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

2. Variant Analysis for General Genome Report
3-5 million variants
Genes
~20,000 Coding/Splice Variants
Published as
Disease-Causing
<1%
Pharmacogenetics
Rare CDS/Splice Variants
5-10 Variants
20-40 “Pathogenic” Variants
LOF in Disease
Associated Genes
PharmGKB Levels of Evidence:
PharmGKB curators use specific criteria to assess the PharmGKB “variant annotations” and determine the level of evidence.
Level 1 annotations require at least one study with at least 1000 cases and 1000 controls of the same ethnicity with statistically significant p-values <0.05.
Level 2 associations are those found in at least one population of >100 with a statistically significant p-value of <0.05, and may or may not be replicated.
Level 3 associations with lower levels of evidence are those that do not meet the above criteria for population size or p-value, or may be in vitro studies.
30-50 Variants
Review evidence for variant pathogenicity
Review evidence for gene-disease association and LOF role

3. Classification of Reported Pathogenic Variants found 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 )
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

7. ClinVar Submitters
Variants
Genes
OMIM
23524
3077
Harvard Medical School and Partners Healthcare
6996
155
InVitae Inc.
5526 4
International Standards For Cytogenomic Arrays
4194 46
GeneReviews
2913
287
ARUP Laboratories
1415 6
LabCorp
1391
140
Sharing Clinical Reports Project
902 2
Finland Institute for Molecular Medicine
840 39
Tuberous Sclerosis Database
431 1
ClinSeq Project
425 35
Leiden Muscular Dystrophy Database
220 10
GeneDx
205 3
Emory Genetics Laboratory 48 13
American College of Medical Genetics and Genomics 23
Osteogenesis Imperfecta Database; University of Leicester 15
Ambry Genetics
Other laboratories (19) 52 25
Total
49130
3848

8. Sequencing Laboratories Which Have Agreed to Share Data
Alfred I Dupont Hospital for Children
Illumina Clinical Services Lab
All Children's Hospital St. Petersburg
Indiana University/Perdue University
Ambry Laboratories
InSiGHT
ARUP
LabCorp / Integrated Genetics / Correlagen
Athena Diagnostics
Masonic Medical Research Laboratory
Baylor Medical Genetic Laboratories
Mayo Clinic
Boston Children's Hospital
Mt. Sinai School of Medicine
Boston University
Nationwide Children's Hospital
Children's Hospital of Philadelphia
Nemours Biomolecular Core, Jefferson Medical
Children's Mercy Hospital, Kansas City
Oregon Health Sciences University
Cincinnati Children's Hospital
Providence Sacred Heart Medical Center
City of Hope Molecular Diagnostic Lab
Quest Diagnostics
CureCMD
SickKids Molecular Genetic Laboratory
Denver Genetic Laboratories
Transgenomics
Detroit Medical Center
University of Chicago
Emory University
University of Michigan
Fullerton Genetics Laboratory
University of Nebraska Medical Center
GeneDx
University of Oklahoma
Cleveland Clinic
University of Penn
Greenwood Genetics
University of Sydney
Harvard-Partners Lab for Molec. Medicine
University of Washington
Henry Ford Hospital
Women and Children's Hospital
Huntington Medical Research Institutes
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
Scope
Number of alleles
Total submitted to ClinVar
997
Multiple assertions
269
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 Committee on the Interpretation of Sequence Variants
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. Uncertain significance Likely benign Benign
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
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
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
Example from a single genome (PM ) – Kalotina’s data
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 – haploinsufficient vs. triplosensitive
Other structural changes (translocations, inversions, etc)
Imprinted loci
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 Project and 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)
Christa/Heidi

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
Data Collection
Structural Variation
Sequence Variation
Other Genomic Data
Phenotype
Curation
Variant Curation – Clinical Significance
Gene-Variant Pairs – Actionability
Clinical Domain Curation
Machine Learning Curation
IT/Biofx
Data Extraction
Data Analysis
Data Dissemination
Laboratory Bioinformatics/IT
EHR Integration
Community
Education
ELSI/
Actionability
Patient Registry
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
Case-level Data
Medical
Lit
External Informatics
Activities Enabled
Crowd-
sourced
Curation
ClinVar
Pharm
GKB
Variant-level Data
Population
Datasets
Expert
Curated
Variants
Data
Application Interface
Gene
Resource
(Medical Exome,
Actionability)
CoreDB
EHR Interface
CNV Curation Tool (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
Over 190 institutional members
Over 2800 individual members
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

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