1. Genome in a Bottle Consortium
January 2014
Stanford University
Reference Materials for Clinical Applications of Human Genome
Sequencing
Marc Salit, Ph.D. and Justin Zook, Ph.D
National Institute of Standards and Technology
Advances in Biological/Medical Measurement Science
(ABMS @ Stanford)

2. Advances in Biological/Medical
Measurement Science Program
• Measurement Science
and Standards for
Quantitative Biology
– enable commercial and
clinical adoption of
innovations
• NIST, Stanford University,
Private Affiliates
– currently Life Technologies
and Agilent
– soliciting more
participation!
• NIST staff engaged in
ABMS to be located on
Stanford campus and at
NIST in Gaithersburg, MD
– about 9 scientists at outset
• great postdoc
opportunities
– embedding postdocs in
faculty groups
– initial portfolio genomics,
functional genomics,
synthetic biology
abms@nist.gov

3. 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

4. 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 for
NA12878 on 2 platforms, 3
analysis methods

5. Measurement Process
– materials will be
certified for their
variants against a
reference sequence,
with confidence
estimates
Sample
gDNA isolation
generic measurement process
• gDNA reference
materials will be
developed to
characterize
performance of a part
of process
Library Prep
Sequencing
Alignment/Mapping
Variant Calling
Confidence Estimates
Downstream Analysis

6. Putting “Genomes” in Bottles
• NIST working with GiaB
to select genomes
• Current plan
CEPH Utah Pedigree 1463
12889
– NA12878 HapMap
sample as Pilot sample
• 8 trios, focus on children
• varying biogeographic
ancestry
12891
12877
• part of 17-member
pedigree
– trios from PGP as more
complete set
12890
12892
12878
11 children, Birth Order Redacted
12879
12880
12881
12882
12883
12884
12885
12886
12887
12888
12893

7. Genome in a Bottle Working Groups
Reference Material
Selection
& Design
Meaurements for
Reference Material
Characterization
Andrew Grupe,
Celera
Mike Eberle, Illumina
•Develop prioritized list
of whole human
genomes for Reference
Materials
•Identify candidate
approaches and
materials for artificial
RMs
•Develop prioritized
list
Bioninformatics,
Data Integration,
and Data
Representation
Steve Sherry, NCBI
•Develop consensus
plan for experimental
characterization of
Reference Materials
•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

8. Agenda
Monday
• 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)

9. Agenda
Tuesday
Monday
• Breakfast and registration
• Breakfast and registration
• Use cases: Experiences using the pilot
• Welcome and Context Setting
Reference Material
• NIST RM Update and Status Report
• Discussion of plans to release pilot
• Charge to Working Groups
Reference Material
• Coffee Break
• Coffee Break
• Slides Group be made available on SlideShare after
Working will Breakout Discussions
• Working Group Breakout discussions
• the workshop (see genomeinabottle.org).
Lunch (provided)
• Lunch (provided)
• Informal Working Group Reports
• Working Group leaders present plans
• Coffee Break
and discussion
• Tweets are Discussions unless• the speaker requests
Breakout Topical welcome
Steering committee Overview
Please Note
– Topic #1: Moving beyond the 'easy'
variants and regions of the genome
– Topic #2: Selecting future genomes for
Reference Materials
•
otherwise. Please use #giab
First meeting of the Steering
as the hashtag
Committee (others adjourn)
.

10. NIST Reference Materials
Pilot RM - NA12878
Personal Genome Project
• 8300 10ug vials of NA12878
gDNA @ NIST 4/2013
• Ashkenazim trio DNA expected
~Dec 2013
• Asian son DNA expected ~Dec
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
– 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?

11. 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/…

12. Steering Committee
• Genome in a Bottle Consortium
Governance
–
–
–
–
decision making
prioritization
guidance
development of resources if
needed
• end-of-day Tuesday
• Agenda
– composition of the steering
committee
– rapporteur
– Consortium scope
•
•
•
•
RM portfolio
interlab studies
cancer
consortium imprimatur
– adopt, or endorse non-NIST
RMs?
• Liaison with other organizations
• Priorities for future genome RMs
• Version strategy for reference
data