1 / 16

www.iccg.org

U41 Grant Session. www.iccg.org. ISCA has e volved!. Established in 2007, ISCA was originally focused on copy number array data. Realizing our goals are not unique to structural variation , in 2012 we evolved into ICCG to include sequence-level variation efforts. . ICCG Membership.

niran
Download Presentation

www.iccg.org

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. U41 Grant Session www.iccg.org

  2. ISCA has evolved! Established in 2007, ISCA was originally focused on copy number array data. Realizing our goals are not unique to structural variation, in 2012 we evolved into ICCG to include sequence-level variationefforts.

  3. ICCG Membership • Over 190 member institutions • Over 2,400individual members worldwide

  4. Timeline CRVR Grant to be Awarded U41 Grant Resubmitted U41 Grant Submitted ACMG Grant GO Grant 2007 2009 2011 2012 2013 ISCA Launched ICCG Launched

  5. Project Goals To raise the quality of patient care by: • Standardizing testing platforms and data interpretation related to structural and sequence-level variation • Creating a centralizeddatabaseof clinically relevant variant annotations to share datafor clinical and research purposes • Implementing a QC and expert consensus processfor curating data submitted across laboratories and developing evidence based classifications

  6. 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) • Soma Das (U Chicago) • Matt Ferber (Mayo) • Birgit Funke (Harvard/Partners) • Elaine Lyon (ARUP) • Heidi Rehm (Harvard/Partners) • AvniSantani (CHOP) • Patrick Willems (Gendia) Structural Variant Workgroup Erik Thorland (co-chair, Mayo) Swaroop Aradhya (co-chair, GeneDx) Deanna Church (NCBI) Hutton Kearney (Fullerton) Charles Lee (Harvard/BWH) Christa Martin (Emory) Sarah South (ARUP) • Phenotyping Workgroup • David Miller (chair, Harvard) • Ada Hamosh (Hopkins) • Mike Murray (Harvard/BWH) • 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 Joyce Mitchell (co-chair) and Sandy Aronson (co-chair) ARUP: David Crockett; Cartagenia: Steven Van Vooren; Emory: Virenkumar Patel; GeneDx: Rhonda Brandon; Mayo: Eric Klee; NCBI: Deanna Church, Donna Maglott; George Riley; Partners Healthcare: Eugene Clark, Larry Babb, Siva Gowrisanker, Matt Varugheese, Tom Venman; University of Chicago TejaNelakuditi; Utah: Karen Eilbeck • Consultants • Les Biesecker, Johan den Dunnen, Robert Green, AdaHamosh, Laird Jackson, Stephen Kingsmore, • Jim Ostell, Sue Richards, Peter Robinson, Lisa Salberg, Joan Scott, Sharon Terry

  7. Structural Variant Workgroup Co-Chairs: • Erik Thorland(Mayo) and SwaroopAradhya(GeneDx) Goals: • Use evidence-based review to assess genes/regions targeted on ISCA array design • Develop a genome-wide dosage sensitivity mapto aid in clinical array interpretation and inform array design • Haploinsufficiency (loss) and/or Triplosensitivity (gain)

  8. ISCA Participants ARUP Sarah South Erica Andersen Birmingham Women's NHS Foundation Dominic McMullan Emory University Christa Martin Erin Kaminsky Erin Riggs Eli Williams Vanessa Horner GeneDx SwaroopAradhya Daniel Pineda-Alvarez Mayo Clinic Erik Thorland Karen Wain Lindsey Waltman DDG2P Matt Hurles Helen Firth David FitzPatrick Mission Health Hutton Kearney NCBI Deanna Church Victorian Clinical Genetics Services Damien Bruno www.ncbi.nlm.nih.gov/projects/dbvar/ISCA

  9. Sequence Variant Workgroup • Sequence Variant Workgroup • Madhuri Hegde(Co-Chair, Emory) Sherri Bale (Co-Chair, GeneDx) Soma Das (U Chicago) Matt Ferber (Mayo) Birgit Funke (Harvard/Partners) Elaine Lyon (ARUP) Heidi Rehm (Harvard/Partners) AvniSantani (CHOP) Patrick Willems (Gendia) TBN from NCBI TBN from CRVR Develop standards for variant classification in conjunction with ACMG, CAP, AMP Guide ClinVar Development Define the Medical Exome Solicit and support labs to submitting data Develop process for expert consensus - 8 pilot projects

  10. Phenotyping Workgroup • Phenotyping Workgroup • David Miller (chair, Harvard/BCH) • Ada Hamosh (Hopkins) • Mike Murray (Harvard/BWH) • Robert Nussbaum (USCF) • Erin Riggs (Emory) • Peter Robinson (Germany) • Steven Van Vooren (Cartagenia) • Patrick Willems(Gendia) Develop approaches to improve the collection of phenotypic data for association with genotypes Ensure the use of consistent and compatible terminologies and ontologies across interconnected phenotype resources

  11. Education, Engagement and Access Working Group • Chair: Andy Faucett (Geisinger) • Members: Genetic counselors and ICCG project managers • Educate stakeholders on ICCG efforts • Publications, webinars, booths at meetings, website • Engage groups to encourage submission of data • Labs, clinicians, researchers, patient advocacy groups • Ensure access to data and resources is appropriately managed

  12. Bioinformatics and IT Workgroup Facilitate communication between laboratories, vendors and NCBI Develop submission standards for ClinVar Evaluate how labs are using ClinVar and recommend enhancements Support activities of other workgroups Co-Chairs: Joyce Mitchell and Sandy Aronson ARUP/Utah: David Crockett, Karen Eilbeck Cartagenia: Steven Van Vooren Emory: Stuart Tinker, Viren Patel GeneDx: Rhonda Brandon Mayo Clinic: Eric Klee NCBI: Deanna Church, Donna Maglott; George Riley Partners Healthcare: Eugene Clark, Larry Babb, Siva Gowrisanker, Matt Varugheese, Tom Venman Univ of Chicago: TejaNelakuditi

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

  14. Proposed U01/U41 Governance Structure Note: pending funding decisions Steering Committee U41, UNC/Geisinger/ACMG, Stanford/Baylor, NHGRI, NCBI Scientific Advisory Board External Stakeholder Committee Stanford/Baylor Executive Committee U41 Executive Committee UNC/Geisinger/ACMG Executive Committee Standards/Data Collection Workgroups Clinical Domain Workgroups Bioinformatics & IT Workgroups Informatics WG PGx Cardio WG Actionability WG EHR WG PGx WG Phenotyping WG Informatics WG Sequence Variant WG Structural Variant WG Cardio WG Bioinformatics and IT WG Sequence Variant WG Structural Variant WG Clinical Domain WGs Sequence Variant WG Structural Variant WG Population Genetics Non-coding Epigenetics Curation Tools WG Medical Exome ClinVar WG Analysis WG Disease Area WGs Prenatal GWAS JIRA CNV ELSI and Genetic Counseling WG Education, Engagement, Access WG Data & Tool Dissemination WG

  15. ClinVar/CRVR System Interactions Note: pending funding decisions 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

  16. Opportunities to get involved • Tell us you are interested • Send us your data! • Send sample export of what you have • Are you interested in curating? • Medical exome project • Disease area variant curation groups • Help support the project by engaging with stakeholders

More Related