Genome in a Bottle Consortium August 2014

NIST, Gaithersburg, MD

Reference Materials for Clinical Applications of Human Genome Sequencing

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

Advances in Biological/Medical Measurement Science (ABMS @ Stanford)

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

• Biannual workshops – August 2013 at NIST– January 2014 at Stanford– August 2014 at NIST– January 29-30 2015 at Stanford

• 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• 2 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

Deanna Church, Personalis

•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

Update

Zook et al., Nature Biotechnology, 2014.

• methods to develop SNP/indel call set described in manuscript

• broad and quick adoption of call set for benchmarking– struck nerve

• use scenarios a highlight of this workshop

Preliminary uses of high-confidence NIST-GIAB genotypes for NA12878

• NIST have released several versions of high-confidence genotypes for its pilot RM

• These data are presently being used for benchmarking– prior to release of RMs– SNPs & indels

• ~77% of the genome

Highlights

This workshop• release plans for pilot RM• characterization plans for

HG-002 – HG-005• prioritization of next

genomes• collaborations

– ABRF– Global Alliance

Upcoming• materials and methods to

support somatic variant calling

• integrating structural variants into the GIAB call sets

• crowdsourcing analysis• data analysis/code

jamboree

Agenda

Thursday• Welcome and Status Update• Charge to Working Groups• Break• Working Group Breakout

Discussions• Lunch (in NIST cafeteria)• FDA Perspective on Future

Needs • ABRF interlaboratory NGS study • Break• Working Group Breakout

Discussions continued

Friday• Working groups meet if needed• Working Group leaders present

plans and discussion• Break• Discussion of NIST Reference

Material Development plans• Discussion of Steering

Committee agenda items• Everyone adjourn except

steering committee• Steering committee meet over

lunch

AgendaMonday• Breakfast and registration• Welcome and Context Setting• NIST RM Update and Status Report• Charge to Working Groups• Coffee Break• Working Group Breakout Discussions• Lunch (provided)• Informal Working Group Reports• Coffee Break• Breakout Topical Discussions

– Topic #1: Moving beyond the 'easy' variants and regions of the genome

– Topic #2: Selecting future genomes for Reference Materials

Tuesday• Breakfast and registration• Use cases: Experiences using the

pilot Reference Material• Discussion of plans to release pilot

Reference Material• Coffee Break• Working Group Breakout

discussions• Lunch (provided)• Working Group leaders present

plans and discussion• Steering committee Overview• First meeting of the Steering

Committee (others adjourn)

Please Note

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.

Plenary sessions are being broadcast as a webinar. Questions from webinar attendees can be submitted via chat

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

12/2014• SNPs, small indels

• Sequenced at 6 labs– 4 technologies, multiple modes

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

Personal Genome Project• Ashkenazim trio DNA

received Feb 2014• Asian son DNA received Feb

2014– Parents’ cell lines at Coriell

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

• What future RMs are needed?

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”• Coriell MTA for PGP genomes now

explicitly permits commercial redistribution/modification/…

AMP Survey Using Pilot RM

AMP Members International

AMP Survey Future RM needs

AMP Members International