81 FR 226 - Genome in a Bottle Consortium-Progress and Planning Workshop

DEPARTMENT OF COMMERCE
National Institute of Standards and Technology

Federal Register Volume 81, Issue 2 (January 5, 2016)

The National Institute of Standards and Technology (NIST) announces the Genome in a Bottle Consortium--Progress and Planning Workshop to be held on Thursday, January 28, 2016, and Friday, January 29, 2016. The Genome in a Bottle Consortium is developing the reference materials, reference methods, and reference data needed to assess confidence in human whole genome variant calls. A principal motivation for this consortium is to enable performance assessment of sequencing and science-based regulatory oversight of clinical sequencing. The purpose of this workshop is to update participants about progress of the consortium work, continue to get broad input from individual stakeholders to update or refine the consortium work plan, continue to broadly solicit consortium membership from interested stakeholders, and invite members to participate in work plan implementation. Topics of discussion at this workshop will include progress and planning of the Analysis Group, which is analyzing and integrating the large variety of sequencing data for four candidate NIST Reference Materials (RMs), with a particular focus on challenging types of variants and challenging regions of the genome. Other potential NIST RMs that might be developed by the consortium will also be discussed.

[Federal Register Volume 81, Number 2 (Tuesday, January 5, 2016)]
[Notices]
[Pages 226-227]
From the Federal Register Online  [www.thefederalregister.org]
[FR Doc No: 2015-33140]


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DEPARTMENT OF COMMERCE

National Institute of Standards and Technology


Genome in a Bottle Consortium--Progress and Planning Workshop

AGENCY: National Institute of Standards and Technology, Commerce.

ACTION: Notice of public workshop.

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SUMMARY: The National Institute of Standards and Technology (NIST) 
announces the Genome in a Bottle Consortium--Progress and Planning 
Workshop to be held on Thursday, January 28, 2016, and Friday, January 
29, 2016. The Genome in a Bottle Consortium is developing the reference 
materials, reference methods, and reference data needed to assess 
confidence in human whole genome variant calls. A principal motivation 
for this consortium is to enable performance assessment of sequencing 
and science-based regulatory oversight of clinical sequencing. The 
purpose of this workshop is to update participants about progress of 
the consortium work, continue to get broad input from individual 
stakeholders to update or refine the consortium work plan, continue to 
broadly solicit consortium membership from interested stakeholders, and 
invite members to participate in work plan implementation.
    Topics of discussion at this workshop will include progress and 
planning of the Analysis Group, which is analyzing and integrating the 
large variety of sequencing data for four candidate NIST Reference 
Materials (RMs), with a particular focus on challenging types of 
variants and challenging regions of the genome. Other potential NIST 
RMs that might be developed by the consortium will also be discussed.

DATES: The Genome in a Bottle Consortium workshop will be held on 
Thursday, January 28, 2016 from 9:00 a.m. to 5:30 p.m. Pacific Time, 
and Friday, January 29, 2016 from 9:00 a.m. to 1:00 p.m. Pacific Time. 
Attendees must register by 5:00 p.m. Pacific Time on Thursday, January 
21, 2016.

ADDRESSES: The meeting will be held on the second floor of the Li Ka 
Shing Conference Center, Stanford University, 291 Campus Drive, Palo 
Alto, CA 94305. Please note admittance instructions under the 
SUPPLEMENTARY INFORMATION section of this notice.

FOR FURTHER INFORMATION CONTACT: For further information contact Justin 
Zook by email at [email protected] or by phone at (301) 975-4133 or Marc 
Salit by email at [email protected] or by phone at (650) 350-2338. To 
register, go to: http://web.stanford.edu/~saracl/GIAB2016.fb

SUPPLEMENTARY INFORMATION: Clinical application of ultra high 
throughput sequencing (UHTS) for hereditary genetic diseases and 
oncology is rapidly growing. At present, there are no widely accepted 
genomic standards or quantitative performance metrics for confidence in 
variant calling. These standards and quantitative performance metrics 
are needed to achieve the confidence in measurement results expected 
for sound, reproducible research and regulated applications in the 
clinic. On April 13, 2012, NIST convened the workshop ``Genome in a 
Bottle'' to initiate a consortium to develop the reference materials, 
reference methods, and reference data needed to assess confidence in 
human whole genome variant calls (www.genomeinabottle.org). On August 
16-17, 2012, NIST hosted the first large public meeting of the Genome 
in a Bottle Consortium, with about 100 participants from government, 
academic institutions, and industry. This meeting was announced in the 
Federal Register (77 FR 43237) on July 24, 2012. A principal motivation 
for this consortium was to enable science-based regulatory oversight of 
clinical sequencing.
    At the August 2012 meeting, the consortium established work plans 
for four technical working groups with the following responsibilities:
    (1) Reference Material (RM) Selection and Design: Select 
appropriate sources for whole genome RMs and identify or design 
synthetic DNA constructs that could be spiked-in to samples for 
measurement assurance.
    (2) Measurements for Reference Material Characterization: Design 
and carry out experiments to characterize

[[Page 227]]

the RMs using multiple sequencing methods, other methods, and 
validation of selected variants using orthogonal technologies.
    (3) Bioinformatics, Data Integration, and Data Representation: 
Develop methods to analyze and integrate the data for each RM, as well 
as select appropriate formats to represent the data.
    (4) Performance Metrics and Figures of Merit: Develop useful 
performance metrics and figures of merit that can be obtained through 
measurement of the RMs.
    The products of these technical working groups will be a set of 
well-characterized whole genome and synthetic DNA RMs along with the 
methods (documentary standards) and reference data necessary for use of 
the RMs. These products will be designed to help enable translation of 
whole genome sequencing to regulated clinical applications. The pilot, 
NIST ``Human DNA for Whole-Genome Variant Assessment (Daughter of Utah/
European Ancestry)'' RM was released in May 2015 and is available at 
http://tinyurl.com/giabpilot. The consortium is currently analyzing and 
integrating data from two trios that are candidate NIST RMs. The 
consortium meets in workshops two times per year, in January at 
Stanford University in Palo Alto, CA, and in August at the National 
Institute of Standards and Technology in Gaithersburg, MD. At these 
workshops, including the last meetings at Stanford in January 2015 and 
at NIST in August 2015, participants in the consortium have discussed 
progress developing well-characterized genomes for NIST Reference 
Materials and planned future experiments and analysis of these genomes 
(see https://federalregister.gov/a/2012-18064, https://federalregister.gov/a/2013-18934, https://federalregister.gov/a/2014-18841 and https://federalregister.gov/a/2015-01158 for past workshops 
at NIST and Stanford). The January 2015 meeting was announced in the 
Federal Register (80 FR 3220) on January 22, 2015, and the meeting is 
summarized at https://docs.google.com/document/d/19J6YDg1MH1iD-8Q8mmV9L7wHOfuyUC3aogctZ2Nh87U/edit?usp=sharing. The August 2015 
meeting was announced in the Federal Register (80 FR 45194) on July 29, 
2015, and the meeting is summarized at https://docs.google.com/document/d/19-KSn0ydF8rsWRbl6OqhIdbt2gGN10dOMRF6inKmrk4/edit?usp=sharing.
    There is no cost for participating in the consortium. No 
proprietary information will be shared as part of the consortium, and 
all research results will be in the public domain.
    All attendees are required to pre-register. Anyone wishing to 
attend this meeting must pre-register at http://web.stanford.edu/
~saracl/GIAB2016.fb by 5:00 p.m. Pacific Time on Thursday, January 21, 
2016, in order to attend.

Richard Cavanagh,
Acting Associate Director of Laboratory Programs.
[FR Doc. 2015-33140 Filed 1-4-16; 8:45 am]
 BILLING CODE 3510-13-P