Canada

stephenl@canceratl.ca

Zurel, Bhérer, et al. (2025)³¹

Gilbert, Zurel, et al. (2023)³²

NLGP protocol was approved by the NL Health REB (#: 2018.243).

Participants consented to secondary use, pending access requests for scientific research through Sequence Bio board.

Random recruit­ment of partic­ipants from general practice clinics across the province aged ≥ 18 years, possessed a valid NL health card, and provided written consent.

2,500 participants total, including people of Indigenous heritage, 1,807 NL individuals of European descent for the NLGP cohort.

Additionally, included data from the Irish DNA Atlas and the People of the British Isles.

Saliva samples were obtained and medical histories provided by all 2,500 participants. Information also collected on religion and the birthplace of their parental ancestors.

Targeted SNP genotyping: 1,110 Y chromosomes from an NL-based cohort were analyzed using 5,761 Y-specific SNPs.

Y-chromosome haplogroup comparison – compared SNP data with Irish DNA Atlas and People of the British Isles.

Rare variant analysis – checked 2,114 Y-SNPs against the gnomAD database to find population-specific markers.

Phylogenic tree was constructed using the SNP data from the haplotype analysis.

WGS was conducted. A quality threshold of 99.2% SNP pass rate per sample resulted in 2,446 individuals and 1,721,246 SNPs passing initial genotyping QC.

Used Linkage disequilibrium and haplotype analyses comparing to SNPs from other datasets to determine participants with European ancestry from this paper. This resulted in 1,807 individuals and 685,221 common SNPs.

performed haplotype-based clustering using fineSTRUCTURE

identified 22 discrete clusters which summarize fineSTRUCTURE’s

DNA extracted from these samples was genotyped using the Illumina Global Diversity Array (GDA; Illumina, San Diego, CA).

fineSTRUCTURE. was used for LD and haplotype analyses.

The genotype and sample metadata from the NLGP are not publicly available due to participant recruitment conditions and consent agreements that protect the privacy of NLGP participants. Researchers interested in accessing the NLGP data are encouraged to contact Sequence Bioinformatics (info@sequencebio.com).

Michael S. Phillips

Sequence Bioinformatics Inc., St. John’s, NL

pgxdoc@gmail.com

Dr Edmund Gilbert

School of Pharmacy and Biomolecular Sciences, Royal College of Surgeons in Ireland, Dublin, Ireland

FutureNeuro SFI Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland

edmundgilbert@rcsi.ie

Rahman, Jones, Curtis, et al. (2003)³³

No mention of consent or REB

200 consecutive unrelated individuals presenting to a blood collection service in St John’s. Recruited subjects from St John’s because it represents the ‘worst case’ scenario in demon­strating extended LD in NL

Blood samples

Genotyped > 1,300 individual SNP sites but > 200 of these sites on the chip consistently failed, yielding most of the no-signal calls so only 1,064 markers were analyzed.

Estimated the LD between 2 SNPs using the standardized multiallelic disequilibrium coefficient D

genotyped 200 done by estimating haplotype frequencies for the 200 subjects using the EH program limited analyses to the 591 marker pairs.

Genotyped using the Affymetrix HuSNP protocol according to the manufacturer’s instructions.

No statements of data availability.

Dr. Proton Rahman had full access to data

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Zhai, Zhou, Woods, et al. (2016)³⁴

Approved by the NL Health REB. As part of a colorectal cancer research study

494 unaffected individuals recruited between 2001 and 2003 by random digital dialing across the NL to serve as controls

Age matched to cancer patients but only inclusion criterion was the absence of a personal history of colorectal cancer. 52 individuals with < 2 generations of NL ancestry were excluded.

Reference populations include Irish (211), British (450), Native American (108) and HapMap3 popu­lations.

Individ­uals with > 3% missing SNP data were excluded, as were SNPs that were not successfully typed in > 5% of partici­pants.

Provided a blood sample for DNA extraction

Gave information on their family sufficient to construct ≥ 3-generation pedigree

Used public records to determine the historic religious affiliation of each family

Provided questionnaire that gave information on personal, parental and grand-parental ethnicity.

Public list of names on the Qalipu Mi'kmaq First Nation Band Order, with genealogical methods, used to confirm ancestral connection to Aboriginal populations.

WGS using 1.2 million SNPs

multidimensional scaling (MDS) analysis were carried out using PLINK. First included all 14 populations; the second included the NL, IRE, BBC and NAS data; the third included only the NL, IRE and BBC data

Linkage disequilibrium was also conducted 86 individuals randomly selected from each population.

genome-wide SNP data

genotyped using an Affymetrix Axiom Genome-Wide Array

The genotype data of the NL samples are available with accession number GSE74392. Religion/ethnicity data of the NL samples are available at request to the author (guangju.zhai@med.mun.ca) subject to an appropriate ethics approval.

genotyping of the NL samples conducted by Dr Stephen B Gruber, USC Norris Comprehensive Cancer Center, University of Southern California as part of the ColoRectal Transdisciplinary Study (CORECT). The study makes use of data generated by the Wellcome Trust Case-Control Consortium.

Dr G Zhai

Discipline of Genetics, Faculty of Medicine, Memorial University of NL, St John’s, NL guangju.zhai@med.mun.ca

Zipperlen, Peddle, Melay et al. (2005)³⁵

Approved by MUN REB. Consent obtained from patients.

128 with Crohn disease and 103 controls, all white and of NL ancestry.

Peripheral whole blood samples

Collected demographic and health data from participants.

DNA extracted from lymphocytes with the Wizard Genomic DNA Purification Kit from Promega (Madison, WI). Genotyped for 5 SNPs of the TNF-Alpha gene

The products cleaned and spotted onto a SpectroChip. Chip scanned with a mass spectrometry workstation (Bruker). Resulting spectra analyzed with Sequenom SpectroTYPER-RT software.

*No statement about data availability

Dr. Proton Rahman had full access to data

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Gladman, Farewell, Pellett, et al. (2003)³⁶

Not specified.

65 sibling pairs from a PsA Clinic in NL (50 pairs affected by PsA, and/or psoriasis), 117 from a clinic in Toronto.

DNA sample not specified.

Collected clinical history, physical, and radiologic data.

Extracted DNA assessed for SNP for each HLA-A, -B, -C, -DR, and -DQ loci. Also, clinical history, physical examination by a rheumatologist, and radiologic assessment

Not specified.

Dafna D Gladman

Centre for Prognosis Studies in The Rheumatic Diseases, Toronto Western Hospital, Toronto, ON

dafna.gladman@utoronto.ca

Butt, Sun, Greenwood, et al. (2005)³⁷

*Letter to the editor, unable to find initial reference

Approved by MUN REB. Consent obtained from all PsA patients

259 PsA probands and 238 ethnically matched controls all from the NL founder population

Not specified.

All subjects genotyped for: 3 SNPs in SLC22A4 (rs3792876, 1050152, rs3763112), 1 SNP in SLC22A5 (rs2631367), 1 SNP in SLC9A3R1 (rs734232), and 1 SNP in RUNX1 (rs2268277)

DNA was extracted using the Promega Wizard Genomic DNA purification kit. The Sequenom MassArray platform using time-of-flight mass spectrometry used for sequencing

Dr. C. Butt provided this in correspondence with:

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Butt, Sun, Peddle, et al. (2005)³⁸

Approved by MUN REB. Consent obtained from all participants.

234 patients with PsA and 88 ethnically matched, unrelated controls from NL founder population.

Whole blood samples

All subjects genotyped using SNP technology for:

NFkB1-94delATTG

RelA rs2009453

RelA rs6591183

NFKBIA-410 (rs2233409)

NFKBIA-673 (rs2233407)

NFKBIA-949 (rs2233406)

NFKBIA 2578 (rs696)

DNA extracted using Promega Wizard Genomic platform. Polymerase chain and extension reactions designed using MassARRAY design software. Primer extension products cleaned and spotted onto a SpectroChip. Genotypes determined using the Sequenom SpectroTYPER-RT software.

*No statement about data availability

Unclear who to contact but this contact is provided in other articles with this group:

Dr. Proton Rahman full access to data.

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Butt, Peddle, Greenwood, et al. (2006)³⁹

Approved by MUN REB and UofT REB. Consent obtained from all participants.

238 NL PsA patients and 149 healthy NL controls. All PsA probands and controls similar ethnicity to the patients (cases).

*410 participants were also included from Toronto.

Whole blood samples

Collected demographic information and data on disease onset and patterns.

All subjects genotyped using SNP technology for polymorphisms: PPTN22 (rs2476601, R620W) and tp53 (rs1042522, Pro72Arg).

DNA extracted using Promega Wizard Genomic DNA purification Kit. PCR and extension reactions designed using MassARRAY design software. Primer extension products cleaned and spotted onto a SpectroChip. Genotypes determined using the Sequenom SpectroTYPER-RT software.

*No statement about data availability

Dr. Proton Rahman had full access to data.

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Rahman, Siannis, Butt, et al. (2006)⁴⁰

Approved by MUN REB and the UofT. Consent obtained from all patients.

237 PsA cases and 103 controls from NL and 203 cases 101 controls from Toronto. Control subjects were of similar ethnicity to cases.

Peripheral blood samples (lymphocytes) Collected demographic information and data on disease onset and patterns.

DNA genotyped for 5 TNF variants by 5 SNPs were in the 5′ flanking region of TNFalpha gene positions:

−1031 (T→C), −863 (C→A),

−857 (C→T),

−308 (G→A), and −238 (G→A).

Genotyped using time of flight mass spectrometry using Sequenom platform. DNA extracted using Wizard Genomic DNA purification kit from Promega. The products cleaned and spotted onto a SpectroChip. The chip scanned with mass spectrometry workstation (Bruker). Resulting spectra analyzed with Sequenom SpectroTYPER-RT software.

*No statement about data availability

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Rahman, Sun, Peddle, et al. (2006)⁴¹

Approved by MUN REB. Consent was obtained from all participants.

212 PsA cases and 150 ethnically matched controls.

Controls were volunteers from NL who participated in as a result of a local campaign seeking controls for genetics studies.

Whole blood samples

Information collected including age at onset of psoriasis and PsA, and disease pattern.

DNA extracted using Wizard Genomic DNA Purification kit.

DNA genotyped by 29 SNPs within the IL1 gene cluster (but specifically located within the IL1A, IL1B, and IL1F5–10 genes).

Genotyped using time of flight mass spectrometry using Sequenom platform. DNA extracted using Wizard Genomic DNA purification kit from Promega. Products cleaned and spotted onto a SpectroChip. Chip scanned with mass spectrometry workstation (Bruker). Resulting spectra analyzed with Sequenom SpectroTYPER-RT software.

*No statement about data availability

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Butt, Lim, Greenwood, et al. (2007)⁴²

Approved by MUN REB. Consent was obtained from all participants.

258 PsA probands and 154 unrelated controls. All from the NL founder population.

Whole blood samples. Information collected including age at onset of psoriasis, PsA and disease pattern

Participants genotyped for SNPs:

VEGF gene (rs3025039, rs699947, rs1570360, and rs2010963)

FGF1 gene (rs34011)

FGF2 gene (rs1048201)

EGF gene (rs4444903, rs11568943 and rs2237051)

DNA extracted using the Promega Wizard Genomic DNA purification kit. Polymorphisms typed using Sequenom chipbased MALDI-TOF mass spectrometry platform using MassArray software (Sequenom).

Products cleaned and spotted onto SpectroChip. Chip scanned with mass spectrometry workstation (Bruker). Resulting spectra analyzed with Sequenom SpectroTYPER-RT software.

*No statement about data availability

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Rahman, Inman, Maksymowych, et al. (2009)⁴³

Approval from MUN REB and UHN, UofT. Specimens collected from patients with PsA with informed consent.

496 (247 NL, 249 Toronto) PsA probands and 476 controls (228 from NL, 248 from Toronto). All patients and controls mostly of North European ancestry. Controls for the NL population were volunteers who participated from a local campaign seeking population-based controls for genetic studies.

DNA: Not specified.

Information collected including age at onset of psoriasis and PsA, and disease pattern.

Cases and controls genotyped for 11 SNPs in IL-23R: (rs1004819, rs7517847, rs7530511, rs10489629, rs2201841, rs11465804, rs11209026, rs1343151, rs10889677, rs11209032, and rs1495965.)

The Sequenom MassARRAY system used to genotype each study participant. Genotypes determined using a MassARRAY compact analyzer (Sequenom).

*No statement about data availability

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Pollock, Chandran, Pellett, et al. (2013)⁴⁴

Study approved by the UHN REB and all subjects provided written informed consent

374 PsA/PsC) probands and 115 health ethnically matched controls recruited from MUN, St. John’s.

*745 cases and 547 controls from Toronto also included.

Whole blood samples

Data including age at onset of psoriasis and PsA, disease pattern, rheumatologist assessment

Genomic DNA extracted using the Gentra Pure Gene Blood Kit (Qiagen, Mississauga, ON). SNP technology used to genotype HLA-B and HLA-C and MICA-129 polymorphism rs1051792

Unclear, genotyping done through Life Technologies, Mississauga, ON. No statement provided regarding data availability.

Dr Dafna D. Gladman

PsA Program

Centre for Prognosis Studies in the

Rheumatic Diseases

Toronto Western Research Institute

University of Toronto

Toronto, ON

dafna.gladman@utoronto.ca

O'Rielly, Pollock, Zhang, et al. (2014)⁴⁵

*Abstract only

*Not stated

Investi­gated the differential methylation pattern among paternally (n = 24) and maternally (n = 24) transmitted PsA.

48 samples provided by 48 participants

*Not stated. Likely a blood sample

Genome-wide DNA methylation profiling was performed.

Methylation analysis was performed on 382,024 of the 485,512 CpG sites after filtering. Revealed 90 significant CpG sites (P < 0.05). The 3 most significant CpG sites were hypermethylated regions located on chromosome 8 that did not reside on or adjacent to a gene.

Genome-wide DNA methylation profiling was performed using Illumina HumanMethylation450k Beadchip, which measures up ∼480,000 different CpG sites per sample and covers 96% of RefSeq genes.

No information on data availability

*Not provided

Chandran, O'Reilly, Haddad, et al. (2014)⁴⁶

*Only abstract available*

*Not provided, only abstract available*

All patients were Caucasians of Northern European Ancestry.

24 PsA patients with mutilans (Patients with ≥ 1 joint with grade 4 damage were classified as having arthritis mutilans) and 24 patients without arthritis mutilans (no damage following similar duration of follow up).

blood DNA samples

to investigate DNA methylation

methylation profiling was performed using Illumina HumanMethylation450k Beadchips, which measures up ~480,000 different CpG sites per sample and covers 96% of RefSeq genes.

No information on data availability.

*Not provided.

O'Rielly, Zhang, Codner, et al. (2015)⁴⁷

*Only abstract available

Not specified.

41 from NL with PsA treated with TNF-alpha Inhibitors (21 considered TNFi responders, 20 secondary TNFi failures

Not specified.

Genome-wide DNA methylation profiling performed using Illumina HumanMethylation450k Beadchip (480,000 different CpG sites per sample and covers 96% of RefSeq genes)

Not specified.

Not specified. All authors from Faculty of Medicine, Memorial University of NL, St. John's, NL

Dr. Darren O’Rielly

St. John’s, NL

Darren.orielly@med.mun.ca

Pollock, Thava­neswaran, Pellett, et al. (2015)⁴⁸

The study was conducted with the approval of the UHN REB, and all subjects provided written informed consent.

Cutaneous psoriasis without arthritis (PsC) and PsA

92 NL PsA probands

DNA-Not specified.

Family history

PsC or PsA susceptibility alleles HLA–C*01, C*02, C*06, C*12, HLA–B*07, B*08, B*27, B*38, B*39, B*57, HLA–DR4, DR7, DQ*0303, and MICA–129

*Included in analysis, not specified how this was collected.

*Not specified.

Dafna D. Gladman, MD, FRCPC,

Full access to data in study

University of Toronto Psoriatic Arthritis Program, Toronto, ON

dafna.gladman@utoronto.ca

Stuart, Nair, Ellinghaus, et al. (2010)⁴⁹

All participating subjects gave informed consent and protocols were reviewed and approved by local institutional review boards.

Replication study following meta analysis, including 4,064 cases and 4,685 controls from Michigan, Toronto, NL (n=368 cases, 358 controls) and Germany

Not stated

Collaborative Association Study of Psoriasis (CASP) was included in the initial meta-analysis (includes 368 cases and 358 controls from NL).

Following meta

selected 102 SNPs for replication based on their p value rankings either in a subset of 350 CASP PsA cases vs. normal controls

Replication sample consisted of up to 4,064 PsV cases and 4,685 controls from Michigan, Toronto, NL, and Germany. a meta-analysis of 2 recent psoriasis genome-wide association studies

First-stage replication genotyped all selected SNPs in the large Michigan sample; 91 SNPs passed all quality control (QC) filters.

Second stage replication typed all but 1 of 51 QC-filtered SNPs from set A of the PsA GWAS in the samples from Toronto and NL, which contain most of the PsA cases.

SNPs with the most promising association results were then followed-up with third stage typing--8 from sets B and C in the 2 Canadian samples, and 6 from all 3 sets in the German sample.

Sequencing software, and data libraries not stated

No statement of data availability.

James T Elder

Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, US, jelder@umich.edu

Stuart, Philip, Nair, et al. (2015)⁵⁰

All participants provided written informed consent and were recruited according to the protocols approved by the institutional review board of each institution.

1430 cases (323 from NL) and 1417 controls (323 from NL) (no PsA or PsC) from multiple studies included*

Also included data from previous studies for meta-analysis. PsC (individuals affected with PsV for ≥ 10 yrs without developing any signs of PsA).

*Not stated, likely blood samples

Wanted to discern differences in genetic risk factors for PsA and cutaneous-only psoriasis (PsC)

Used GWAS of 1,430 PsA case subjects and 1,417 unaffected control subjects (yielded high-quality genotypes at 791,217 SNPs for 1,430 PsA case subjects and 1,417 control subjects).

After replication, also identified a PsV-associated SNP near CDKAL1 (rs4712528, odds ratio = 1.16, P = 8.4 × 10⁻¹¹).

All PsV case subjects were diagnosed by a dermatologist; a large subset were also evaluated for PsA by a rheumatologist.

Samples for the PsA GWAS were genotyped with the Illumina HumanOmni1-Quad BeadChip array (Illumina). Genotypes were obtained for 1,020,596 autosomal SNPs

genotyped 23 markers to validate and replicate promising signals from the discovery analysis.

*No statement of data availability or where sequencing was conducted.

James T Elder

Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, US, jelder@umich.edu

Rahmati, O'Rielly, Li, et al. (2020)⁵¹

Ethics approval was granted for this study by the Health Research Ethics Authority in NL (2016.195). All patients consented to be part of study

40 PsA patients

recruited by the PsA clinic at MUN. All patients satisfied the Classi­fication of Psoriatic Arthritis (CASPAR) criteria

Blood sample. Both DNA and total RNA extracted. Peripheral blood mononuclear cells separated from whole blood with Ficoll-Paque Plus density gradient (Cat # GE-1440-02, Millipore Sigma).

Isolated CD4⁺ cells and CD14⁺ cells from PsA patients to determine the most discriminatory cell type. Consecutive patients initiating TNFi or IL-17Ai therapy were invited to participate in this study

Assessed PsA patients initiating either TNFi (golimumab, adalimumab, etanercept, infliximab, and certolizumab pegol) or interleukin-17A inhibitors (17Ai) 17Ai (secukinumab and ixekizumab) for active PsA at baseline and 3-months after initiating use.

CD4⁺ transcript profiling performed using transcriptomic data at initiation of therapy. Identified > 100 DEGs that differentiated IL-17Ai response from non-response and TNFi response from non-response.

Regarding PsA, 161 genes were down-regulated, and 27 genes were upregulated in patients treated with etanercept as compared with untreated controls

Network and pathway analysis: only overlap of DEGs (fold change ≥ 1.4 and raw p value ≤ 0.05) between response groups to each biologic at baseline and DEGs between responders to the 2 biologics were selected: generated 2 lists of statistically significant DEGs. To capture biologically meaningful DEGs, gene sets were obtained by overlaying differential expression values onto physical protein interaction network obtained from Integrated Interaction Database (IID, version 2018 to 11). Obtained ROCK2 and RAC1 protein expression data across 19 different tissues from the Human Protein Atlas

Gene expression analysis: Raw FASTQ files with RNA reads aligned to the human hg19 reference genome. Gene expression for each sample quantified as fragments per kilobase of transcript per million mapped reads using Cufflinks (version 2.2.1) and normalized within-sample to transcripts per million reads values.

Also collected DAPSA activity scores (includes a 68/66 joint count summed with a patient global score, patient pain score, and CRP level) at baseline and 3 months into treatment.

NEBNext Ultra II Directional RNA Library Prep Kit for Illumina (Cat # NEB-E7760L, D-Mark Biosciences) and the NEBNext rRNA Depletion Kit (Cat # NEB_E6310X, D-Mark Biosciences) used to create sequencing libraries from total RNA.

Double-stranded cDNA purified with Agencourt AMPure XP beads (Cat # A63881, Beckman Coulter). Followed by end repair and dA-tail addition before adaptor ligation. Adaptor-ligated DNA further purified then unique dual index barcodes attached (NEBNext Dual Indexed Primer Set 1, Cat # E7760D-Mark)

Final libraries size-selected with bead purification and the quality and quantity assessed with Tape Station D1000 kit (Agilent) and the KAPA Library Quantification Kit (Cat# KK4828, Roche). Library concentrations normalized and pooled for sequencing on Illumina NovaSeq 6000 for 2 × 150 bp reads and ~ 40 million reads/sample.

No statement of data availability.

Does not state where DNA analysis was completed

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Nair, Duffin, Helms, et al.  (2009)⁵²

*A letter

Protocols reviewed and approved by local institutional REBs.

All participants subjects gave consent.

Pulled samples from multiple sources (identified psoriasis susceptibility loci, by genotyping 1,409 psoriasis cases and 1,436 controls of European ancestry. Followed up 21 SNPs in 5,048 psoriasis cases (368 cases, 358 controls from NL)

*NL involvement stated in supple­mental materials

Not specified.

Identified psoriasis susceptibility loci in initial samples (1,359 psoriasis cases and 1,400 controls to impute). WGS genotyped for 438,670 autosomal SNPs. From these, 21 SNPs (representing 18 loci) with strongest evidence for association genotyped in an additional 5,048 cases and 5,051 controls (including the NL cases and controls)

Follow-up samples genotyped using Applied Biosystems Taqman assays, Sequenom single base extension assays, or allele-specific kinetic PCR.

dbGAP: genotype and phenotype data deposited with the accession code phs000019.v1.p1. NCBI GEO: microarray data were deposited under accession number GSE13355.

James T Elder

Ann Arbor Veterans Affairs Hospital, Ann Arbor, Michigan, US, jelder@umich.edu

Gerald G Krueger

Department of Dermatology, University of Utah, Salt Lake City, Utah, US

gerald.krueger@hsc.utah.edu

Anne M Bowcock

Division of Human Genetics, Department of Genetics, Washington University School of Medicine, St. Louis, Missouri, US, bowcock@wustl.edu

Gonçalo R Abecasis

Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, Michigan, US

goncalo@umich.edu

Das, Stuart, Ding, et al. (2015)⁵³

Not specified.

5067 subjects of European ancestry from 5 collaborating centers, including

783 (470 psoriasis cases, 313 controls) from NL *58 samples pulled from Tsoi et al (a previous study)

Not specified.

All subjects genotyped to include all genes of interest in their entirety and all SNPs in 8 psoriasis susceptibility regions (MHC, IL12B, IL23A, IL23R, TNIP1, TNFAIP3, IL13 and RNF114)

Illumina technology used.

Information uploaded to NCBI dbGaP database at (dbGaP accession number: phs000019.v1.p1).

Dr GR Abecasis

Department of Biostatistics, Center for Statistical Genetics, University of Michigan, Ann Arbor, MI

goncalo@umich.edu

O’Rielly, Uddin, Codner, et al. (2016)⁵⁴

The REBs from all partici­pating hospitals approved study (HREA #1999.172). Patient consent obtained.

Single multi­generational family from NL with Axial spondyl­oarthritis conditions (number of partici­pants unclear). Replication cohorts provided by The Spondylo­arthritis Consortium of Canada: provided clinical and radiographic data, as well as DNA samples for the replication cohorts.

Whole blood samples

HLA-B*27 genotyping and exome sequencing performed by Life Technologies (US)

Samples sequenced targeting whole genome exons using Illumina HiSeq 2000. Mapping of reads aligned using Burrows Wheeler Alignment V.0.7.10, and the genome analysis toolkit V.1.1.28 used to call variants against the reference genome.

*No statement about data availability

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Lehr, Rahman, and O’Rielly (2017)⁵⁵

*Letter to the editor

Institutional ethics was approved from the Health REB at MUN (Health Research Ethics Authority reference #15.051). Patient consent was obtained.

1,000 consecutive patient samples (572 men and 428 women) received by the clinical genetics laboratory at Eastern Health to determine the HLA-B*27 genotyping status. There were 172 HLA-B*27–positive and 828 HLA-B*27– negative patients.

Whole blood samples

Targeted analysis of the HLA-B locus by Genotyping of rs4349859 (NM_001289154.1:­c.2921G > A) and rs116488202 (NC_000006.12:­g.31377139C > T) as a test of who has axial spondylo­arthritis

Targeted analysis of the HLA-B locus was performed using LABType SSO HLA-B locus kit on a Luminex 100/200 platform (One Lambda, ThermoFisher Scientific). Genotypes of rs4349859 (NM_001289154.1: c.-2921G > A) and rs116488202 (NC_000006.12:­g.31377139C > T) were assigned using the end point genotyping analysis software (Applied Biosystems).

*Conducted at the Molecular Genetics Laboratory, Eastern Health,

Dr. Darren O’Rielly

Faculty of Medicine, Memorial University of NL, Craig L. Dobbin Genetics Research Centre,

St. John’s, NL

darren.orielly@med.mun.ca

Spector, Reneland, Mah, et al. (2006)⁵⁶

Approved by REBs at each clinical centre. All partici­pants provided consent for the study.

London, UK:

343 cases with OA, 303 controls without OA

NL Canada:

378 cases with OA (211 with knee OA, 99 with hand OA, and 68 with hip OA), 264 controls without OA

*All European ancestry

Not specified.

Health history and rheumatologist examination

Genotyping of all participants:

A set of 25,494 SNP markers located within 10 kb of 13,735 Entrez Gene annotated genes.

SNP annotation based on the NCBI dbSNP database, reference SNP, build 118. Genomic annotation was based on NCBI genome build 34. Gene annotation based on Entrez Gene genes for which NCBI was providing positions on the Map Viewer FTP site.

*No statement of data availability, but NF and UK data analyzed together. Site of processing and data library not specified.

Dr. Tim D. Spector

St. Thomas' Hospital, London, UK

Twin Research and Genetic Epidemiology Unit, St. Thomas' Hospital, London UK

tim.spector@kcl.ac.uk

Aref-Eshghi, Zhang, Liu et al. (2015)⁵⁷

And

Gill, Liu, Sun, et al. (2024)⁵⁸ are both

part of the NFOAS is ongoing, initiated in 2011, Aref-Eshghi (above), Gill (Below)

Approved by the HREA of NL

(NFOAS-# 2011.311 and CODING- #10.33)

Consent obtained from participants.

5 patients with hip OA, 6 with knee OA, and 7 OA-free hip controls. OA Patients having joint replace­ments due to primary OA recruited between 2011 and 2013, and OA-free controls (joint replacement for alternate reason) recruited in same NL hospital.

Cartilage samples, pathology reports, Demographic information (obtained by a self-administered questionnaire) height and weight from medical records.

Looked at the methylation status of 485,000 methylation sites throughout genome, covering 99% of RefSeq genes at an average of 17 CpG sites per gene across the 5-UTR, gene promoter regions, first exon, gene body, and 3-UTR.

Genome wide DNA methylation analysis conducted using the Illumina Infinium HumanMethylation450 BeadChip.

The genome-wide DNA methylation data available with accession number GSE73626.

Guangju Zhai

Memorial University of NL, St. John’s, NL

gzhai@mun.ca

Aref-Eshghi, Zhang, Liu et al. (2015)⁵⁷

and

Gill, Liu, Sun, et al. (2024)⁵⁸ are both

part of the NFOAS is ongoing, initiated in 2011, Aref-Eshghi (above), Gill (Below)

Approved by the Health Research Ethics Authority of NL

(NFOAS-# 2011.311 and CODING- #10.33)

Consent obtained from participants.

559 OA patients (172 hip, 387 knee), 118 healthy controls (from CODING study) study all from NL.

*Replication cohort from UK

Whole blood samples

WGS done by the Illumina Human Omni2.5 to 8 microarray platform (genotypes 2.5 million SNPs) or the Human Global Diversity Array (genotypes 1.9 million SNPs) at The Centre for Applied Genomics in Toronto .

Data imputed against 1000 Genome Project phase 3 data by the Sanger Imputation Server which generated data on a total of 81,706,022 SNPs across the entire genome.

Datasets available from the corresponding author on reasonable request

Guangju Zhai

Memorial University of NL, St. John’s, NL

gzhai@mun.ca

Zhai, Aref-Eshghi, Rahman, et al. (2014)⁵⁹

The study was approved by Health Research Ethics Authority (HREA) of NL and written consent was obtained from all the participants.

A case-control study (part of the NFOAS). 126 patients undergoing total hip/knee joint replace­ments between 2011 and 2013 in local hospital due to severe OA (cases). 348 healthy controls who did not have any evidence of either knee or hip OA were selected from previous genetic association study for type 2 diabetes and obesity. Controls had no musculo­skeletal pain, a prior diagnosis of osteo­arthritis, were not taking aceta­minophen or NSAIDs and had a normal physical examin­ation, as it relates to the skeletal system

Blood samples obtained from all study participants. DNA was extracted by using the standard protocol.

Controls completed questionnaire regarding ongoing symptoms, previous diagnosis and medication history. Each patient examined by a rheumatologist. Height and weight measurements were obtained from patient’s hospital medical record. Body mass index (BMI) was calculated

105 SNPs were genotyped

(selected based on SNPs reported to be associated with OA in GWAS and some candidate studies).

Genotyped using either the Sequenom iPLEX Gold method (OA cases) using 384-well plate chip and loaded onto the Mass Spectrometer for reading, or using Illumina HumanHap550-Duo BeadChip at Centrillion Biosciences at Palo Alto, California (completed previously for controls). Cross-validation of genotyping quality was carried out on 31 controls that were genotyped by both Sequenom iPLEX Gold method and IlluminaHumanHap550-Duo BeadChip.

Data availability not reported.

Quebec Genome and Innovation Centre and Centrillion Biosciences, CA, conducted gentyping.

Guangju Zhai

Memorial University of NL, St. John’s, NL

gzhai@mun.ca

Aref-Eshghi, Liu, Harper, et al. (2015)⁶⁰

*See below

The study protocol was approved by the Health Research Ethics Authority of NL and written consent was obtained from all participants.

Part of the ongoing NFOAS that was initiated in 2011, A total of 32 OA cases (25 hip OA and 7 knee OA) and 21 healthy controls were included.

*See below

Human cartilage samples were collected from patients undergoing total hip/knee joint replacement surgery due to primary OA or hip fractures as controls.

*See below

Compared the expression levels of TGFB1 and BMP2 as ligands, SMAD3 as an intracellular mediator, and MMP13 as a targeted gene between human osteoarthritic and healthy

*See below, same processes used.

*Sequencing performed in-house.

Guangju Zhai

Memorial University of NL, St. John’s, NL

gzhai@mun.ca

Aref-Eshghi, Liu, Razavi-Lopez, et al. (2016)⁶¹

Refer to above

Part of the NFOAS initiated in 2011. 58 patients with OA undergoing total hip/knee replace­ments and 55 controls with hip fractures. Recruited between November 2011 and December 2013 in St. Clare’s Mercy Hospital and Health Science Centre General Hospital in St. John’s, NL.

DNA/RNA: Four pieces (∼ 200 mg each) of cartilage tissues retained from either tibial plateaus or femoral heads collected from cases and controls.

Also, pathology reports, demographic information (self-administered questionnaire), and

Anthropometric data including BMI from hospital admission and medical records and age was at the time of surgery.

Investigated SMAD3 gene expression and its promoter DNA methylation in cartilage tissues.

PCR was performed to measure gene expression.

One microlitre of the converted cDNA was subject to quality control by PCR amplification of the SMAD3 and GAPDH genes followed by agarose gel electrophoresis.

Sequenom EpiTyper was used to assay DNA methylation.

Complementary DNA (cDNA) synthesis from the extracted RNA was done using the Maxima H Minus First Strand cDNA Synthesis Kit (K1682; Thermo Scientific, Vilnius, Lithuania).

Quantification of SMAD3 was performed using the ABI-7900HT Fast Real-Time PCR system on a 96-well plate.

Bisulfate conversion of DNA was conducted using the EpiTect Bisulfite Kit

SMAD3 promoter DNA methylation was quantified using the Sequenom EpiTyper platform

The mass signals generated were translated into quantitative DNA methylation levels (beta value range 0 to 1) by MassArray EpiTyper Analyzer software.

No statement of data availability.

Guangju Zhai

Memorial University of NL, St. John’s, NL

gzhai@mun.ca

Werdyani, Liu, Xie, et al. (2021)⁶²

*Only Abstract Available

Refer to above

Primary OA patients from the NFOAS that comprised total knee or hip replacement and recruited before 2016. 83 primary OA patients (44 responders, 39 non-responders) included in analysis.

Whole blood DNA samples

Study participants completed their pre-operation and 3.99 ± 1.38 years post-surgery outcome assessment using the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC).

WGS completed. Pre-association quality control filtering conducted for raw genotyping data using PLINK 1.7 program, and genotype imputation performed using IMPUTE2 algorithm with multiple population reference data (1000 Genome Project). The imputed data with ∼3.1 million variants used to test the association with non-responders to TJR using the additive genetic model.

DNA samples were genotyped using the genome-wide Illumina HumanOmni2.58 genotyping microarray containing 2.4 million SNPs.

Werdyani, Liu, Xie, et al (2020)

*Only Abstract Available

Werdyani, Liu, Furey, et al (2022)⁶³

*Only Abstract Available

Refer to above

Part of the NFOAS

total hip or knee replacement patients due to primary OA, recruited before 2017 in St John’s, NL. Self-reported OA-free controls derived from same source population, originally recruited to the CODING study.

566 OA patients and 120 unaffected passed the QC check and were included in the analysis.

DNA samples were extracted from whole blood

WGS conducted. 2 genotype datasets were merged and the common SNPs between both genotyping microarrays were used in the analysis.

Pre-association quality control filtering and population structure analyses performed for study participants based on genotyping data. Individuals excluded from cohort if they: a) had a heterozygosity rate > 3SD, b) had discordant sex information; c) were non-Caucasian; and d) had call rate < 95%. Also, variants quality control filtering was performed to exclude SNPs that had call rate < 0.0001).

genotyped using the Illumina HumanOmni2.58 and Infinium Global Diversity 8 v1.0 genotyping microarrays.

No statement of data availability in the abstract.

Werdyani, Liu, Furey, et al (2022)

*Only Abstract Available

Maksymowych, Rahman, Reeve, et al. (2006)⁶⁴

Ethical approval for the study was obtained from the MUN Bioethics Research Committee. The ethnic composition of this cohort is relatively restricted to individuals of Irish/southwest English descent.

3 independent case-control cohorts

AB, NL (112 unrelated white AS patients attending the outpatient rheuma­tology department of MUN, 10 had IBD, 20 had psoriasis, and 4 had reactive arthritis. Controls were 150 healthy unrelated white blood donors from St. John's, NL. Cohort is relatively restricted to individuals of Irish/ southwest English descent), and Toronto that have been pheno­typically well-characterized in a systematic manner by investi­gators collab­orating in the Spondylo­arthritis Research Consortium of Canada disease network.

DNA was extracted from peripheral blood and the final concentration adjusted to 5 ng/μL.

Samples were genotyped using a panel of 38 single-nucleotide polymorphism (SNP) markers within the IL1 gene cluster. Data from 20 informative and nonredundant SNP markers were analyzed using several association test strategies. First, we used the program WHAP to identify single-marker associations. Second, we used WHAP to analyze “sliding windows” of 3 contiguous markers along the entire extent of the IL1 gene cluster to identify haplotypic associations. Third, we used the linkage disequilibrium mapping program DMLE to estimate the posterior probability distribution of a disease locus.

First, 2.5 ng of genomic DNA was amplified under standard conditions using forward and reverse primer pairs.

Genotyped by time-of-flight mass spectrometry using the Sequenom platform (Sequenom, San Diego, CA)

The primer extension products were then cleaned and spotted onto a SpectroChip.

Measures of pairwise LD were determined using Haploview

Dr. W. P. Maksymowych

University of Alberta Department of Medicine, Edmonton, AB

walter.maksymowych@ualberta.ca

*has full access to all the data

Snelgrove, Lim, Greenwood, et al. (2007)⁶⁵

*Only had access to article draft

Approved by MUN REB. Consent obtained from all patients.

101 AS patients and 100 ethnically matched controls (all Caucasian).

Controls from volunteers from local campaign seeking controls for genetic studies.

Whole-blood samples

Data collected included measures of disease activity and function

Index

SNP testing of 2 functional variants in the TLR4 gene: Asp299Gly (A/G polymorphism) and Thr399Ile (C/T polymorphism)

DNA extracted using the Promega Wizard Genomic DNA purification kit. polymorphisms typed using Sequenom chipbased MALDI-TOF mass spectrometry platform using MassArray software (Sequenom).

Products cleaned and spotted onto a SpectroChip. Chip scanned with mass spectrometry workstation (Bruker). Resulting spectra analyzed with the Sequenom SpectroTYPER-RT software.

*No statement about data availability

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Rahman, Inman, Gladman, et al. (2008)⁶⁶

Ethics approval for this study was obtained at each of the participating universities.

3 cohorts (NL, AB, ON) of AS patients from established rheumatic disease centers in Canada. (majority of Caucasians of northern European descent), (NL: 121 AS probands and 219 controls)

Whole-blood samples

Data collected included measures of disease activity and function

Index

SNPs were rs1004819 (C > T), rs7517847 (t > G), rs10489629 (G > A), rs2201841 (t > C), rs11465804 (t > G), rs11209026 (G > A), rs1343151 (t > C), rs10889677 (A > C), rs11209032 (G > A), and rs1495965 (G > A). (of these were incorporated in the haplotype analysis. Allele and haplotype associations were calculated using the WHAP software package. P values for haplotype associations were calculated using a permutation test.

The MassArray system (Sequenom, San Diego, CA) was used to genotype each study participant using a single multiplex reaction that was designed using AssayDesigner 3.0. T

*No statement about data availability

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

*had full access to all of the data in the study

Maksymowych, Inman, Gladman, et al. (2009)⁶⁷

*Earlier study Rahman (2008) drew from same cohort

Approval obtained from each participating university. Patients provided consent.

992 AS cases and 1,437 controls from 3 centers (472 cases and 451 controls from AB, 138 (22 had IBD, 28 had psoriasis in addition to AS) cases and 392 controls from NL founder population, and 382 cases and 594 controls from Toronto).

Whole blood sample

All genotyped for 13 coding-region SNPs, 6 in the ERAP1 gene, 4 in the TAP2 gene, 1 in the TAP1 gene, 1 in the LMP2 gene, and 1 in the LMP7 gene

The MassARRAY system (Sequenom, San Diego, CA) used to genotype study participants.

Genotypes determined using MassARRAY Typer software, version 4.0.

*No statement regarding data availability

Dr. W. P. Maksymowych has full access to all of the data

University of Alberta Department of Medicine, Edmonton, AB walter.maksymowych@ualberta.ca

Uddin, Maksymowych, Inman, et al. (2013)⁶⁸

Informed consent for partici­pation in the study was obtained from partici­pants or, where partici­pants are children, a parent or guardian.

approved by the MUN Human Investi­gation Committee.

NL:

298 cases

299 controls

AB:

289 cases

285 controls

All cases and controls were of North European ancestry.

*Cases satisfied the modified New York criteria

Each individual was assessed clinically including imaging studies.

Custom genome-wide tiling microarray consisted of 2 × 1 million probes covering the genome with a mean spacing of 280 bp. Approximately 1700 CNVs were detected in each individual sample.

Segregated gene-centric CNV analysis (i.e., a CNV that consists of or overlaps with a gene) revealed that 56 CNVs are enriched in affected family members (at least three) and absent in the unaffected family members.

Affected family members carried 2 copies of the UGT2B17 gene, whereas unaffected members carried a single copy.

The breakpoint encompassing the UGT2B17 gene region was covered with probes with 280 bp spacing, providing high resolution to detect genomic aberrations.

*Analysis conducted in Quebec and Toronto.

Samples were analyzed using the ViiA™ 7 Real-Time PCR System (Life Technologies) and analyzed using CopyCaller Software (Life Technologies, PN 4412907).

*No statement of Data Availability

Dr. Proton Rahman

Memorial University of NL, St. John’s, NL

prahman@mun.ca

Young, Ives, Lynch (2001)⁶⁹

Obtained informed consent from each individual including relatives

6-gen family from NL with mutations in the Wolfram Syndrome Gene (WFS1). 62 family members identified with low frequency hearing loss. Additionally unaffected family members were included.

150 unrelated individuals also included as controls for genetic analyses.

peripheral blood (83 people) DNA was isolated using a salting out extraction method.

family and medical histories (from 314 informative relatives) and pure tone audiometric evaluations (performed on 81 relatives.)

Linkage analysis: 47 family members included in genome-wide scan using 386 polymorphic markers. Additional polymorphic markers were genotyped on family members in the vicinity of D4S431 to define the DFNA38 critical region.

Sequencing: Coding sequence, regulatory regions and flanking intronic sequence of candidate genes were sequenced from genomic DNA. 11 variant sites in WFS1 were detected in all deaf individuals. 5 variants were known polymorphisms; 6 novel, of which 3 were amino acid substitutions: Gly107Arg, Ala716Thr and Val871Met. The A716T mutation abolishes an HaeII restriction enzyme site, all family members who were not included in the genome scan were tested for the mutation by restriction enzyme analysis using WFS1 specific primers. Restriction digest analysis was also used to test for mitochondrial mutations associated with hearing impairment: A1555G, A3243G, A7445G, 7472 ins C, T7510C, T7511C, T7512C, and 961_TC (n) ins. 150 controls were also genotyped for the A716T mutation.

Genome wide scan completed using the ABI Prism Linkage Mapping Set-MD10. PCR products were size fractionated on an ABI 377 sequencer machine and alleles were scored with Genotyper software (v. 2.0 Applied Biosystems). 2-point linkage analyses were performed using the MLINK subroutine of FASTLINK (V4.0P) Genome-wide.

No statement of data availability. Unclear where analysis was performed.

Dr. Terry-Lynn Young

Memorial University of NL

St. Johns, NL

tlyoung@mun.ca

Ahmed, Cindy Li, Powell, et al. (2004)⁷⁰

Approval from the NL Labrador Medical Genetics Program, Health Sciences Centre REB. Participants provided consent.

32 people from a large six-generation pedigree from Labrador

Addition­ally, families in Pakistan were in­cluded.

Whole blood samples

Family pedigrees, pure tone air and bone conduction audiometry and Pneumatic otoscopy results

WES to identify mutant alleles of TMPRSS3 locus.

PCR amplified products were sub-cloned into pGEM-T Easy vector (Promega) and sequenced.

Dr. Zubair M Ahmed performed DNA sequencing. No additional information on data availability.

Dr. Edward R Wilcox

Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, National Institutes of Health, Rockville, MD, US US wilcoxe@nidcd.nih.gov

Abdelfatah, McComiskey, Doucette, et al. (2013)⁷¹

Informed consent, family history and permission to access medical records and audio­grams were obtained as per approved protocol #01.186 (Human REB, St John’s, NL).

A 6 gener­ation (n = 28 affected) family of English extract­ion from NL with sensory neural hearing loss. part of a large study of heredi­tary hearing loss in province.

DNA extracted from peripheral leukocytes of all available family members. Phenotypic data reviewed by audiologists and classified according to the GENDEAF study group recommend­ations

1. Genomic DNA from a proband (Figure 1; IV-11) was screened by Sanger sequencing for population specific mutations in WFS1, TMPRSS3 and PCHD15, a mutations in GJB2 and GJB6.

2. Targeted sequencing of exons 5 to 7 in KCNQ4, exons 4, 5, 12 in COCH and exons 5, 9 to 14, 17, 18, 20 in TECTA based on their association with bilateral symmetric, sloping, SNHL

3. To check for other potential pathogenic mutations in the DFNA2 locus, we fully sequenced the remaining exons of KCNQ4 and the entirety of GJB3 (DFNA2B) in selected family members

4. Variants of interest subjected to cascade sequencing (affected n = 23; unaffected n = 19) and allele frequencies determined using ethnically matched population controls from NL.

5. To identify other candidate genes to screen, audiograms from selected subjects were submitted to Audiogene for computerized comparison with known average audiograms of 16 AD loci.

6. All available family members were genotyped for DFNA2A/B-linked. Haplotypes were manually constructed.

7. Two-point linkage analysis was carried out using MLINK on 4 microsatellite markers (D1S195, D1S472, D1S2706 and D1S2130

Determined using ethnically matched population controls from NL. Sanger sequencing was carried out on an ABI PRISM 3130XL DNA Analyzer (Applied Biosystems, Foster City, CA, US)

Markers and alleles scored with GeneMapper software (v.4.0; Applied Biosystems) used for step 6.

Linkage calculations were performed using the Linkage Program MLINK, version 5.1.9

Dr. Terry-Lynn Young

Memorial University of NL

St. Johns, NL

tlyoung@mun.ca

Pater, Benteau, Griffin, et al. (2017)⁷²

Approval from Human REB, St. John’s, NL). Protocol #01.186

Consent for family history and permission to access medical records and audiograms obtained from all participants

4 members of a NL family with HL, relatives, 169 HL cases and 175 from NL founder population.

Whole blood samples

Family histories

Retrospective and prospective audiograms

Medical data from medical charts

Family pedigrees

4 cases vetted for population-specific deafness alleles. More loci selected based on audiograms. WES libraries created using the Ion Torrent AmpliSeq RDY Exome Kit. Based on these results, samples from relatives and 175 controls and 169 HL cases had Cascade sequencing and haplotype analysis on potential mutations in Microsatellites flanking candidate genes.

Bidirectional Sanger sequencing

Used Mutation Surveyor Software to select quality reads and analyze DNA sequences. Purified libraries obtained from WES of 4 probands quantified using the Ion Library Quantification Kit (Life Technologies, Cat. #4468802) and loaded onto a PI v3 chip and sequenced with Ion Torrent Proton Sequencer. SNVs and insertion/deletions were called (GATK, v3.5) and annotated using SnpEff (v4.1;). Cascade and haploid screening using GeneMapper software v4.0.

Dr. Terry-Lynn Young

Memorial University of NL

St. Johns, NL

tlyoung@mun.ca

Pater, Penney, O’Rielly, et al. (2022)⁷³

Approval from Human REB, St. John’s, NL). Protocol #01.186

Consent for family history.

Partici­pant consent obtained.

5 affected and 2 unaffected family members of a 6 generation NL family with a variable form of bilateral sensori­neural HL, 202 sensori­neural HL cases and 326 ethnically matched controls all from NL.

Peripheral blood sample

1 family member sequenced for all pathogenic variants causing HL in NL population, the 34 select autosomal dominant genes matching proband’s audiometric data.

Next 4 affected and 2 unaffected family members had genome-wide SNP genotyping.

Candidate variants amplified using standard touchdown PCR protocol and sequenced in family members and compared to sensorineural HL cases and controls using Gene Mapper software.

Genomic DNA libraries (using the Lucigen Shotgun NxSeq AmpFREE Low DNA Library Kit) were prepared on 4 affected and 2 unaffected members of the NL family. Prepared libraries were loaded on Illumina.

The datasets generated during and/or analyzed during study available from the corresponding author on reasonable request.

Dr. Terry-Lynn Young

Memorial University of NL

St. Johns, NL

tlyoung@mun.ca

Abdelfatah, Mostafa, French, et al. (2022)⁷⁴

Approved by MUN REB (#1.186), Western University (#103,679) and the Danish Research Ethical Committee (KF 01-234/02 and KF 01-108/03).

Participants consented regarding publishing their data

5 people with otosclerosis and 17 relatives in 1 NL family. As well as 2 controls with no HL for first pass screening. Unrelated cases with otosclerosis recruited from NL (n = 82), Finland (n = 35) and the Faroe Islands (n = 20) and used as validation cohorts.

Leukocytes isolated from peripheral blood samples

5 affected family members and 2 controls genotyped for markers spanning each OTSC disease interval and bracketing 3 OTSC susceptibility genes using WES. Unaffected family members and cases genotyped with 9 extra markers (D16S518, D16S3049, D16S3098, D16S422, D16S2625, D16S520, D16S413, D16S3023, D16S3026) mapping qter of the OTSC4 disease interval.

WES was outsourced to the Genome Centre (McGill University, QC,) including library preparation (TrueSeq Prep Kit).

Positional candidate genes selected based on function and/or gene expression.

Samples Sanger sequenced on an ABI 3130xl/3730.

Samples run on Illumina Hiseq 2000. Variants of interest validated by cascade sequencing in NL family. Heterozygous variants co-segregating with otosclerosis in an autosomal dominant pattern tested in the unrelated otosclerosis cases.

The datasets generated during and/or analysed during study available from the corresponding author on reasonable request.

Dr. Terry-Lynn Young

Memorial University of NL

St. Johns, NL

tlyoung@mun.ca

Singh, Penney, Griffin, et al. (2023)⁷⁵

Approval from Human REB. St. Johns (protocol #01.186), Consent from participants to access medical/audiometric records, collect biological samples.

22 people from a NL family (first Canadian family known to have profound HL and be POU4F3 c.37del carriers)

Plus 187 HL cases and 71 ethnically matched controls from NL

Peripheral blood or saliva samples of 22 family members (8 for WGS, 14 for WES)

Additionally, audiogram, and 7 generation family pedigree Data

Blood samples from HL cases and controls.

A WGS and WES done with SNP technology done with Human610-Quad chip on family members. Sanger sequencing used to screen cases and controls variants that co-segregated with significant sensory neural HL identified with WGS and WES of affected family.

Libraries multiplexed and sequenced using a S2 Reagent Kit (200 cycles) NovaSeq 6000 (Illumina Inc.) Sequence data analyzed by Mutation Surveyor and Alamut Visual on the combined linkage analysis with WES. Exome library preparation made with the Nextera DNA kit (Illumina Inc.)

Datasets generated and analyzed are available from the corresponding author on reasonable request. Have been uploaded to ClinVar (accession SCV002556358).

Dr. Terry-Lynn Young

Memorial University of NL

St. Johns, NL

tlyoung@mun.ca

Green, O’Rielly, Pater, et al. (2020)⁷⁶

Approved by Human REB of Eastern Health in St. John’s NL. (protocol # 02.116)

Population-based clinical recruitment of patients with STGD1/STGD1 like disease and their extended families (29 families [DNA samples from 82 people]

since 1978)

Whole blood samples

Family interviews and public archival records providing historical religious affiliations and community of origin

WGS of the ABCA4 gene

Location of sequencing and data library not specified.

Primer sequences are available upon request.

Data from this study have been submitted to the public Leiden Open Variation Database.

Dr. Terry-Lynn Young

Memorial University of NL

St. Johns, NL

tlyoung@mun.ca

Fan, Rahman, Peddle, et al. (2004)⁷⁷

Not specified. Recruit­ment through advertise­ments in local newspaper and family doctors.

200 people with BMI ≥ 30 and 200 controls with BMI ≤ 30. All European ancestry from west coast of NL.

Plus, previously collected data from 6 BBS1 families from same region (8 affected, 37 carriers, 18 noncarriers)

Whole blood samples

DNA extracted using simple saltingout method. BBS1 exons screened for the M390R mutation by direct sequence analysis.

Location of sequencing and data library not specified.

Sequencing was carried out with ABI 377 automated sequencer. Sequences analyzed using Sequencer 3.1.1.

*No statements about data availability.

Dr. William S. Davidson,

Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, British Columbia william_davidson@sfu.ca

Service, DeYoung, Karayiorgou, et al. (2006)⁷⁸

Approved by

University of California, Los Angeles Institutional REB.

Consent obtained from participants.

Samples from 12 populations including NL.

200 independent persons geno­typed from each population.

Not specified.

SNP technology used to analyze magnitude and distribution of linkage disequilibrium across the entire length of chromosome 22.

Genotyping reactions performed using Illumina BeadLab kit reagents and protocols25. Performed genotyping, using 250 ng of normalized genomic DNA from each sample as template for the Illumina GoldenGate genotype assay, on the Illumina BeadLab 1000 platform.

Data collection accomplished using the BeadScan (Illumina) software package.

No statement regarding data availability.

Dr. Nelson Freimer

(nfreimer@mednet.ucla.edu).

Dawson, Smith, Werdyani, et al. (2010)⁸⁰

Approval from Human Research Ethics Authority of NL (protocols #2016.1914 and #2018.0391) Consent and permission to access medical records obtained from all participants.

70 cases recruited from Provincial Medical Genetics Program and NL HBOC Study and extended family members from 5 cases.

880 NL ethnically matched controls screened for the RAD51C c.571 + 4A > G variant.

Whole blood samples from all 70 case participants and 880 controls.

Family history and pedigree evaluations and clinical risk for 5 probands

Performed panel of moderate-high-risk CA susceptibility genes for 5 probands at external facilities using the OncoGeneDx Custom Panel (GeneDX), the Common Hereditary CAs Panel (Invitae) or the Ovarian CA Focus Panel (Fulgent Genetics). Performed WES and WGS microarray analysis to detect additional variants. Based on this, remaining 65 cases, family members, and 880 controls screened for RAD51C c.571 + 4A > G variant. Haplotype analysis on markers flanking the recurrent RAD51C c.571 + 4A > G conducted on family members

WES and WGS performed at Centre for Translational Genomics (St. John's, NL)

WES Libraries were quantified by quantitative PCR and loaded onto the Ion Proton platform for high-throughput sequencing.

DNA sequences analyzed using Mutation Surveyor Software v5.0.0 (SoftGenetics LLC). Data analyzed using TaqMan Genotyper Software v1.4 (Applied Biosystems). GeneMapper Software used to conduct haplotype analysis on family members.

Dr. Darren O’Rielly

Faculty of Medicine, Memorial University of NL, Craig L. Dobbin Genetics Research Centre, St. John’s, NL

darren.orielly@med.mun.ca

Pedram, Zhai, Gulliver et al. (2017)⁸¹

Approved by the Health Research Ethics Authority (HREA), MUN project identification code: #10.33, (latest date of approval: February 10, 2016). All partici­pants provided consent.

Stage 1: 24 subjects 8 obese with high FA, 8 obese with low/zero FA clinical symptom score (FAO, NFO), and 8 healthy controls with normal BMI and low/zero FA symptom score (Ctrl).

Stage 2: 752 subjects

(all taken from the CODING study)

DNA sample: 5 ml of whole blood

Stage 1: Genome-wide screening study using a whole-exome sequencing method (sent to BGI Americas). Top 100 SNPs identified and categorized into 5 subgroups based on gene functions: addiction (Ad), psychological disorders, energy metabolism and obesity, and cancer, unknown function or with other diseases.

Stage 2: Top 19 SNPs in the Addiction subgroup genotyped in all subjects (Génome Québec Innovation Centre).

Exome sequencing done using latest Illumina HiSeq 4000 system with 100 bp and 150 bp paired-end sequencing

Sequencing of top 19 SNPs done using Sequenom iPLEX Gold genotyping technology

*No statement of data availability.

E-mail addresses:

Dr. Pardis Pedram

p.pedram@mun.ca

Guangju Zhai guangju.zhai@med.mun.ca

Dr. Hongwei Zhang hzhang@mun.ca

Dr. Guang Sun

gsun@mun.ca

Young, Woods, Parfrey, et al. (1998)⁸²

Appropriate informed consent was obtained and medical records were reviewed.

17 NL families

WBCs from whole blood

medical records

A physical examination was performed and measurements were made of height and weight.

includedD3S1776, D3S1251, D3S1752, D3S1271, D3S1753,D11S1298, D11S480, FGF3, D11S1369, D15S216,D15S131, D15S204, D15S114, D15S211, D16S419,D16S390, D16S408, D16S526, and D16S265. Additional markers typed for haplotype analysis on chromo-some 3

*Here only Department of Biochemistry, Memorial University of NL, St. John’s, NL, was mentioned

Dr. Terry-Lynn Young, Faculty of Medicine, Memorial University of NL, St. John’s, NL

tlyoung@mun.ca

Woods, Young, Parfrey, et al. (1999)⁸³

Protocol for clinical investi­gation approved by the Human Investi­gations Committee of the Faculty of Medicine, MUN, and the Medical Advisory Council of the St. John’s General Hospital.

*Patient consents not specified.

Genotyped members of 17 NL families (20 males and 14 females with BBS and from 111 unaffected family members) identified through the registry of the Canadian National Institute of the Blind and the Nephrol­ogy Unit at the Health Science Center, St. John’s, NL.

DNA was prepared from whole blood using a simple salting-out method.

≥ 4 polymorphic microsatellite markers spanning the critical regions of the 4 known the 4 known loci (BBS1 (11q), BBS2 (16q), BBS3 (3p), and BBS4 (15q), were examined in all families. PCR using 100 to 200 ng of template DNA was conducted with primers purchased from Research Genetics, Inc.

Haplotypes were constructed for each of the 4 known loci and linkage analysis was tested with two-point linkage Two-point linkage analysis was performed using the MLINK subroutine of FASTLINK to corroborate haplotype analysis.

*Information on likability with administrative data and availability of data not provided.

Dr. Micheal O. Woods

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL

mwoods@mun.ca

Young, Woods, Parfrey, et al. (1999)⁸⁴

Stated that Informed consent had been obtained previously.

17 BBS families of English ancestry were haplotyped at the BBS1, BBS2, BBS3, and BBS4 loci.

DNA was extracted from the lymphocytes of venous blood by a simple salting-out procedure

Markers D11S1298, D11S956, D11S480, D11S4205, D11S1883, D11S4945, PYGM, D11S4946, D11S4940, D11S4938, D11S449, D11S4941, D11S913, and FGF3 were typed in key family members. 1 family was excluded from the study, because several samples failed to amplify. Haplotypes were constructed, for each family, to give the minimum number of recombinations. Disease haplotypes (DH) were identified from alleles that were transmitted from both unaffected parents to affected offspring. LOD scores were calculated by the MLINK subroutine program of FASTLINK (V3.0P).

marker-allele frequencies in disease and normal (non-transmitted) chromosomes of the 10 obligate BBS carriers (parents) were compared. Normal alleles from each parent were used as population controls, to avoid the possibility of inadvertently including BBS1 disease alleles from random carriers in the population. DHs were compared between families in the search for (i) common BBS1 haplotypes that would indicate that the parents of ≥ 2 families were distantly related and (ii) a common ancestral DH.

Accession number and URLs for data in this article are as follows: Online Mendelian Inheritance in Man (OMIM), (for BBS [MIM 209900]) Sixth International SCW 11 Workshop (Nice, France, 1998).

Institute of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia

Credited in paper.

Dr. Terry-Lynn Young, Faculty of Medicine, Memorial University of NL, St. John’s, NL

tlyoung@mun.ca

Katsanis, Beales, Woods, et al. (2000)⁸⁵

*Letter

Full informed consent was obtained in concert with the Institu­tional Review Boards for Human Subject Research at the sponsoring institutions

Included 5 NL and 2 European American BBS pedigrees. (40 total individuals, 31 individuals from NL)

extracted DNA from venous lymphocytes

A detailed family history and pedigree were obtained through personal inter views with appropriate family members. Available pediatric, ophthalmologic, electrophy­siologic, otologic, renal, orthopedic, endocrino­logic and genetic records were recovered and reviewed.

Haplotype and mutation analysis.

lymphocytes for exclusion studies from all known BBS loci by genotyping all available individuals with published markers from the respective critical intervals and constructing haplotypes. Suitable pedigrees were subsequently used for a genome screen with the CHLC 10 cM screening set version 8 (Research Genetics); alleles were analysed and lod scores were tabulated. Fine-mapping studies used additional microsatellites derived from the Genome Database.

Amplified PCR products from patients, relatives and control samples were purified with the Qiagen 96-PCR purification kit (Qiagen) and sequenced with dye-primer chemistry (Applied Biosystems) in an ABI 377 automated sequencer (Applied Biosystems). PCR products were also cloned into the TA vector (Invitrogen) and sequenced to separate the different alleles. Resulting sequences were aligned and mutations were evaluated by the Sequencher sequence alignment program (ACGT Codes). MKKS exon amplification primers are available.

*Unclear if data can be linked to administrative data or who holds the data.

Dr. James R. Lupski,

Department of Molecular and Human Genetics

Baylor College of Medicine, Room 609E, One Baylor Plaza, Houston, TX jlupski@bcm.tmc.edu

Beales, Katsanis, Lewis, et al. (2001)⁸⁶

Informed consent obtained from patients. Protocols approved by the appropriate oversight committees at each institution

163 BBS pedigrees were screened for mutations in MKKS (BBS6). 50 (27 North American/ European and 2 NL pedigrees for which BBS1 was excluded through haplotype analysis, and 21 con­sanguineous pedigrees of Turkish, Iraqi, Pakis­tani, and Indian origin) were included.

BBS6 gene McKusick-Kaufman (MKKS) syndrome gene

(MKKS) on chromosome 20 and for potential assignment of the disorder to any of the other known BBS loci in the human genome.

*unclear how many individuals from NL are included.

Blood samples provided and DNA was extracted by a salting-out process

In several cases, the diagnosis was ascertained by local physicians and verified through extensive examination of medical records.

Combinatorial strategy of linkage disequilibrium and haplotype analysis.

For the genetic analyses, a total of 54 custom-synthesized (MWG/Sigma-Genosys) fluorescent microsatellite STRPs (short-Tandem-repeat polymorphisms) were typed for each family member: for BBS1: D11S4205, D11S1883, D11S599, D11S449, D11S1889, D11S4909, D11S4946, PYGM, D11S4945, and D11S4944; for BBS2: D16S411, D16S415, D16S419, D16S390, D16S408, D16S526, D16S3089, D16S265, D16S3034, D16S408, D16S3057, D16S514, D16S503, D16S400, D16S421, and D16S515; for BBS3: D3S1566, D3S1276, D3S3634, D3S1603, D3S1251, D3S2419, D3S1271, and D3S1278; for BBS4: D15S117, D15S153, D15S125, D15S988, D15S814, D15S650, D15S131 D15S204, D15S114, and D15S205; for BBS5: D2S151, D2S142, D2S156, D2S2330, D2S335, and D2S326; and for BBS6: D20S115, D20S851, D20S189, and D20S186.

mutations in the MKKS gene

Products were resolved on an ABI 377 automated sequencer, and alleles were assigned with GENESCAN v2.3 and GENOTYPER v2.1 software (Applied Biosystems). Sequence data were managed on Sequencher (Genecodes Corporation). Linkage analysis was performed, where appropriate, with the LINKAGE package of programs: two-point linkage data were generated with MLINK (assuming a gene frequency of 0.005 and a penetrance of 0.9); multipoint analyses were performed with LINKMAP.

No information provided on data availability or ability to link with administrative data.

Primers were provided by the Lupski lab in Houston, TX.

Dr. James R. Lupski,

Department of Molecular and Human Genetics

Baylor College of Medicine, Room 609E, One Baylor Plaza, Houston, TX jlupski@bcm.tmc.edu

Moore, Green, Fan et. al (2005)⁸⁷

Approval obtained from Human Investi­gation Committee of MUN and Simon Fraser University REB. Informed consent was obtained for all partici­pants in the study

46 patients (26 males, 20 females) from 26 families.

Blood sample; Also, neurologic assessments, anthropometric measurements, and clinical photographs

Linkage to BBS1, BBS2, BBS3, BBS4, or BBS5 was assessed using microsatellite markers. Linkage to BBS7 or BBS8 was examined by haplotype analysis

*No statement regarding where genetic data was deposited

*No statement on data availability.

Dr. Patrick S. Parfrey

Clinical Epidemiology Unit, Health Sciences Centre, Memorial University, St John’s, NL

pparfrey@mun.ca

Stuckless, Parfrey, Woods, et al. (2007)⁸⁸

Informed consent obtained from all subjects or an appropriate proxy. Ethics approval was granted by the Human Investi­gations Committee of the Faculty of Medicine, MUN, the Health Care Corporation of St. John’s and the Avalon Peninsula Health Board.

More than 300 families with high or intermediate risk for hereditary CRC have been referred to the Medical Genetics Program of NL. 52 families met either the Amsterdam I or Amsterdam II criteria. 290 people from 18 families confirmed to have MSH2 mutation

Mut.: intron 5 splice site; fam #: 12;

# Individ: 151

Mut.: exon 8 deletion; fam. #: 5;

# individ.: 74

Mut.: exon 4-16 deletion; fam #: 1; individ.: 65

235 individuals (81%) found to be mutation positive, remaining 55 (19%) considered presumed positive

DNA from all available family members at 50% risk of inheriting an MSH2 mutation was prepared from whole blood using a simple salting-out method.

The point mutation in the splice donor site of intron 5 in MSH2 (c.942 + 3A > T) was determined by restriction fragment analysis. Exon deletions in MSH2 were detected by Multiplex Ligation-dependent Probe Amplification (MLPA) using genomic DNA

Genotyping, using microsatellite markers, for families segregating the exon 8 deletion performed on either an ABI 3100 Genetic Analyzer (Applied Biosystems) or a Beckman Coulter CEQ 8000 Genetic Analysis System (Beckman Coulter Inc., Fullerton, CA, US). M. MLPA, using the HNPCC probes (kit no. SALSA P003) conducted and analyzed according to protocol provided by MRC-Holland (Amsterdam, Holland) on an ABI 377 Genetic Analyzer (Applied Biosystems, Foster City, CA, US). Marker positions on chromosome 2 were identified using the Genome Browser from the UCSC Genome Bioinformatics website.

Dr. Jane S. Green

Department of Genetics,

Faculty of Medicine, Health Sciences Centre, Memorial University of NL, A1B 3V6, St. John’s, NL

Campbell, Edwards, McLaughlin, et al. (2007)⁸⁹

Written informed consent was obtained from all subjects for use of their DNA samples for research purposes consistent with this study. The ethics review board of the MUN approved this study.

Genotyped 146 Caucasian people with a Lynch syndrome mutation (5′-untrans­lated region poly­morphism in cytochrome P450 17A1 (CYP17; c.−34T→C, exon 4). Included (n = 161). From 161 samples, 15 were excluded for low DNA yield. 92 DNA samples from population-based controls in NL to compare allele frequencies in the current study with that of the general population (identified through random-digit dialing and frequency-matched on age and sex to the case popu­lation)

Genomic DNA was extracted from leukocytes using a common salting out procedure

People had data on age and site of cancer diagnoses, colon screening history, polyp detection, and vital status

genotyped 146 Caucasian Lynch syndrome mutation carriers for a 5′-untranslated region polymorphism in cytochrome P450 17A1 (CYP17; c.−34T→C) and an exon 4 polymorphism in catechol O-methyltransferase (COMT; c.472G→A); 50 mutation carriers had developed colon or rectal cancer at last contact.

Genotypes determined blinded to the subjects' cancer status. YP17 and COMT genotypes determined by PCR and RFLP techniques. 459 bp fragment of CYP17 was amplified using the following primers: forward 5′-TTC TTC CAC AAG GCA AGA GA-3′; reverse 5′-TTG GGC CAA AAC AAA TAA GC-3′. The 25 μL PCR reaction for CYP17 included 100 ng of genomic DNA, 1 × reaction buffer, 3.0 mmol/L of MgCl₂, 0.2 mmol/L of each deoxynucleotide triphosphate, 0.04 units/μL of Taq polymerase, and 0.6 μmol/L each of forward and reverse primers. The region containing the COMT exon 4 polymorphism was amplified using the primers: forward 5′-TAC TGT GG CTA CTC AGC TGT GC-3′; and reverse 5′-GTG AAC GTG GTG TGA ACA CC-3′. The 20 μL PCR reaction for COMT included 200 ng of genomic DNA, 1 × reaction buffer, 0.2 mmol/L of each deoxynucleotide triphosphate, 0.05 units/μL of Taq polymerase, and 0.2 μmol/L each of forward and reverse primers.

Dr. Micheal O. Woods

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL mwoods@mun.ca

Woods, Williams, Careen, et al. (2007)⁹⁰

Kohonen-Corish., Macrae, Genuardi, et al. (2011)⁹¹

Plazzer, Sijmons, Woods, et al. (2013)⁹²

Thompson, Spurdle, Plazzer, et al. (2014)⁹³

N/A

The InSiGHT data­base is the primary store of public information of inherited gastro­intestinal cancer gene variants. The intended uses of the data­base are to assist clinicians in providing accurate health care to their patients and to facilitate biological and clinical studies on variants associated with hereditary GI syndromes.

As of May 2012, there are 12,538 entries for 3,072 unique variants across the MMR genes in the InSiGHT database.

If the InSiGHT database can be realized by detailed analysis of the variant spectrum, by gene and exon, especially when cross-referenced to patient demographics and disease information. Additionally, the results of the interpretation process will allow the calibration of automated methods of variant classification

A database entry is defined as a single record of a variant in the database. A unique variant is a summary account of all the entries of a variant. sharing of variant information from individual clinics and regional or national organisations. 1 central and public web-accessible database powered by the Leiden Open Variation Database (LOVD) [1] platform

InSiGHT which had 3 separate databases which could be combined. Thus, the InSiGHT database became a model system of the HVP for other gene/disease groups to emulate.

“Probably the most used and referenced database is that which is associated with the International Society for Gastro-intestinal Hereditary Tumours (InSiGHT; www.insight-group.org). However, this is primarily a submission catalogue and INSIGHT has made no attempt to actively assemble published data. It does have the advantage, however, of having an extensive list of unpublished variants describing the geographical locale of the variant carrier and whether the alteration was considered pathogenic or nonpathogenic by the submitter.”

This database was then merged into the InSiGHT database

The International Society for Gastrointestinal Hereditary Tumours (InSiGHT) is a database with information on variants contributing to GI cancers. It includes information on the. There has been data submitted on NL participants.

In 2007, a public database was established at MUN: the Mismatch Repair Genes Variant Database (MMRGVD Literature) [4]. The curators of this database obtained variants solely from published articles, consisting of 6,136 entries on 2,260 unique variants. This would go on to represent the largest single component of the InSiGHT database with 49% of total entries and covering 74% of unique variants. Of these, 1366 unique variants had not been submitted directly by any other contributor to the InSiGHT database (Table 2). 580 disease phenotype descriptions were listed, associated with 372 unique variants. 259 reports had Amsterdam or Bethesda criteria (positive or negative) listed. All of this information was obtained from 1,100 published articles

InSiGHT, as a GDSDb will receive data from HVP Country Nodes, such as the Australian Node which is currently expanding to cover 15 laboratories.

The Human Variome Project (HVP) aims to collect all human genetic variation affecting health to a central resource that is freely available, and mobilize the scientific and medical community worldwide to participate in this effort. The International Society for Gastrointestinal Hereditary Tumours (InSiGHT, www.insight-group.org) established a pilot program with the HVP in 2007 to collect all inherited variation affecting colon cancer susceptibility genes.

multiple gene mutation/variant repositories have been merged or linked forming the InSiGHT Colon Cancer Gene Variant Databases

Other work includes fostering the worldwide MMR consortium, which is an initiative between InSiGHT and the NCI Colon Cancer Family Registry, born at the Washington meeting of the 2 groups on April 27, 2010. The InSiGHT Databases now have over 3,800 unique variants listed. Initially, gene-specific data from the original InSiGHT Mutation database was merged with 2 other MMR gene databases from NL⁹⁰ and from the Netherlands. accompanying phenotype information was absolutely essential for the genotypic data to be useful.

Curator of the InSiGHT database:

John-Paul.Plazzer@mh.org.au

MMR Genes Variant Database:

Dr. Micheal O. Woods

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL

mwoods@mun.ca

Win, Dowty, Reece, et al. (2021)⁹⁴

Study approved by the institutional human ethics committees, institutional review boards, or central national authorities of participating centres. Partici­pants provided written or oral informed consent, when­ever required by these commit­tees.

Data from the Inter­national Mismatch Repair Consort­ium (IMRC) (organized by InSiGHT Used secondary from 5585 (173 families from Canada) families (collected between July 11, 2014, and Dec 31, 2018)

For each family, data were collected on identification number; the mismatch repair gene with the pathogenic variant; method of ascertainment of the family (ie, a population-based source, such as a cancer registry, or after presentation to a familial cancer clinic or genetics clinic); the date the family was ascertained; and the person in the family first identified as carrying the pathogenic variant (the proband). For each family member, data were collected on the personal, mother, and father identification numbers; sex; carrier status of a pathogenic variant (ie, a carrier, non-carrier, or untested); genetic testing date; cancer diagnoses (anatomic site and age at diagnosis); polypectomies and bowel surgery (age at the time of surgery); ages at the time of pedigree collection and at last contact or death; and country of residence.

—

Data for this study were contributed by the IMRC investigators. Availability of these data will depend on the agreement of the investigators who contributed the data to the IMRC. Upon agreement, deidentified, individual participant data that underlie the results reported in this Article will be made available, together with data dictionaries and the study protocol, with publication of all IMRC prespecified manuscripts. Data will be available to researchers who provide a methodologically sound proposal for use in achieving the goals of the approved proposal. Proposals can be submitted according to the instructions provided. To gain access, data requestors will need to sign a data access agreement with the University of Melbourne and participating IMRC centres.

Dr. Micheal O. Woods

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL mwoods@mun.ca

Woods, Hyde, Curtis, et al. (2005)⁹⁵

*Only abstract available.

Wish, Hyde, Parfrey, et al. (2010)⁹⁶

Woods, Younghusband, Parfrey, et al. (2010)⁹⁷

Clarke, Green, Green, et al. (2012)⁹⁸

DeRycke, Gunawardena, Middha, et al. (2013)⁹⁹

Haja Mohideen, Hyde, Squires, et al. (2014)¹⁰⁰

Haja Mohideen, Dicks, Parfrey, et al. (2015)¹⁰¹

Xu, Green, Green, et al.(2015)¹⁰²

Zhu, Wang, Zhai, et al. (2017)¹⁰³

Zhu, Wang, Zhai, et al. (2018)¹⁰⁴

Curtis, Yu, Carey, et al. (2022)¹⁰⁵

Savas, Xu, Werdyani, et al. (2015)¹⁰⁶

Ethics approval obtained from the REB of MUN. All patients or their proxies provided informed consent for access to previously collected tumour/tissue samples and medical records.

*Secondary use studies approved, including studies doing additional sample testing

NL Familial Colon Cancer Registry (NFCCR): Patients were eligible for the study if diagnosed with colorectal carcinomas (pure adenomas not included) between 1 January 1999 and 31 December 2003 and were <75 years of age at diagnosis. 750 (64%) from 708 different families consented to be in study.

Controls were identified by random digit dialing from the residents of the province, and matched to the cases on sex and 5 year age group. Controls provided a blood sample and filled out a risk factor question­naire.

*Cohort 2 in Haja Mohideen, Hyde, Squires, et al. (2014)¹⁰⁰

Blood sample (552 people), Tumour tissue (772 tumours from 750 cases) people) and medical records (728 patients from 685 families)

Family questionnaire collected, which enabled pedigrees to be constructed. From the family history questionnaire, recorded the type of cancer, age at diagnosis, and age at death or age at last follow-up for all first-degree relatives (FDR). Cancer diagnoses in consenting family members confirmed by medical records when possible.

Pathology reports available.

16 families selected based on the presumption of a genetic predisposition to disease due to 1) large numbers of affected relatives and 2) younger ages at diagnosis

Forty affected individuals were chosen for sequencing based on genetic relatedness (preferring distant relatives), including 3 cases per family where possible.⁹⁹

149 controls, 118 probands (only 4 with the variant inputted into the LOVID CRC database)⁹⁸

Pannels: DNA sequencing and multiplex ligation-dependent probe amplifications of MMR genes and APC was undertaken. DNA from all patients was screened for MUTYH mutations. The presence of the BRAF variant, p.V600E, and of MLH1 promoter methylation was also tested in tumours.^96-98

Genotyping experiments were performed for 539 patients with available prognostic data at a service provider (Centrillion Biosciences, US) using the Illumina Human Omni1-Quad SNP genotyping platform. This cohort contains > 1 million SNP markers. After quality control, 505 had usable data.⁹⁷

Investigate the associations of polymorphisms from the selected genes (HIF1A, HIF1B, HIF2A, LOX, MIF and CXCL12) in a larger patient cohort. 77 SNPs to be included. the 77 SNPs were obtained as a part of a whole genome SNP genotyping study (535 patients).

Primer sequences for each of the 10 exons of GALNT12 were described by Guda et al. All exons andintron/exon boundaries were screened for variants using standard protocols for automated direct sequencing.⁹⁸

Patients were genotyped 6 (Mitochondrial DNA) mtDNA polymorphisms (16189 (T/C; rs55749223), 10398 (A/G; rs2853826), (MitoT479C, rs41442247; MitoT491C, rs28625645; MitoT10035C, rs41347846; MitoA13781G, rs41358152). In addition, out of 736 patients, 276 patients (274 have results) were investigated for the mtDNA copy number change based on the availability of their DNA samples extracted from both the tumour and non-tumour colon or rectum tissue; 210 of these patients were also investigated in the genotyping analysis. (performed at an outsourced genotyping facility (Centrillion Genomics Services, CA, US).)

The nucleotide positions of these SNPs are annotated based on the Cambridge Reference Sequence (NC_001807.4), whereas the positions of the TaqMan® genotyped polymorphisms are based on the revised Cambridge Reference Sequence (NC_012920.1)¹⁰¹

Initially, a total of 539 patients with available prognostic data and germline DNA were subject to whole-genome SNP genotyping.

QC analyses on the genetic data were performed using PLINK v1.07 and Eigensoft 4.2. After QC analyses, a total of 505 subjects and 729,737 SNPs were included in the final analysis.¹⁰²

Genotyping of peripheral blood DNA samples was performed using the Illumina Human Omni-Quad Bead chip that contains about 1.1 million SNPs at Centrillion Biosciences (US). For quality control purposes, genomic DNA from 200 duplicate samples were sent to the Laboratory of Dr Stephen Gruber (Director, USC Norris Comprehensive Cancer Center, Los Angeles) for genotyping using the Affymetrix Axiom my Design GW Array Plate, which contains 1.3 million probes. SNPs with genotype concordance < 97% between the 2 platforms were dropped from all analyses.”¹⁰³

Genotyping for the GC rs2282679 allele

To monitor quality and consistency between the 2 platforms, DNA samples from 200 CRC patients were typed on both platforms. As the DNA from cases and controls were genotyped on different platforms, a genotype imputation strategy was implemented to integrate the 2 datasets using IMPUTE2 with multi-population reference panels from 1000 Genomes (Phase 1). The imputation approach was validated based on the overlapping SNPs between the 2 platforms and the genotypes from 200 CRC samples that were typed on both platforms. SNPs with genotype concordance < 97% across the 2 platforms were removed from further analysis. For the purpose of the current study, directly measured data from both arrays on rs2282679 were retrieved from the genome-wide SNP genotype database of the NFCCR.¹⁰⁴

Whole exome sequencing was completed using SNP technology to identify new colon cancer associated loci. This was done differently in different families. It is unclear how NL families conducted sequencing and library preparation.⁹⁹

Pannels: Methylation was detected using the MS-MLPA kit ME001B (MRC-Holland)

Automated sequencing was done on an ABI 3700 DNA Analyzer (Applied Biosystems). Transgenomic Wave 3500HT System, Omaha, Nebraska, US) was used to detect MUTYH mutations.^96-98

In total, 2 pathogenic variants were identified in at least 11 probands (3: c.907G > A (p.Asp303Asn, 1: c.1187A > G (p.Tyr396Cys)) variant) from 4 different families All variants have been submitted to the LOVD CRC database (www.lovd.nl/GALNT12) (this was only 4 people)

Genotypes were obtained using the Illumina Human Omni1-Quad Bead Chip at a service provider (Centrillion Genomic Services, US).¹⁰⁰

Whole-genome SNP genotyping using the Illumina® Omni1-Quad human SNP genotyping platform (service provider: Centrillion Biosciences, US).¹⁰²

Genotyping conducted using the Illumina Human Omni-Quad Beadchip that contains about 1.1 million SNPs at Centrillion Biosciences (US). Control individuals were genotyped in the Laboratory of Dr. Stephen Gruber (Director, USC Norris Comprehensive Cancer Center, Los Angeles) using the Affymetrix Axiom® myDesign™ GW Array Plate, which contains 1.3 million probes.¹⁰⁴

Patrick S. Parfrey

Health Sciences Centre, 300 Prince Philip Drive, St. John's, NL A1B 3V6

pparfrey@mun.ca

Dr. Micheal O. Woods

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL

mwoods@mun.ca

Dr. Sevtap Savas

Memorial University,

Division of Biomedical Sciences, Human Genetics and Genomics

savas@mun.ca^100,101

Peizhong Peter Wang

Division of Community Health and Humanities, Faculty of Medicine, Memorial University of NL, St. John’s, NL

pwang@mun.ca¹⁰⁴

Request to access the datasets should be directed to NL Colorectal Cancer Registry (PP; pparfrey@mun.ca) and Research, Grant, and Contract Services (rgcs@mun.ca) at Memorial University of NL, St. John’s, NL, and the ethics approval shall be obtained from the Health Research Ethics Board (HREB), Ethics Office, Health Research Ethics Authority.¹⁰⁵

Dorani, Hu, Woods, and Zhai. (2018)¹⁰⁷

Schumacher, Schmit, Jiao, et al. (2015)¹⁰⁸

Bien, Su, Conti, et al. (2019)¹⁰⁹

Guo, Lin, Wen, et al. (2021)¹¹⁰

Thomas, Sakoda, Hoffmeister et al. (2020)¹¹¹

Archambault, Su, Jeon, et al. (2020)¹¹²

Archambault, Jeon, Lin, et al. (2022)¹¹³

Schmit, Edlund, Schumacher, et al (2019)¹¹⁴

Huyghe, Bien, Harrison, et al. (2019)¹¹⁵

Huyghe, Harrison, Bien, et al. (2021)¹¹⁶

Original data collection approved by MUN Health Research Ethics Authority (HREA) with the approval number HIC 01.70. Present studies recog­nized by HREA as the use of second­ary data which have already been collected and de-identified, and did not require a clearance.

NFCCR dataset used, see above.

These samples were processed for larger studies developed by the colorectal cancer Trans­disciplinary (CORECT) consort­ium

(672 people: 195 cases, 477 controls on the Affymetrix Axiom platform. This was also stated as being part of the CORECT study (supple­mental materials.¹⁰⁸ 17 cases and 68 controls from NFCCR, collected from 2000 to 2004)^112,113

See above.

GWAS array data (with approximately 1.3 million SNPs and indels on 2 physical genotyping chips (pegs). Prior to imputation, SNPs with < 95% call rate, concordance < 95% with 1000 Genomes in samples genotyped for quality control, or HWE P < 10^-4 in controls were excluded. All SNPs overlapping 1000 Genomes were matched to the forward strand.) from NL was done at McGill University and Génome Québec Innovation Centre, Montréal, QC, for genotyping the Sequenom panel in on the Affymetrix Axiom Platform) the NFCCR samples

For 65 SNPs initially discovered in the GECCO and CORECT studies, estimated the log-odds ratios from a model fit with overall CRC (no age restrictions) as the outcome and the 141 SNPs as independent variables, adjusted for age, sex, principal components, and genotype platform^112,113

Huyghe, Bien, Harrison, et al. (2019)¹¹⁵

imputed genotype datasets (BAM files) from previous studies to the Haplotype Reference Consortium panel (39.2 million variants) using the University of Michigan Imputation Server.

The CRC Transdisciplinary (CORECT) consortium coordinated the genotyping of data. Genotyping was conducted using a custom Affymetrix genome-wide platform (the Axiom CORECT Set) on 2 physical genotyping chips (pegs) for 2 datasets with around 1.2 and 1.1 million SNPs. The first dataset has 1,236,084 SNPs and 696 samples with 200 cases and 496 controls and the genotyping rate was 0.997. In GWAS, genotyping rate is computed as the percentage of samples (including both cases and controls) that are successfully genotyped. The second dataset has 1,134,514 SNPs and 656 cases with a genotyping rate of 0.888. Using PLINK, a tool for analyzing genetic data, we merged these 2 datasets based on their common SNPs and obtained a dataset of 265,195 SNPs and 1,152 unique samples. Among the samples, 656 were cases and 496 were controls. After the steps of quality control and imputation, the final preprocessed and balanced dataset had 186,251 SNPs and 944 samples (472 being cases and 472 being controls)

Data availability: Colorectal Transdisciplinary (CORECT) Study

GitHub

Data underlying article (SNP (ex, rs72647484), Locus (ex. 1p36.12), Risk/other (ex. T/C), allele Risk allele freq (ex. 0.9107), and PMID (ex. 25990418) provided for 141 risk variants.) accessed from the Fred Hutchinson Cancer Center. The derived data generated shared on reasonable request to the corresponding author with permission of the Fred Hutchinson Cancer Center.^112,113

Dr. Ting Hu

Department of Computer Science, Memorial University, St. John’s, NL

ting.hu@mun.ca

Dr. Micheal O. Woods

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL

mwoods@mun.ca

Contact:

Ulrike Peters, Email: upeters@fredhutch.org.¹¹¹

Dr. Richard B. Hayes

NYU Langone Health

New York, NY Richard.B.Hayes@nyulangone.org).^112,113

Savas, Hyde, Stuckless, et al. (2012)¹¹⁷

Haja Mohideen, Hyde, Squires, et al. (2014)¹⁰⁰

Haja Mohideen, Dicks, Parfrey, et al. (2015)¹⁰¹

Dan, Werdyani, Xu, et al. (2016)¹¹⁸

Approved by the Human Investigation Committee of MUN and the Regional Health Boards.

Informed consent not required by local ethics board as study was considered an anonymous chart review.

(#12.206, #10.133).

Population-based retrospective cohort of 280 patients followed for ≤ 12.5 yrs after diagnosis.

From the Avalon Peninsula of NL, new cases (diagnosed in 2 St. John’s health facilities, ascer­tained between Jan 1, 1997 and Dec 31, 1998.

*Cohort 1 in Haja Mohideen, Hyde, Squires, et al. (2014)¹⁰⁰

Surgical specimens available for 280 (272 could be genotyped) of 292 patients identified. DNA extracted from formalin-fixed paraffin-embedded non-tumour colon and rectum tissues.

For all 280 patients the clinical data was collected. Prognostic data of these patients was collected from the medical and hospital records and the NL and Labrador Centre for Health Information.

DNA samples were extracted from either peripheral blood samples (n = 40) or the nontumour colon or rectum tissues obtained during the surgery (n = 207)

initially selected 5 tagSNPs in SLC6A4 (rs11080121, rs12150214, rs2066713, rs4251417, and rs140700) and 2 tagSNPs in BDNF (rs7124442 and rs6265) and 1 tagSNP in AVPR1B (rs35369693) but, rs11080121 and rs2066713 in SLC6A4 and rs7124442 in BDNF could not be genotyped.

Data from the 5 remaining SNPs were included in this study. At least 5% of the samples were genotyped 2 and all duplicated genotypes were concordant.¹¹⁷

Selected 6 hypoxia pathway genes (HIF1A, HIF1B, HIF2A, LOX, MIF and CXCL12). 49 SNPs from these genes (both tagged and untagged) were successfully genotyped.¹⁰⁰

No linkability. Due to lack of consents

Genotyped using the Sequenom MassArray® technology by The Centre for Applied Genomics Facility, Toronto, ON ¹¹⁷

Sequenom MassArray technology at an outsourcing genotyping facility (UHN Analytical Genetics Technology Centre, ON; n = 35 SNPs) or in-house TaqMan SNP genotyping assays (n = 14 SNPs).¹⁰⁰

Out of the 6 SNPs genotyped, 2 SNPs [16189 (T/C; rs55749223) and 10398 (A/G; rs2853826)] were genotyped using the TaqMan^® SNP genotyping technique.

The genotype data for the remaining 4 mtDNA polymorphisms (MitoT479C, rs41442247; MitoT491C, rs28625645; MitoT10035C, rs41347846; MitoA13781G, rs41358152) were obtained using a genome wide SNP genotyping technique (Illumina Human Omni1-Quad genome wide SNP genotyping platform) as part of another project of our team.¹⁰¹

Sequenom MassArray^® technique at a service provider (Clinical Genomics Centre, Mount Sinai Hospital, Toronto, ON). 15 DNA samples genotyped twice (6%) and in all cases the genotypes obtained were identical. All SNPs in this cohort had MAFs ≥ 5% and their genotype frequencies were in HWE equilibrium.¹¹⁸

Dr. Sevtap Savas

Memorial University,

Division of Biomedical Sciences, Human Genetics and Genomics

savas@mun.ca

Fernandez, Fox, Bhatia, et al. (2012)¹¹⁹

MUN’s Human Investi­gations Committee approved this study (#02.26) and all individuals consented to be in the study.

Recruited people with pulmonary fibrosis with the 5 respirol­ogists in NL from January 2006 to July 2011 (90% consented to study. 78 pulmonary fibrosis patients (28 familial plus the recruitment of an additional 49 affected relatives [first degree relatives] and 50 sporadic cases). Excluded patients with significant environ­mental exposures known to be associated with lung fibrosis, or with known collagen vascular diseases,

DNA was extracted from whole blood using either a simple salting out method or by using the Wizard Genomic DNA Purification Kit.

Additional: family history form, medical history form, questionnaire on environmental exposures, medical records, biopsy proven UIP on a clinical pathology report or, in the absence of surgical lung biopsy, met American Thoracic Society/European Respiratory Society criteria for IPF

Relatives completed Pulmonary Function Tests (PFTs) and a high-resolution chest CT scan (HRCT).

DNA sequencing in both directions was performed for all exons and exon/intron boundaries for 4 of the known genes causing familial pulmonary fibrosis were sequenced in 28 FPF probands and 50 sporadic PF patients: TERT (telomerase reverse transcriptase) and TERC (telomerase RNA component) Autosomal dominant mutations in surfactant protein C (SFTPC) and in surfactant protein A2 (SFTPA2). Variant nomenclature and primers were derived from the following RefSeq accession numbers: NG_009265.1 (TERT), NG_016363.1 (TERC), NG_016968.1 (SFTPC) and NG_013046.1 (SFTPA2).

Telomere length assays carried out on 5 affected individuals with TERT mutations from 2 families.

Automated sequencing was performed on either an ABI 3130 Genetic Analyzer or an ABI 3730 Genetic Analyzer (Applied Biosystems, Foster City, CA).

*Only NL researchers credited with DNA sequencing. Likely housed in NL. Was connected with medical records and therefore linkable with administrative data.

*No stamen of data availability.

Dr. Micheal O. Woods

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL

mwoods@mun.ca

Powell, Bridget, Fernandez, et al, (2019)¹²⁰

The Health REB (Reference Number 04.89) for MUN approved this study, and all participants provided consent.

Over a 5-year recruitment period assembled 53 IA families containing 154 affected individuals and 415 unaffected family members for study. through collab­oration between MUN’s Discipline of Genetics and the Department of Surgery (Division of Neuro­surgery, only neuro department in NL) at Eastern Health. Referred to study if presented or had family member that presented with ruptured or unruptured IA. *Not all partici­pants couple provide a DNA sample. For this specific paper, 100 controls from CRC study (described in CRC section also included).

Whole blood samples provided by people affected by IA and family members.

Diagnosis of IA confirmed through CT imaging of the Circle of Willis or by magnetic resonance angiography. Consenting relatives obtained through family history offered CT angiography, underwent a comprehensive medical and family history assessment.

For this specific paper: WES completed for a cohort of 12 affected individuals (5 from 1 family, 7 from the other) from 2 multiplex families (> 11 affected family members)

Filtered variants were prioritized based on validation by Sanger sequencing and segregation within the families. Following this filtering process, variants C4orf6 c.A1G (p.M1V) and SPDYE4 c.C103T (p.P35S) were sequenced using Sanger sequencing in 100 population controls.

Genomic DNA was extracted from whole blood using either a simple salting out method or the Wizard® Genomic

WES was completed at McGill University and Genome Quebec Innovation Center (MUGQIC, Montreal, QC). The Agilent SureSelect 50 Mb All Exon kit was used for exome capture and paired-end sequencing was completed on the Illumina® HiSeq 2000 platform.

*No statement of data availability. Seems to be on-going.

Likely likable with administrative data through medical insurance number since obtained through clinical interactions and findings from this study can impact patient health.

Dr. Micheal O. Woods

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL

mwoods@mun.ca

Hodgkinson, Parfrey, Bassett, et al. (2005)¹²¹

Consent for analysis of past and current cardio­logy records and for DNA analysis was obtained from each subject (or surro­gate) in compli­ance with the Human Investi­gation Committee require­ments of the Health Care Corpor­ation of St. John's. All available clinical records and autopsy reports were obtained.

367 subjects (212 male, 155 female) from “well-ascertained” sibships (those where ≥ 50% of siblings were known to be at high or low risk of ARVC as determined on the basis of clinical, pedigree, and/or haplotype data.) from 11 families were studied.

Blood sample: DNA extracted from peripheral lymphocytes (201 out of the 367 subjects)

Part 1: A NL family with autosomal-dominant ARVC was reported in 1988. An affected-only linkage analysis was performed. 17 affected individuals who had DNA samples available for molecular analysis. Linkage of disease to 3p25 was confirmed with a maximum multipoint logarithm of the odds score of 9.3 at D3S1585. Analysis of 8 markers allowed the construction of a chromosome 3p25 HR haplotype with D3S3610-Fibulin2-D3S2385-D3S1585-D3S1554 to 708d1CA-316A10CA-D3S3613 ordered from telomere to centromere shared by all affected family members.

Part 2: 10 additional families with ARVC were studied, and the critical region was reduced to 2cM, at which locus the identical set of DNA markers (haplotype) co-segregates with ARVC. The presence or absence of the 2cM HR haplotype was determined for each family member assessed.

Part 2: Fluorescent-labelled primers used to amplify di-, tri-, or tetra nucleotide repeats by the polymerase chain reaction, and fragments analyzed by capillary gel electrophoresis by the use of an ABI 310 genetic analyzer (Applied Biosystems, Foster City, California).

Dr. Kathleen Hodgkinson

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL,

khodgkin@mun.ca

Merner, Hodgkinson, Haywood, et al. (2008)¹²²

Informed consent was obtained in compliance with the Human Investi­gation Committee require­ments of the Eastern Health Corpor­ation of St. John's, NL (study number 00-176).

15 unrelated families referred to the NL Provincial Medical Genetics Program or the NL Labrador genetics cardio­myopathy clinic for family history of cardio­myopathy and sudden death. Families deter­mined to have ARVC on the basis of clinical testing with estab­lished criteria. Total of 496 subjects born at a priori 50% risk (clinically affected and their first-degree relatives) available for study. Only subjects from well-ascertained sibships in study.

Blood samples from 295 subjects born at a priori 50% risk collected. (201 not DNA tested for mutation)

Clinical data prospectively collected over 11 years.

Step 1: Screening candidate genes. Mutation-screening panel established with genomic DNA from 4 clinically affected subjects from 3 families and 3 spouses (controls). All coding and noncoding exons and intron-exon boundaries of positional candidate genes for ARVD5 sequenced. Sequencing variants found exclusively in clinically affected subjects on the mutation-screening panel were experimentally determined to reside on the ARVD5 haplotype by segregation analysis.

Step 2: Genotyped 18 polymorphic microsatellite markers on clinically affected subjects across all families to identify a disease-associated haplotype at 3p25. Identified key recombinations and reduced the disease region to a 2.36 Mb interval containing 20 annotated genes. Bidirectional resequencing of the 20 physical candidate ARVD5 genes revealed 240 variants. Nineteen variants found exclusively in clinically affected subjects on the mutation-screening panel (based on also screening 161 population controls from a colorectal study, and 47 spouses), and 11 were determined to reside on the ARVD5 ancestral haplotype through segregation analysis in 1 family. Only 1 of the 5, TMEM43 1073C→T (S358L), shared by all clinically affected subjects

Step 3: Sequenced genomic DNA from all available subjects born at a priori 50% risk (n = 295) across the 15 ARVC families for the presence of the 1073C→T TMEM43 mutation.

Clinical data: Annual visits by subjects to genetics cardiomyopathy clinic in which 12 lead ECGs, Holter monitors, MRIs, signal-averaged ECGs, and echocardiograms were done. Clinical data obtained retrospectively from medical records including “at-risk” relatives not seen in clinic and autopsy results. Subjects categorized as affected, unaffected, or unknown. (in which disease status was known in ≥ 50% of siblings) were included in this study.

Step 1: Purified PCR products were cycle sequenced in both forward and reverse directions with the use of BigDye Terminator V3.1 cycle sequencing kit on an automated ABI 3700 DNA analyzer (Applied Biosystems)

Sequencing electropherograms were inspected manually and analyzed with Mutation Surveyor software (Transition Technologies).

The URLs for data presented herein are as follows:

• NCBI dbSNP

• Online Mendelian Inheritance in Man (OMIM)

• UCSC Genome Browser

Dr. Terry-Lynn Young

Memorial University of NL

St. Johns, NL

tlyoung@mun.ca

Haywood, Merner, Hodgkinson, et al. (2013)¹²³

Study complies with the Declar­ation of Helsinki; informed consent was obtained in compli­ance with the Human Investi­gation Committee requirements of the Eastern Health Care Corporation of St John's, NL (study # 00-176)

*Study included both UK and NL probands.

NL population-based controls (n = 161) were obtained through random phone dialling, as part of a large colo­rectal cancer study.

Blood samples.

To identify which recurrent mutations were due to potential founder effects, comparison of the ARVC-haplotypes was carried out. DNA from NL probands was genotyped for 5 microsatellite markers spanning TMEM43 on chromosome 3p25, and disease haplotypes inferred by comparing alleles in UK probands to those residing on the disease haplotypes in NL patients with the same mutation.

33 variants identified. 15 variants identified from bidirectional sanger sequencing of UK cohort had been found in control NL population previously so were non-pathogenic. Of the 18 variants remaining from the original 33 identified in UK probands and not seen in the NL controls, 5 were present in > 1% of the UK population control panels and therefore classified as ‘no known pathogenicity’. This included 2 synonymous (p.P74P and p.S303S) and 3 intronic (c.443 to 48 G > A, c.1203 + 719 G > T, c.1203 + 771_775 delCAAAA) variants (Table 2). Our data support the current classification of 3 of these 5 variants (p.P74P, p.S303S, c.443 to 48 G > A) as having unknown pathogenicity in the ARVD/C database.

Variant analysis was carried out using the Mutation Surveyor v3.25 software (SoftGenetics, LLC, PA, US).

No mention of data availability.

Dr. Terry-Lynn Young

Memorial University of NL

St. Johns, NL

tlyoung@mun.ca

Hodgkinson, Connors, Merner, et al. (2013)¹²⁴

Human REB of the Eastern Health Care Corpor­ation of St. John's study # 00-176

Partici­pants provided informed consent

15 NL families referred to a genetic cardio­myopathy clinic with a history of sudden cardiac death and were found to have a p.S358L mutation in TMEM43 gene.

Subjects were unaffected (n = 164) if they did not have TMEM43 p.S358L.

412 subjects were included in the study: 258 affected) and 154 unaffected.

DNA was extracted from peripheral lymphocytes using standard methods Additionally accessed medical records for all subjects. Prospective serial 12-lead ECGs [≥ 1 available for 300 subjects], echocardiograms [≥ 1 available for 248 subjects] and Holter monitors were [≥ 1available for 239 subjects] available from 1998 onward. All clinical assessments were repeated at 1- to 3-year intervals.

Subjects (n = 295) initially had DNA haplotype analysis at the 3p25 ARVD5 locus and subsequent direct mutation analysis for the p.S358L mutation in TMEM43 (present = 144, absent n = 151).

No information provided on sequencing software or data availability.

Dr. Kathleen Hodgkinson

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL

khodgkin@mun.ca

Hodgkinson, Howes, Boland, et al. (2016)¹²⁵

Consent for retrospective and current chart review and for genetic analysis was obtained from each indiv­idual (or surrogate) in compliance with institu­tional review committee and regional ethics board (study no. 00.176).

Studied 24 multiplex families followed for ≤ 20 years segregating an autosomal dominant p.S358L mutation in TMEM43. 229 unaffected, 393 affected, 240 unknown.

Family histories obtained from which 862 indi­viduals who were born at an a-priori 50% pedigree risk were identified

*No new information provided, see above*

Genetic results obtained initially using a research-generated disease-associated haplotype²⁴ and later direct mutation analysis.

Managed at the Provincial Cardiac Genetics Clinic

No information provided on sequencing software or data availability.

Dr. Kathleen Hodgkinson

Discipline of Genetics, Faculty of Medicine, Health Sciences Centre, St. John’s, NL

khodgkin@mun.ca

Bourassa, Meijer, Merner, et al. (2012)¹²⁶

Approved by the relevant ethic commit­tees, and informed consent was obtained from all subjects

110 study participants

(107 from 4 NL families and 3 from ON probands) + 169 NL popu­lation controls (used from previous NFCCR cohort)

blood was collected for DNA analyses.

Diagnosed by single neurologist

A mutation screening panel of 53 genes, composed of 2 affected individuals with the ancestral disease haplotype from 2 different families and an unaffected control, was established. PCR analysis of all coding exons and flanking intron regions of the 53 genes and predicted genes located in the 1.9 Mb disease haplotype (sequenced at the McGill University and Génome Québec Innovation Centre) was conducted. Searched for rare variants (those with less than 1% allele frequency) that were exclusively present in the 2 affected individuals

Then, determined the allele frequency of remaining interesting variants by screening 169 NL population controls who were previously collected for NFCCR study.

single variant of interest was observed in vesicle-associated membrane protein 1 (VAMP1 [MIM 185880]) at position chr12: g.6574054T > G. VAMP1 has 3 annotated isoforms, VAMP1A, VAMP1B, and VAMP1D, that only differ by their last exon: VAMP1A and VAMP1B is c.340 + 2T > G, and the VAMP1D mutation is c.342T > G (p.Ser114Arg). The c.340 + 2T > G variant is thought to be the disease-causing variant.

Segregation of this particular variant was tested with genomic DNA from every participant, and the variant segregated with the disease in all 4 families, as well as in the 3 single cases from ON. The nucleotide mutation was also assessed in variant databases.

PCR analysis: analyzed with Mutation Surveyor v.3.0 (SoftGenetics)

Dr. Guy A. Rouleau

Department of Medicine, Université de Montréal, Montréal, Quebec

guy.rouleau@umontreal.ca

Abdel-Razek, Collier, Predham, et al. (2017)¹²⁷

Not stated.

66 total (33 affected, only 16 diag­nosed by mutation) and both those affected and their family members (indi­viduals born at an a-priori 50% risk) from 3 pedigrees.

Uknown

*May not be relevant, just a chart review*

Individuals were included if disease status of ≥ 50% of their sibship was known (n = 66), but this included people diagnosed through testing for mutation and/or obligate carriers (OC) and/ or documented SCD < 50 years so not necessarily genomic data.

66 total (33 affected, only 16 diagnosed by mutation) and both those affected and their family members.

Collected genetic and clinical records from medical data.

Unknown

Unknown

Etchegary, Pike, Puddester, et al. (2022)¹²⁸

study was approved by the provincial Health REB and Eastern Health’s Research Proposal Approvals Committee (Ref#: 2022.125).

Not available

Not available.

This is a protocol for a dataset of BRCA and LS mutation carriers in NL (identified from 2006 (CPS testing start date) to present day) To assess (1) Health care utilization (uptake of risk management interventions—screening, surgeries, including prophylactic surgery, specialist appointments), (2) adherence to recommended risk management interventions, (3) cancer outcomes (cancer incidence, stage at cancer diagnosis). NLCHI will link the data collected from the PMGP in Obj. 1. Wiil include people with or without a history of cancer with any molecularly confirmed hereditary cancer syndrome [HCS] (any 1 or a combination of any hereditary cancer genes including LS genes, BRCA1/2, ATM, CHEK2, PALB2, RAD51C, CDH1, MEN1, VHL, etc.)

This will also include qualitative data.

*Data about the mutations themselves is not the priority but the mutations of the people will likely be included*

Unclear if this has actually been established.

Not available.

Dr. Holly Etchegary

Department of Clinical Epidemiology, Faculty of Medicine, Memorial University of NL, St. John’s

holly.etchegary@mun.ca

Dyer, Lin, Shapoval, et al. (2024)¹²⁹

Not available

Not available

Not available

MethMotif is a database publicly available database that provides a comprehensive repository of transcription factor (TF)-binding profiles, enriched with DNA methylation patterns. It includes multiple species. Incorporates a vast array of ChIP-seq and Whole Genome Bisulfite sequencing (WGBS) or Enzymatic Methyl Sequencing (EM-seq) datasets from diverse sources

Release Notes

At least 1 set of Human NL samples is available in the database:

GEO Accession viewer

Not available

Touati Benoukraf

Division of BioMedical Sciences, Faculty of Medicine, Memorial University of NL, St. John’s

tbenoukraf@mun.ca

Newfoundland

Researchers:

1. Dr. Kathy Hodgkinson (Ph.D.): Memorial University

2. Dr. Darren O’Rielly (Ph.D., FCCMG. Memorial University Molecular Genetics Laboratory (Director), Eastern Health

3. Dr. Proton Rahman (MD., FRCPC.): Memorial University

4. Dr. Neetu Singh (Ph.D.): Marathon of Hope - Atlantic Cancer Consortium

5. Dr. Curtis French (Ph.D.): Memorial University

6. Dr. Touati Benoukraf (Ph.D.): Memorial University, Bioinformatics for Personalized Medicine (Canada Research Chair)

7. Dr. Sevtap Savas (Ph.D.): Memorial University, Beatrice Hunter Cancer Research Institute

8. Dr. Michael Woods (Ph.D.): Memorial University, National Board of Directors of the Canadian Cancer Society

9. Dr. Terry-Lynn Young (Ph.D.): Memorial University, Craig L. Dobbin Genetic Research Centre (Director, Genomics Research), Laboratory Medicine Program, Eastern Health (Medical Scientist)

10. Dr. Guangju Zhai (Ph.D.): Memorial University

11. Dr. Gerald Mugford (Ph.D): Memorial University

12. Dr. Dennis O’Keefe: The NL Genome Project (Co-Principal Investigator)

Institutions:

1. Provincial Medical Genetics Program

2. Central Newfoundland Satellite Genetics Centre

Nova Scotia

Researchers:

1. Lynette Penney (MD.): Dalhousie University, IWK Health (Division Head of Medical Genetics)

2. Steve Armstrong (Ph.D): Genome Atlantic (President/CEO)

3. Kristin Tweel (Ph.D): Genome Atlantic (Director, Sector Innovation)

4. Britta Fiander (Peng): Genome Atlantic (Director, Innovation Programs)

5. Dr. Victor Martinez (Ph.D): Dalhousie University, IWK Health (Clinical Genomics Specialist)

6. Dr. Karen Bedard (Ph.D): Dalhousie University

7. Dr. Jo-Ann Brock (MD.): IWK Health (Medical geneticist, Division Head, Pathology and Laboratory Medicine)

8. Dr. Sarah Dyack (MD.): IWK Health (Medical geneticist, Division Head, Medical Genetics): Dalhousie University

9. Dr. Anthony Vandersteen (MD. Ph.D FRCP. FRCPC. FCCMG.): IWK Health (Medical Geneticist)

10. Dr. Robin Urquhart (PH.D.): Dalhousie University, Population Cancer Research (Endowed Chair), Atlantic PATH (Scientific Director)

11. Dr. Jason Hicks (M.Sc.): Atlantic PATH (Executive Director)

12. Dr. Ellen Sweeney (Ph.D.): Atlantic PATH (Research Director), Dalhousie University

13. Yunsong Cui (M.Sc.): Atlantic PATH (Data Analyst)

14. Dr. Luke Chen (MD., FRCPC., MMEd.): Dalhousie University

15. Dr. Dan Gaston (PhD.): Dalhousie University

16. Dr. Manuel Mattheisen (MD.): Dalhousie University

17. Dr. Christopher McMaster (Ph.D): Dalhousie University, CIHR Institute of Genetics

18. Dr. Johane Robitaille (MDCM.): Dalhousie University

Institutions:

1. Maritime Medical genetics

2. Genome Atlantic

New Brunswick

Researchers:

1. Dr. Rodney J. Ouellette (MD.): Atlantic Canada Research Institute (Founder and Senior Scientist), CHU Dumont (Laboratory Medical Head-Molecular Genetics)

2. Dr. Gilles Robichaud (Ph.D): Université de Moncton, BHCRI (Senior Scientist), Atlantic Canada Research Institute (Adjunct Scientist)

3. Dr. Mouna Ben Amor (MD.): Clinical Genetics Vitalité Health Network, Université de Moncton

4. Dr. Eric Allain (Ph.D.): Université de Moncton, Vitalité Health Network, Atlantic Cancer Research Institute, BHCRI (Associate member)

5. Dr. Nicolas Crapoulet (Ph.D.): Vitalité Health Network (Clinic Specialist in Molecular Genetics)

6. Dr. Dominique Comeau (Ph.D.): Vitalité Health Network

7. Dr. Nadia Bouhamdani (Ph.D.): Vitalité Health Network (Clinical Specialist and Researcher)

Prince Edward Island

1. Dr. Denise Lockhart: PEI Cancer Treatment Centre (Manager)