Heidi L. Rehm, PhD

Partners Healthcare and Harvard Medical School

ClinGen Clinical Genome Resource

The Problem

> 100 million genomic variants in humans

>20,000 genes

Most we don’t understand

0

200

400

600

800

1000

1200

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

0

2

4

6

8

10

12

14

16

18

20

Lung Cancer

KRAS EGFR

G12C L858R

GJB2

35delG

GJB2

M34T PTPN11

N308D

MYBPC3

R502W

68% of

pathogenic/

likely pathogenic

variants are seen

only once

96% of variants are

seen <10 times

Number of Probands

Num

ber

of V

ariants

Histogram of Pathogenic Variants from Diagnostic Testing of 15,000 Probands

(cardiomyopathy, hearing loss, rasopathies, aortopathies, somatic and hereditary cancer

pulmonary disorders, skin disorders, other genetic syndromes)

31%

VUS

25%

Positive 61%

Negative 14%

Inconclusive nclusive

52%

Benign

17%

Path

Clinical Domain WGs

Chairs: Jonathan Berg & Sharon Plon

Cancer co-chairs: Matthew Ferber, Ken

Offit, Sharon Plon

Cardiovascular co-chairs: Euan Ashley,

Birgit Funke, Ray Hershberger

Metabolic co-chairs: Rong Mao, Robert Steiner, David Valle

Pharmacogenomic co-chairs: Teri Klein, Howard McLeod

ClinGen Working Groups (WG) ClinGen Working Groups (WG)

Actionability WG

Chair: Jim Evans

Informatics WG

Chair: Carlos Bustamante

EHR WG

Chair: Marc Williams

ClinVar IT Standards and Data Submission

WG

Chairs: Sandy Aronson & Karen Eilbeck

Gene Curation WG

Chairs: Jonathan Berg & Christa Martin

Sequence Variant WG

Chairs: Sherri Bale, Heidi Rehm, &

Madhuri Hegde

Structural Variant WG

Chairs: Swaroop Arahdya & Erik

Thorland ELSI and Genetic Counseling WG

Chair: Andy Faucett & Kelly Ormond

Education, Engagement, Access

WG

Chair: Andy Faucett

Phenotyping WG

Chair: David Miller

ClinGen The Clinical Genome Resource

Launched Sept 2013

NCBI ClinVar Leads Melissa Landrum

Jennifer Lee Donna Maglott

George Riley Steve Sherry

U41 Grant PIs David Ledbetter Christa Martin Bob Nussbaum

Heidi Rehm

U01 PIs Jonathan Berg

Jim Evans David Ledbetter

Mike Watson

U01 PIs Carlos Bustamante

Sharon Plon

NHGRI Program Directors

Lisa Brooks Erin Ramos

ClinVar vs. ClinGen? • ClinVar is a database

• ClinGen, The Clinical Genome Resource, is an NIH funded program supporting a wide range of activities encompassing both support for ClinVar (funded through NCBI) as well as other projects

• ClinGen includes 3 grants primarily funded by the National Human Genome Research Institute at NIH

Clinical Domain WGs

Chairs: Jonathan Berg & Sharon Plon

Cancer co-chairs: Matthew Ferber, Ken

Offit, Sharon Plon

Cardiovascular co-chairs: Euan Ashley,

Birgit Funke, Ray Hershberger

Metabolic co-chairs: Rong Mao, Robert Steiner, David Valle

Pharmacogenomic co-chairs: Teri Klein, Howard McLeod

ClinGen Working Groups (WG) ClinGen Working Groups (WG)

Actionability WG

Chair: Jim Evans

Informatics WG

Chair: Carlos Bustamante

EHR WG

Chair: Marc Williams

ClinVar IT Standards and Data Submission

WG

Chairs: Sandy Aronson & Karen Eilbeck

Gene Curation WG

Chairs: Jonathan Berg & Christa Martin

Sequence Variant WG

Chairs: Sherri Bale, Heidi Rehm, &

Madhuri Hegde

Structural Variant WG

Chairs: Swaroop Arahdya & Erik

Thorland ELSI and Genetic Counseling WG

Chair: Andy Faucett & Kelly Ormond

Education, Engagement, Access

WG

Chair: Andy Faucett

Phenotyping WG

Chair: David Miller

ClinGen The Clinical Genome Resource

Launched Sept 2013

NCBI ClinVar Leads Melissa Landrum

Jennifer Lee Donna Maglott

George Riley Steve Sherry

U41 Grant PIs David Ledbetter Christa Martin Bob Nussbaum

Heidi Rehm

U01 PIs Jonathan Berg

Jim Evans David Ledbetter

Mike Watson

U01 PIs Carlos Bustamante

Sharon Plon

NHGRI Program Directors

Lisa Brooks Erin Ramos

Goals of ClinGen 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

• Developing machine-learning algorithms to improve the throughput of variant interpretation

• Implementing an evidence-based expert consensus process for curating genes and variants

• Assessing the actionability of genes and variants and supporting their use in clinical care systems

Public LSDBs

>600

Pharm

GKB

Population

Databases

EVS

1000G

dbSNP

Medical

Literature

Clinical Lab

Databases

OMIM

Variant Databases

COSMIC

HGMD

$$$

HGMD

$$$

Research Lab

Databases

Largely absent from

the public domain

Largely without

standardized

assertions

Review of Published Pathogenic Variants Found in WGS

3-5 million variants 3-5 million variants

~20,000 Coding/Splice Variants ~20,000 Coding/Splice Variants

20-40 “Pathogenic”

Variants

20-40 “Pathogenic”

Variants

Published as Disease-Causing

Genes

<1%

Rare CDS/Splice Variants Rare CDS/Splice Variants

LOF in Disease Associated Genes

10-20 Variants 10-20 Variants

Review evidence for

gene-disease association

and LOF role

Review evidence for

variant pathogenicity

92%

Excluded 67% Excluded

Acknowledgements:

Heather McLaughlin

Kalotina Machini

Ozge Ceyhan Birsoy

Matt Lebo

Danielle Metterville

Weak disease association 65%

Not medically relevant 33%

Somatic 2%

MedSeq Project:

PI: Robert Green

Rating System for Gene Dosage

Highest -- 3, 2, 1, 0, unlikely dosage sensitive -- Lowest

Proposed Revisions to ACMG

Guideline for Interpretation of

Sequence Variants

ACMG

Sue Richards, Chair Heidi Rehm, Co-chair

Sherri Bale Wayne Grody

David Bick Madhuri Hegde

Soma Das Elaine Spector

AMP

Elaine Lyon Julie Gastier-Foster

CAP

Karl Voelkerding Nazneen Aziz

On behalf of the ACMG Laboratory Quality Assurance Committee

Terminology

Mendelian disease variant terminology

• Pathogenic

• Likely pathogenic ← (≥90% confidence)

• Uncertain significance (VUS)

• Likely benign

• Benign

Replace terms “mutation” and “polymorphism” with “variant”

Defined other areas that need variant terminology:

Complex traits, Pharmacogenetics, Cancer

Population Data

Computational And Predictive Data

Segregation Data

Other Database

Prevalence in affecteds statistically increased over controls PS4

MAF frequency is too high for disorder BSI OR observation in controls inconsistent with disease penetrance BS2

Truncating variant in a gene where LOF is a known mechanism of disease PVS1

De novo (paternity & maternity confirmed)

PS2

Well-established functional studies show a deleterious effect PS3

Novel missense change at an amino acid residue where a different pathogenic missense change has been seen before PM5

Multiple lines of computational evidence support a deleterious effect on the gene /gene product PP3

De novo (without paternity & maternity confirmed) PM6

Non-segregation with disease BS4

Patient’s phenotype or FH highly specific for gene PP4

For recessive disorders, detected in trans with a pathogenic variant PM3

Found in case with an alternate cause BP5

Missense in gene where only truncating cause disease BP1

Multiple lines of computational evidence suggest no impact on gene /gene product BP4

Well-established functional studies show no deleterious effect BS3

Located in a mutational hot spot

and/or known functional domain PM1

In-frame indels in a repetitive region without a known function BP3

Same amino acid change as an established pathogenic variant PS1

In-frame indels in a non-repeat region or stop-loss variants PM4

Observed in trans with a dominant variant BP2

Functional Data

Co-segregation with disease in multiple affected family members PP1

De novo Data

Allelic Data

Absent in 1000G and ESP PM2

Strong

Observed in cis with a pathogenic variant BP2

Reputable database = benign BP6

Strong Very Strong Moderate Supporting Supporting

Reputable database = pathogenic PP5

Missense in gene with low rate of benign missense variants and path. missenses common PP2

Other Data

Benign Pathogenic

Increased segregation data

The Scoring Rules for Classification

Pathogenic

1 Very Strong AND

1 Strong OR

≥2 (Moderate OR Supporting)

2 Strong

1 Strong AND

≥3 Moderate OR

≥2 Moderate and 2 Supporting OR

≥1 Moderate and 4 Supporting

Likely Pathogenic

1 Very strong or Strong AND

≥1 Moderate OR

≥2 Supporting

≥3 Moderate

≥2 Moderate AND 2 Supporting

≥1 Moderate AND 4 Supporting

Very Strong: PVS1

Strong: PS1-PS4

Moderate: PM1-PM6

Supporting: PP1-PP5

Stand-Alone: BA1

Strong: BS1-BS4

Supporting: BP1-BP6

Benign

1 Stand Alone OR

≥ 2 Strong

Likely Benign

1 Strong and ≥1 Supporting OR

>2 Supporting

Uncertain Significance

If other criteria are unmet or

arguments for benign and

pathogenic are equal in strength

www.ncbi.nlm.nih.gov/clinvar

ClinGenDB ClinGenDB

Data Flows in ClinGen

Expert

Curated

Variants

Case-level Data

Variant-level Data

ClinVar

Data

Locus-Specific Databases Locus-Specific Databases

Clinical Labs Clinical Labs Clinics Clinics Patients Patients

Sharing Clinical Reports Project

Curation Interface

Free-the-Data Campaign

Patient Registries

Researchers Researchers

Unpublished or Literature Citations

InSiGHT

CFTR2 PharmGKB

Submitter Variants Genes Clinical Labs Harvard Medical School and Partners Healthcare 6996 155 Emory Genetics Laboratory 5252 507 International Standards For Cytogenomic Arrays 4134 17711 University of Chicago 3687 462 Sharing Clinical Reports Project 2045 2 GeneDx 1436 40 ARUP Laboratories 1417 7 LabCorp 1391 140 University Pennsylvania Genetic Diagnostic Lab 68 1 American College of Med Genetics and Genomics 23 1 Ambry Genetics 10 1

26459

General Databases OMIM 24443 3360 GeneReviews 3738 406

28181 LSDB/Researcher – Assertions Submitted Breast Cancer Information Core (BIC) 3793 2 InSiGHT 2360 4 Juha Muilu Group; FIMM, Finland (FIMM) 840 39 ClinSeq Project 425 35 Martin Pollak (Nephrology, BIDMC, Harvard) 234 39 CFTR2 133 1

7785 LSDB/Researcher – No Assertions 111 Submitters 50063 >6957

ClinVar – 117,115 submissions/104,217 unique variants

50,063 variants

without assertions

from 111 submitters

62,425 variants

with assertions

from >3360 genes

The Sharing Clinical Reports Project and Free-the-Data Campaign for BRCA1 and BRCA2

Goal: Improve the care and safety of patients through

data sharing

Method: Request clinical lab reports from clinics and

patients

Status: >60 clinics and > 200 patients have submitted

de-identified reports leading to 4278 variants collected

sharingclinicalreports.org

Acknowledgements:

Bob Nussbaum (UCSF)

Danielle Metterville (ICCG)

Laura Swaminathan

George Riley (NCBI)

Larry Brody (BIC)

Sharon Terry (Genetic Alliance)

Genetic Alliance Staff and SC

www.free-the-data.org

ClinVar BRCA1/2 Variants

Total 9703 variants – Pathogenic (2232)

– Likely pathogenic (26)

– Uncertain significance (2191)

– Likely benign (565)

– Benign (169)

– Conflicting interpretations (397)

– Literature reference only (4223)

Pathogenic

Uncertain Significance

Likely Benign

Benign

Not Provided

Conflicting

Likely Pathogenic

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

20% discrepant

ClinVar Pilot Project

Scope Number of alleles

Total submitted to ClinVar 997

Multiple assertions 269

Comparison of three laboratories classifications for variants in 12 RASopathy genes: BRAF, CBL, HRAS, KRAS, MAP2K1, MAP2K2, NRAS, PTPN11, RAF1, SHOC2, SOS1, SPRED1

Summary Assertions in ClinVar

Clinical Assertions

ClinVar Evidence Tab

Expert Panel

Single-Source

Evidence and Methods Provided

1. Assertions without evidence and method provided

2. Literature references without assertions

3. Inconsistency in assertions

Multi-Source Consistency

Evidence and Methods Provided

Practice

Guideline

ClinVar Review Levels

Mendelian Categories:

Pathogenic

Likely pathogenic

Uncertain significance

Likely benign

Benign

(e.g. InSiGHT and CFTR2)

(e.g. 23 CF)

No stars

ClinVar Expert Panel Designation (3 stars)

• Download submission form on ClinVar website

• Panel should include multiple institutions and expertise

– medical specialists in disease area

– medical geneticists

– clinical laboratory diagnosticians/ molecular pathologists

– researchers relevant to the disease, gene, functional assays and statistical analyses

• Process for COI review and updating assertions

• Publications or links that describe annotation process

• Information provided is reviewed by ClinGen Executive Committee and posted on ClinVar w/designation

Proposal to Develop Level 2 Environment for

Submitting and Accessing Case-Level Data

ICCG Annual Conference

June 10-12, 2014, Bethesda, MD

www.iccg.org

clinicalgenome.org

ClinGen Acknowledgements

Jonathan Berg

Carlos Bustamante

Jim Evans

David Ledbetter

Christa Martin

Robert Nussbaum

Sharon Plon

Heidi Rehm

Michael Watson

Erica Anderson

Swaroop Arahdya

Sandy Aronson

Euan Ashley

Larry Babb

Erin Baldwin

Sherri Bale

Louisa Baroudi

Les Biesecker

Chris Bizon

David Borland

Rhonda Brandon

Lisa Brooks

Michael Brudno

Damien Bruno

Atul Butte

Hailin Chen

Mike Cherry

Eugene Clark

Soma Das

Johan den Dunnen

Edwin Dodson

Karen Eilbeck

Marni Falk

Andy Faucett

Xin Feng

Mike Feolo

Matthew Ferber

Penelope Freire

Birgit Funke

Monica Giovanni

Katrina Goddard

Robert Green

Marc Greenblatt

Robert Greenes

Ada Hamosh

Bret Heale

Madhuri Hegde

Ray Hershberger

Lucia Hindorff

Sibel Kantarci

Hutton Kearney

Melissa Kelly

Muin Khoury

Eric Klee

Patti Krautscheid

Joel Krier

Danuta Krotoski

Shashi Kulkarni

Melissa Landrum

Matthew Lebo

Charles Lee

Jennifer Lee

Elaine Lyon

Subha Madhavan

Donna Maglott

Teri Manolio

Rong Mao

Daniel Masys

Peter McGarvey

Dominic McMullan

Danielle Metterville

Laura Milko

David Miller

Aleksander Milosavljevic

Rosario Monge

Stephen Montgomery

Michael Murray

Rakesh Nagarajan

Preetha Nandi

Teja Nelakuditi

Elke Norwig-Eastaugh

Brendon O’Fallon

Kelly Ormond

Daniel Pineda-Alvaraz

Erin Ramos

Darlene Reithmaier

Erin Riggs

George Riley

Peter Robinson

Wendy Rubinstein

Shawn Rynearson

Cody Sam

Avni Santani

Neil Sarkar

Melissa Savage

Jeffery Schloss

Charles Schmitt

Sheri Schully

Alan Scott

Chad Shaw

Steve Sherry

Weronika Sikora-Wohlfield

Bethanny Smith Packard

Tam Sneddon

Sarah South

Marsha Speevak

Justin Starren

Jim Stavropoulos

Greer Stephens

Christopher Tan

Peter Tarczy-Hornoch

Erik Thorland

Stuart Tinker

David Valle

Steven Van Vooren

Matthew Varugheese

Yekaterina Vaydylevich

Lisa Vincent

Karen Wain

Meredith Weaver

Kirk Wilhelmsen

Patrick Willems

Marc Williams

Eli Williams