Genome-in-a-Bottle Consortium August 2013

Reference Materials for Clinical Applications of Human Genome Sequencing

Marc Salit, Ph.D. and Justin Zook, Ph.DNational Institute of Standards and Technology

Genome in a Bottle Consortium Development

• NIST met with sequencing technology developers to assess standards needs– Stanford, June 2011

• Open, exploratory workshop– ASHG, Montreal, Canada– October 2011

• Small, invitational workshop at NIST to develop consortium for human genome reference materials– FDA, NCBI, NHGRI, NCI, CDC, Wash

U, Broad, technology developers, clinical labs, CAP, PGP, Partners, ABRF, others

– developed draft work plan– April 2012

• Open, public meeting at NIST to formally establish consortium, present draft work plan– formed working groups– identified candidate genomes– established principles of:

• reference material selection• characterization• informatics• performance metrics

– August 2012

• Open, public workshop at XGen Congress– March 2013

• Website– www.genomeinabottle.org

Well-characterized, stable RMs• Obtain metrics for validation,

QC, QA, PT• Determine sources and types

of bias/error• Learn to resolve difficult

structural variants• Improve reference genome

assembly• Optimization

– integration of data from multiple platforms

– sequencing and analysis

• Enable regulated applications

Comparison of SNP Calls forNA12878 on 2 platforms, 3

analysis methods

Measurement ProcessSample

gDNA isolation

Library Prep

Sequencing

Alignment/Mapping

Variant Calling

Confidence Estimates

Downstream Analysis

• gDNA reference materials will be developed to characterize performance of a part of process– materials will be certified

for their variants against a reference sequence, with confidence estimates

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• NIST working with GiaB to select genomes

• Current plan– NA12878 HapMap

sample as Pilot sample• part of 17-member

pedigree

– trios from PGP as more complete set• 8 trios, focus on children• varying biogeographic

ancestry

CEPH Utah Pedigree 1463

Putting “Genomes” in Bottles

11 children, Birth Order Redacted

Genome in a Bottle Working Groups

Reference Material Selection& Design

Andrew Grupe,Celera

•Develop prioritized list of whole human genomes for Reference Materials

• Identify candidate approaches and materials for artificial RMs•Develop prioritized list

Meaurements for Reference Material Characterization

Mike Eberle, Illumina

•Develop consensus plan for experimental characterization of Reference Materials

Bioninformatics, Data Integration, and Data Representation

Steve Sherry, NCBI

•Develop plan for integrating experimental data and forming consensus variant calls and confidence estimates

•Develop consensus plan for data representation

Performance Metrics & Figures of Merit

Justin Johnson

•User interface to the Genome-in-a-Bottle Reference Material• “Dashboard”•what an end user will

see and report to understand and describe the performance of their experiment• variant call accuracy•process performance

measures to enable optimization

AgendaThursdayWelcome and IntroIntegrating large scale sequencing into clinical practice

Heidi Rehm

Personal GenomicsMichael Snyder

Break/Poster SessionUpdate on GIAB Progress

Marc Salit

Comparison of NIST, Platinum Genomes, and other NA12878 call-sets to understand sequencing performance

Justin Zook

Presentations from related projectsPlatinum Genomes

Michael Eberle

NA12878 Trio AnalysisFrancisco De La Vega

GeT-RM Project and Genome BrowserDeanna Church

Lunch (on your own in NIST cafeteria)

Working Group MeetingsReference Material Selection & Design (Lecture Room E)Measurements for Reference Material Characterization (Dining Room A&B)Bioinformatics, Data Integration, and Data Representation (Lecture Room A)Performance Metrics and Figures of Merit (Lecture Room C)

FridayDiscussion between working groupsWorking group reports (Green Auditorium)Workplan refinement, timelineLunch (on your own in NIST cafeteria)Discussion: Scope of consortium, how to make decisionsResource needs, how to meet them, and next steps

AgendaThursdayWelcome and IntroIntegrating large scale sequencing into clinical practice

Heidi Rehm

Personal GenomicsMichael Snyder

Break/Poster SessionUpdate on GIAB Progress

Marc Salit

Comparison of NIST, Platinum Genomes, and other NA12878 call-sets to understand sequencing performance

Justin Zook

Presentations from related projectsPlatinum Genomes

Michael Eberle

NA12878 Trio AnalysisFrancisco De La Vega

GeT-RM Project and Genome BrowserDeanna Church

Lunch (on your own in NIST cafeteria)

Working Group MeetingsReference Material Selection & Design (Lecture Room E)Measurements for Reference Material Characterization (Dining Room A&B)Bioinformatics, Data Integration, and Data Representation (Lecture Room A)Performance Metrics and Figures of Merit (Lecture Room C)

FridayDiscussion between working groupsWorking group reports (Green Auditorium)Workplan refinement, timelineLunch (on your own in NIST cafeteria)Discussion: Scope of consortium, how to make decisionsResource needs, how to meet them, and next steps

Please Note

The plenary sessions of this workshop are being webcasted (audio & slides) – please use the microphones when asking questions. Web attendees can ask questions with chat. Slides will be made available on SlideShare after the workshop (see genomeinabottle.org).

Tweets are welcome unless the speaker requests otherwise. Please use #giab as the hashtag.

Status Update, Consortium Business

Marc Salit and Justin Zook

Consenting Genomes for use as Reference Materials

• Risk of re-identification– this is a real risk– privacy– implications for family members

• Meaning of possibility of withdrawal

• Commercial application– indirect, research– direct, derived products

• PGP project currently state-of-art– broad and direct– test to demonstrate

understanding

• “Wild West”

NIST Reference Materials

Pilot RM - NA12878• 8300 10ug vials of NA12878

gDNA @ NIST 4/2013– Available for sequencing by GIAB

participants– target for release as NIST RM

2/2014• SNPs, small indels

• Will be sequenced at ~10 labs– ~4 technologies, multiple modes

• Received “Human Subjects Approval” for release of NA12878 as NIST RM

Personal Genome Project• Ashkenazim trio DNA expected

~Dec 2013• Asian son DNA expected ~Dec

2013– Parents’ cell lines in process at Coriell

• “Human subjects review” close to approval for release of PGP genomes as NIST RMs

• Plan is 5-6 additional trios of diverse ancestry– Ideally, african, asian, hispanic– What should we do if PGP doesn’t

have trios from each of these groups?

Planned Measurements on NA12878 candidate RM

• NIST– ~300x total 2x150bp Illumina

over 6 vials of NA12878– ~100x SOLiD 5500W 2x50bp

coverage – ~50x SOLiD 5500W 2x50bp

coverage of parents

• Illumina– PCR-free– Mate-pair

• Complete Genomics– Normal pipeline– LFR pipeline

• NCI– Ion Proton – Illumina– Various libraries

• Garvan– Illumina exome

• Celera– Targeted panels

• Cornell Weill– Illumina

• MTAs pending– Univ. of Nebraska Medical– Univ. of Michigan

HOW DO WE WANT TO FUNCTION AS A CONSORTIUM?

What’s our scope?How do we make decisions?

Spectrum of Possibilities

• NIST develops and disseminated gDNA RMs with consortium input

• Consortium functions as a Standards Body, with dynamic portfolio and broad influence

Spectrum of Possibilities

NIST develops and disseminates gDNA RMs with consortium input

Consortium functions as a Standards Body, with dynamic portfolio and broad influence

Scope

Basic Scope• Develop/disseminate pilot

genome and 8 trios as RMs– gDNA and reference data

• Develop/disseminate “Performance Metrics Suite”– data repository?

• Documentary Standards to describe methods?– through a clinical SDO? CLSI?

IFCC?

Extended Scope• Other RMs as part of GiaB

portfolio?– tumor/normal pair– artifical spike-in controls

• pDNA from NCI– derived commercial materials

• Cell lines for which we have reference gDNA

• Such cell lines embedded in FFPE

– engineered cell lines• designed as controls for

specific variants

Extended Scope

• need process to include new material/product in portfolio– what does it mean to put

the GiaB imprimatur on something?

• some possible requirements– guidelines for usage– methods for characterization– conduct interlab studies to

establish utility

• how do we decide what to do?– need to be

• open, transparent, public• form consensus

– pragmatic consensus needs champion and commitment• e.g. proposer pilots interlab• consortium members

participate in interlab

• how do we decide policy matters?– see draft data release policy

discussion on this tomorrow after lunch…