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Melissa J Landrum
HVP6
June 2, 2016
 Archive of interpretations of variants relative to conditions
 Variant-level information
 Fully public and freely available
 Submission-driven database
 Primary submissions
 Expert-curated submissions
 Curation support from NCBI staff
Variation Condition
Interpretation Evidence
Content Authorities
Short variants HGVS
Structural variants ISCN (being developed)
Accessions for the variant location dbSNP, dbVar
Genes HGNC
Reference sequence Assembly: Genome Reference Consortium
(GRC)
Gene-specific: RefSeqGene/LRG
Type of variation, location in gene Sequence Ontology
Conditions Orphanet: group terms
OMIM: disease-specific terms
Human phenotype ontology: clinical features
Clinical significance ACMG, CPIC?
Variant effects VAriO, Sequence ontology
Variant
Condition
Submitter
BRCA2:c.9875C>T
Familial cancer of breast
Lab A
SCV000000010
Variant
Condition
BRCA2:c.9875C>T
Familial cancer of breast
RCV000000050
BRCA2:c.9875C>TVariant
BRCA2:c.9875C>T
Familial cancer of breast
Lab B
SCV000000020
BRCA2:c.9875C>T
Breast-ovarian cancer, familial 2
Lab C
SCV000000030
BRCA2:c.9875C>T
Breast-ovarian cancer, familial 2
RCV000000070
ClinVar: Aggregating Data to Improve Variant Interpretation - Melissa Landrum
ClinVar: Aggregating Data to Improve Variant Interpretation - Melissa Landrum
Practice guideline
Reviewed by expert panel
Multiple interpretations with assertion criteria that agree
One interpretation with assertion criteria
OR multiple interpretations with assertion criteria but
conflicting
No interpretations with assertion criteria
OR no interpretation provided
http://www.ncbi.nlm.nih.gov/clinvar/docs/assertion_criteria/
Country Submitters Submissions
United States 170 156201
United Kingdom 26 7423
Australia 17 2462
Finland 4 2121
Germany 34 1794
Canada 19 1607
France 24 1513
China 22 1345
Singapore 3 1102
Switzerland 5 970
Country Submitters Submissions
Netherlands 26 787
Estonia 1 761
Saudi Arabia 4 549
Sweden 9 459
Japan 10 388
Belgium 8 374
India 24 333
Brazil 10 243
Iran 9 121
Italy 15 81
 Submitters are acknowledged on web pages
 Links to the submitter’s website are provided, when
available
 The submitting organization owns its submissions (SCV)
 Only the submitter can update or delete a submission
• Register your organization
• Use the wizard to submit
single variant
interpretations
• Upload files of batch
submissions
http://www.ncbi.nlm.nih.gov/clinvar/
docs/submit/
 Updates are encouraged and expected
 Variant reclassification
 Refining the condition for the interpretation
 New evidence
 Updates must be provided by the submitter
 Clinical laboratories and LSDBs may consider regular
update cycles
ClinVar: Aggregating Data to Improve Variant Interpretation - Melissa Landrum
 Clinical significance/pathogenicity for disease
 Therapeutic effect
 Functional/pharmacological effect
Mark Benson
Garth Brown
Chao Chen
Shanmuga Chitipiralla
Baoshan Gu
Jennifer Hart
Douglas Hoffman
Wonhee Jang
Brandi Kattman
Ken Katz
Jennifer Lee
Zenith Maddipatla
Donna Maglott
Adriana Malheiro
Michael Ovetsky
George Riley
Wendy Rubinstein
Amanjeev Sethi
Ray Tully
Ricardo Villamarin
Steve Sherry
Jim Ostell
David Lipman
Follow us on Twitter
Send questions, comments, suggestions to
clinvar@ncbi.nlm.nih.gov

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ClinVar: Aggregating Data to Improve Variant Interpretation - Melissa Landrum

  • 2.  Archive of interpretations of variants relative to conditions  Variant-level information  Fully public and freely available  Submission-driven database  Primary submissions  Expert-curated submissions  Curation support from NCBI staff
  • 4. Content Authorities Short variants HGVS Structural variants ISCN (being developed) Accessions for the variant location dbSNP, dbVar Genes HGNC Reference sequence Assembly: Genome Reference Consortium (GRC) Gene-specific: RefSeqGene/LRG Type of variation, location in gene Sequence Ontology Conditions Orphanet: group terms OMIM: disease-specific terms Human phenotype ontology: clinical features Clinical significance ACMG, CPIC? Variant effects VAriO, Sequence ontology
  • 5. Variant Condition Submitter BRCA2:c.9875C>T Familial cancer of breast Lab A SCV000000010 Variant Condition BRCA2:c.9875C>T Familial cancer of breast RCV000000050 BRCA2:c.9875C>TVariant BRCA2:c.9875C>T Familial cancer of breast Lab B SCV000000020 BRCA2:c.9875C>T Breast-ovarian cancer, familial 2 Lab C SCV000000030 BRCA2:c.9875C>T Breast-ovarian cancer, familial 2 RCV000000070
  • 8. Practice guideline Reviewed by expert panel Multiple interpretations with assertion criteria that agree One interpretation with assertion criteria OR multiple interpretations with assertion criteria but conflicting No interpretations with assertion criteria OR no interpretation provided http://www.ncbi.nlm.nih.gov/clinvar/docs/assertion_criteria/
  • 9. Country Submitters Submissions United States 170 156201 United Kingdom 26 7423 Australia 17 2462 Finland 4 2121 Germany 34 1794 Canada 19 1607 France 24 1513 China 22 1345 Singapore 3 1102 Switzerland 5 970 Country Submitters Submissions Netherlands 26 787 Estonia 1 761 Saudi Arabia 4 549 Sweden 9 459 Japan 10 388 Belgium 8 374 India 24 333 Brazil 10 243 Iran 9 121 Italy 15 81
  • 10.  Submitters are acknowledged on web pages  Links to the submitter’s website are provided, when available  The submitting organization owns its submissions (SCV)  Only the submitter can update or delete a submission
  • 11. • Register your organization • Use the wizard to submit single variant interpretations • Upload files of batch submissions http://www.ncbi.nlm.nih.gov/clinvar/ docs/submit/
  • 12.  Updates are encouraged and expected  Variant reclassification  Refining the condition for the interpretation  New evidence  Updates must be provided by the submitter  Clinical laboratories and LSDBs may consider regular update cycles
  • 14.  Clinical significance/pathogenicity for disease  Therapeutic effect  Functional/pharmacological effect
  • 15. Mark Benson Garth Brown Chao Chen Shanmuga Chitipiralla Baoshan Gu Jennifer Hart Douglas Hoffman Wonhee Jang Brandi Kattman Ken Katz Jennifer Lee Zenith Maddipatla Donna Maglott Adriana Malheiro Michael Ovetsky George Riley Wendy Rubinstein Amanjeev Sethi Ray Tully Ricardo Villamarin Steve Sherry Jim Ostell David Lipman
  • 16. Follow us on Twitter Send questions, comments, suggestions to clinvar@ncbi.nlm.nih.gov