www.iccg.org

1. A Unified Clinical Genomics Database NHGRI - U41 Genomic Resource Grant www.iccg.org

2. Variant Analysis for General Genome Report 3-5 million variants • Genes ~20,000 Coding/Splice Variants • <1% • Published as • Disease-Causing • Pharmacogenetics 5-10 Variants Rare CDS/Splice Variants 20-40 “Pathogenic” Variants • LOF in Disease • Associated Genes 30-50 Variants • Review evidence for variant pathogenicity • Review evidence for gene-disease association and LOF role

3. Classification of Reported Pathogenic Variantsfound in Human Genomes Likely Path – 1% Pathogenic – 2% Benign 18% Uncertain significance – 52% Likely Benign 26%

4. U41 Genomic Resource Grant: • A Unified Clinical Genomics Database To raise the quality of patient care by: • Standardizing the annotation and interpretation of genomic variants • Sharing variant and case level data through a centralized database for clinical and research use • Implementing an evidence-based expert consensus process for curating genes and variant interpretations

5. Supporting data collection, submission and curation Work with NCBI to design ClinVar to meet the needs of the community Develop data dictionary, ontologies, and work with standards bodies Define data submission and access policies for variant and case-level data including genotypes and phenotypes Work with labs to solicit and support data submission Evidence-based curation of structural variants - (Riggs et al. 2012 ) Evidence-based curation of sequence variants (ACMG Committee work in progress) Develop a gene-centric resource to define the medical exome and provide tools to support use in genomic medicine Work with vendors to improve reagents for genomic analysis (CMA, WES, WGS)

6. NIH NCBI ClinVar • www.ncbi.nlm.nih.gov/clinvar

8. Sequencing Laboratories Which Have Agreed to Share Data Alfred I Dupont Hospital for Children All Children's Hospital St. Petersburg Ambry Laboratories ARUP Athena Diagnostics Baylor Medical Genetic Laboratories Boston Children's Hospital Boston University Children's Hospital of Philadelphia Children's Mercy Hospital, Kansas City Cincinnati Children's Hospital City of Hope Molecular Diagnostic Lab CureCMD Denver Genetic Laboratories Detroit Medical Center Emory University Fullerton Genetics Laboratory GeneDx Cleveland Clinic Greenwood Genetics Harvard-Partners Lab for Molec. Medicine Henry Ford Hospital Huntington Medical Research Institutes Illumina Clinical Services Lab Indiana University/Perdue University InSiGHT LabCorp / Integrated Genetics / Correlagen Masonic Medical Research Laboratory Mayo Clinic Mt. Sinai School of Medicine Nationwide Children's Hospital Nemours Biomolecular Core, Jefferson Medical Oregon Health Sciences University Providence Sacred Heart Medical Center Quest Diagnostics SickKids Molecular Genetic Laboratory Transgenomics University of Chicago University of Michigan University of Nebraska Medical Center University of Oklahoma University of Penn University of Sydney University of Washington Women and Children's Hospital Wayne State University School of Medicine Yale University

9. Documenting arguments will improve the • evidence-based assessment of variants

10. U41/ClinVar pilot project Comparison of three laboratories classifications for variants in 12 RASopathy genes: BRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NRAS, PTPN11, RAF1, SHOC2, SOS1, SPRED1 20% discrepant 53 discrepancies: 60% differ based upon likelihood (Benign vs LB, P vs LP) 34% differed VUS vs Likely Pathogenic/Likely Benign 6% differed VUS vs Pathogenic

11. Lab Classification Differences 84% differences were Lab A reporting a more aggressive assertion (Pathogenic/Benign) than Lab B/C (LP, LB, VUS) 16% of differences were Labs B/C reporting a more aggressive assertion than Lab A

12. ACMG Lab QA Committeeon theInterpretation of Sequence Variants ACMG Sue Richards (chair), Heidi Rehm (co-chair) Sherri Bale, David Bick, Soma Das, Wayne Grody, Madhuri Hegde, Elaine Spector AMP Julie Gastier-Foster, Elaine Lyon CAP Nazneen Aziz, Karl Voelkerding

13. 5 Categories: Pathogenic Likely Pathogenic Uncertain significance Likely benign Benign Pathogenic = 1 stand-alone OR 2 strong OR 1 strong + ≥3 supporting Likely Pathogenic = 1 strong + 2 supporting OR ≥4 supporting Benign = 1 stand-alone OR 2 strong OR 1 strong + ≥3 supporting Likely benign = 1 strong + 2 supporting OR ≥4 supporting

14.  *Variants should be classified as Uncertain Significance if other criteria are unmet

15. QC and Expert Concensus Guideline Practice guidelines Expert Curation Evidence-based review ClinVar Multi-Source Curation Inter-laboratory Single-Source Curation Intra-laboratory Uncurated Large variant datasets dbSNP/dbVar

16. Curation - ClinVar

17. Analysis of LOF Variants - single genome 82 LOF variants below 5% MAF from one case Common 33 8 Reported Rare LOFs Novel/Rare - 41 Pathogenic - 2 (Both AR 1 novel 1 known) VUS – 1 (novel) Update database Not Mendelian 14 Excluded 46 False Positives 13 LOF not a disease Mechanism - 2

18. Gene-centric resource • Define genes with medical relevance • Technical challenges • High GC • Pseudogenes/homologies • Repeat expansions • Common sites of structural variation • Variant types (denote common vs rare types) • Sequence variants (substitutions, small indels) • Loss-of-function vs. Gain-of-function • CNV – haploinsufficientvs. triplosensitive • Other structural changes (translocations, inversions, etc) • Imprinted loci • Repeat expansions • Medically relevant transcripts • Gene regions of pathogenic relevance • Patterns of inheritance (dominant, recessive, X-linked, mitochondrial, de novo, etc) • Phenotypes and evidence base for phenotype associations • Available approaches to define variant pathogenicity (assays, tools, etc) • Clinical utility measures • Clinical decision support opportunities Initiated through collaboration amongst CHOP, Emory, and Harvard/Partners and Structural Variant workgroup

19. U41 - Working with Existing Efforts • NCBI (ClinVar, dbSNP, dbVar, dbGaP, GTR) and EBI • NHGRI (CRVR, eMERGE, CSER, ROR), IRDiRC • Regulatory and Standards: ACMG, CAP, CDC, FDA, ASHG, AMP, CMGS, Global Alliance • Locus Specific Databases (LSDBs – LOVD and non-LOVD) • InSiGHT, PharmGKB, MSeqDB, CFTR2, ENIGMA, etc • Human Variome Projectand HGVS • PhenoDB (Ada Hamosh) and Human Phenotype Ontology (Peter Robinson) • OMIM (Ada Hamosh) and GeneReviews (Bonnie Pagon) • Patient Advocacy Groups (Genetic Alliance, Patient CrossRoads, UNIQUE, Disease Specific Groups) • Industry partners (reagents, instruments, software, etc)

20. ClinGen: The Clinical Genome Resource Program Collaboration between: • NHGRI U41 Grant • PIs: Ledbetter (Geisinger), Martin (Geisinger), Nussbaum (UCSF), Mitchell (Utah), Rehm (Partners/Harvard) • NHGRI U01 “Clinically Relevant Variant Resource” Grants • Grant 1 PIs: Bustamante (Stanford), Plon (Baylor) • Grant 2 PIs: Berg (UNC), Ledbetter (Geisinger), Watson (ACMG) • NCBI • ClinVar

21. ClinGen Delegation of Responsibilities U41 UNC Geisinger ACMG U01 Stanford Baylor U01

22. ClinGen System Interactions Private Labs Labs Patient Registries Controlled Access Public Access LSDBs Labs (Genotypes & Phenotypes) dbGaP OMIM Medical Lit Case-level Data External Informatics Activities Enabled Crowd- sourced Curation ClinVar Pharm GKB Variant-level Data Population Datasets Expert Curated Variants Data Application Interface CoreDB EHR Interface Gene Resource (Medical Exome, Actionability) CNV CurationTool (JIRA) Machine Learning Algorithms Portal for the Public Disease Area Curation Tool Disease WGs Clinical Domain WGs Expert Curation of Genes and Variants by Clinical Domain and Disease Area Workgroups

23. International Collaboration for Clinical Genomics • Annual Conference June 10-12, 2014, Bethesda, MD • Attendees include laboratory directors, physicians, genetic counselors, researchers, parents, government employees, regulatory agency representatives, and vendor partners • Over 190 institutional members • Over 2800 individual members

24. U41 Principal Investigators and Workgroups • NIH U41 PIs: David Ledbetter (Geisinger), Christa Martin (Geisinger), • Joyce Mitchell (Utah), Robert Nussbaum (UCSF), Heidi Rehm (Harvard) • Sequence Variant Workgroup • Madhuri Hegde(co-chair, Emory) • Sherri Bale (co-chair, GeneDx) • Carlos Bustamante (Stanford) • Soma Das (U Chicago) • Matt Ferber (Mayo) • Birgit Funke (Harvard/MGH) • Marc Greenblat (UVM) • Elaine Lyon (ARUP) • Dona Maglott (NCBI) • Sharon Plon (Baylor) • Heidi Rehm (Harvard/Partners) • Avni Santani (CHOP) • Patrick Willems (Gendia) Structural Variant Workgroup Erik Thorland (co-chair, Mayo) Swaroop Aradhya (co-chair, InVitae) Deanna Church (NCBI) Hutton Kearney (Fullerton) Charles Lee (Jackson Labs) Christa Martin (Emory) Sarah South (ARUP) Chad Shaw (Baylor) Karin Wain (Utah) • Phenotyping Workgroup • David Miller (chair, Harvard) • Ada Hamosh (Hopkins) • Karen Eilbeck (Utah) • Monica Giovanni (Geisinger) • Robert Green (Harvard/BWH) • Mike Murray (Geisinger) • Robert Nussbaum (USCF) • Erin Riggs (Emory) • Peter Robinson (Berlin) • Steven Van Vooren (Cartagenia) • Patrick Willems (Gendia) • Engagement, Education and Access Workgroup • Andy Faucett (chair, Geisinger) • Erin Riggs (Emory) • Danielle Metterville (Partners) • Genetic Counselors from participating laboratories Bioinformatics and IT Workgroup Karen Eilbeck (co-chair) and Sandy Aronson (co-chair) ARUP: Brendon O’Fallon; Cartagenia: Steven Van Vooren; Emory: Stuart Tinker; GeneDx: Rhonda Brandon, Lisa Vincent; Mayo: Eric Klee; NCBI: Deanna Church, Jennifer Lee, Donna Maglott; George Riley; Partners Healthcare: Eugene Clark, Larry Babb, Matt Varugheese; University of Chicago Teja Nelakuditi; Utah: Karen Eilbeck, Shawn Rynearson • Consultants • Les Biesecker, Johan den Dunnen, Robert Green, Ada Hamosh, Laird Jackson, Stephen Kingsmore, • Jim Ostell, Sue Richards, Peter Robinson, Lisa Salberg, Joan Scott, Sharon Terry