U41 Grant Session
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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.

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U41 Grant Session

www.iccg.org


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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.


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ICCG Membership

  • Over 190 member institutions

  • Over 2,400individual members worldwide


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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


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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


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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


Structural variant workgroup

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)


Isca participants

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


Sequence variant workgroup

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


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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


Education engagement and access working group

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


Bioinformatics and it workgroup

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


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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


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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


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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


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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


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