The Genome-in-a-Bottle Consortium aims to develop reference materials for clinical applications of human genome sequencing. The National Institute of Standards and Technology is partnering with the Food and Drug Administration and other organizations to produce reference genomes that can be used to evaluate the performance of sequencing instruments and ensure consistency across platforms. The consortium will select candidate reference genomes, experimentally characterize the materials, integrate the data to produce consensus variant calls, and define performance metrics for end users. The goal is to provide a trusted source of reference materials to support regulatory oversight and commercial use of genome sequencing.
January 23, 2017
The Fifth Annual Health Law Year in P/Review symposium featured leading experts discussing major developments during 2016 and what to watch out for in 2017. The discussion at this day-long event covered hot topics in such areas as health policy under the new administration, regulatory issues in clinical research, law at the end-of-life, patient rights and advocacy, pharmaceutical policy, reproductive health, and public health law.
The Fifth Annual Health Law Year in P/Review was sponsored by the Petrie-Flom Center for Health Law Policy, Biotechnology, and Bioethics at Harvard Law School, Harvard Health Publications at Harvard Medical School, Health Affairs, the Hastings Center, the Program On Regulation, Therapeutics, And Law (PORTAL) in the Division of Pharmacoepidemiology and Pharmacoeconomics at Brigham and Women’s Hospital, and the Center for Bioethics at Harvard Medical School, with support from the Oswald DeN. Cammann Fund.
Learn more on our website: http://petrieflom.law.harvard.edu/events/details/5th-annual-health-law-year-in-p-review
From Bits to Bedside: Translating Big Data into Precision Medicine and Digita...Dexter Hadley
Lecture Objectives:
1) To use examples from my research to define and introduce the ideals of precision medicine and digital health. 2) To introduce how large scale population-wide analysis of data can be used to facilitate these two ideals. 3) To introduce how freely available open data can be used to facilitate these two ideals. 4) To show how mobile technology can be used to facilitate these two ideals.
Complete Sequencing – Clifford Reid, PhD; CEO, Complete Genomics as presented at the Personalized Health Care Conference at Ohio State. Dr. Reid discussed what complete human sequencing looks like and costs now and in the near future.
A Grand Challenge of Genome Sequencing: Complete Genomics of Human and Microb...Larry Smarr
11.06.15
Enabling Genomic Medicine Roundtable: A Grand Challenge of Genome Sequencing: Complete Genomics of Human and Microbiome DNA: Comparing Healthy with IBD
Presented by: Larry Smarr, UCSD (Calit2)
San Francisco California
January 23, 2017
The Fifth Annual Health Law Year in P/Review symposium featured leading experts discussing major developments during 2016 and what to watch out for in 2017. The discussion at this day-long event covered hot topics in such areas as health policy under the new administration, regulatory issues in clinical research, law at the end-of-life, patient rights and advocacy, pharmaceutical policy, reproductive health, and public health law.
The Fifth Annual Health Law Year in P/Review was sponsored by the Petrie-Flom Center for Health Law Policy, Biotechnology, and Bioethics at Harvard Law School, Harvard Health Publications at Harvard Medical School, Health Affairs, the Hastings Center, the Program On Regulation, Therapeutics, And Law (PORTAL) in the Division of Pharmacoepidemiology and Pharmacoeconomics at Brigham and Women’s Hospital, and the Center for Bioethics at Harvard Medical School, with support from the Oswald DeN. Cammann Fund.
Learn more on our website: http://petrieflom.law.harvard.edu/events/details/5th-annual-health-law-year-in-p-review
From Bits to Bedside: Translating Big Data into Precision Medicine and Digita...Dexter Hadley
Lecture Objectives:
1) To use examples from my research to define and introduce the ideals of precision medicine and digital health. 2) To introduce how large scale population-wide analysis of data can be used to facilitate these two ideals. 3) To introduce how freely available open data can be used to facilitate these two ideals. 4) To show how mobile technology can be used to facilitate these two ideals.
Complete Sequencing – Clifford Reid, PhD; CEO, Complete Genomics as presented at the Personalized Health Care Conference at Ohio State. Dr. Reid discussed what complete human sequencing looks like and costs now and in the near future.
A Grand Challenge of Genome Sequencing: Complete Genomics of Human and Microb...Larry Smarr
11.06.15
Enabling Genomic Medicine Roundtable: A Grand Challenge of Genome Sequencing: Complete Genomics of Human and Microbiome DNA: Comparing Healthy with IBD
Presented by: Larry Smarr, UCSD (Calit2)
San Francisco California
Crowd-Sourced Intelligence Built into Search over HadoopDataWorks Summit
Search is increasingly being used to gather intelligence on multi-structured data leveraging distributed platforms such as Hadoop in the background. This session will provide details on how search engines can be abused to use not text, but mathematically derived tokens to build models that implement reflected intelligence. The session will describe how to integrate Apache Solr/Lucene with Hadoop. Then we will show how crowd-sourced search behavior can be looped back into analysis and how constantly self-correcting models can be created and deployed. Finally, we will show how these models can respond with intelligent behavior in realtime.
My presentation at the http://neuroinformatics2017.org (Kuala Lumpur, Malaysia) on FAIR and FAIRsharing (previously BioSharing); metadata standards and their implementation by databases/repositories and adoption by journals' and funders' data policies.
Crowd-Sourced Intelligence Built into Search over HadoopDataWorks Summit
Search is increasingly being used to gather intelligence on multi-structured data leveraging distributed platforms such as Hadoop in the background. This session will provide details on how search engines can be abused to use not text, but mathematically derived tokens to build models that implement reflected intelligence. The session will describe how to integrate Apache Solr/Lucene with Hadoop. Then we will show how crowd-sourced search behavior can be looped back into analysis and how constantly self-correcting models can be created and deployed. Finally, we will show how these models can respond with intelligent behavior in realtime.
My presentation at the http://neuroinformatics2017.org (Kuala Lumpur, Malaysia) on FAIR and FAIRsharing (previously BioSharing); metadata standards and their implementation by databases/repositories and adoption by journals' and funders' data policies.
Genome in a Bottle - Towards new benchmarks for the “dark matter” of the huma...
March 2013 Introduction
1. Genome-in-a-Bottle Consortium
Reference Materials for Clinical Applications of
Human Genome Sequencing
Marc Salit, Ph.D. and Justin Zook, Ph.D
National Institute of Standards and Technology
3. NIST in partnership with FDA
• FDA calls for NIST RMs for • FDA funding work at NIST
WGS to develop reference
– “An RM from NIST has materials suitable to
great potential to facilitate support regulatory
FDA's regulatory approach oversight
to WGS, and would help
provide assurance that – materials to be used as
different sequencers at part of evaluation of
different locations had a technical performance of
particular level of ongoing sequencing instruments as
performance.” devices
• Elizabeth Mansfield,
Director, Personalized
Medicine Staff,
OIVD/CDRH/FDA
4. Value of a NIST RM
• NIST commitment to:
– Maintain availability of RM
– Maintain data on RM – ongoing
aggregation of sequence data to
increase accuracy and minimize
biases
– Be a neutral arbiter in aggregation
of data from different platforms
• NIST infrastructure to distribute
RM
• NIST investment in genomic
measurement science
• NIST imprimatur as an
internationally recognized source
of “higher order” RMs for
regulatory and commercial
purposes
7. Genome in a Bottle
Consortium Development
• NIST met with sequencing • Open, public meeting at NIST to
technology developers to assess formally establish consortium,
standards needs present draft work plan
– Stanford, June 2011 – formed working groups
• Open, exploratory workshop – identified candidate genomes
– ASHG, Montreal, Canada – established principles of:
– October 2011 • reference material selection
• characterization
• Small, invitational workshop at • informatics
NIST to develop consortium for • performance metrics
human genome reference – August 2012
materials • Expect to be sequencing
– FDA, NCBI, NHGRI, NCI, CDC, Wash candidate genomes Q4 2012
U, Broad, technology developers,
clinical labs, CAP, PGP, Partners, – developing large RM batches to
ABRF, others characterize in 2013
– developed draft work plan • Website
– April 2012 – www.genomeinabottle.org
8. Genome in a Bottle Working Groups
Reference Material Meaurements for Bioninformatics, Dat Performance Metrics
Selection Reference Material a Integration, and & Figures of Merit
& Design Characterization Data Representation
Andrew Grupe, Elliott Margulies & Steve Sherry, NCBI Justin Johnson,
Celera Mike Eberle, Illumina EdgeBio
•Develop prioritized list •Develop consensus •Develop plan for •User interface to the
of whole human plan for experimental integrating Genome-in-a-Bottle
genomes for Reference characterization of experimental data and Reference Material
Materials Reference Materials forming consensus •“Dashboard”
•Identify candidate variant calls and •what an end user will
approaches and confidence estimates see and report to
materials for artificial •Develop consensus understand and
RMs plan for data describe the
•Develop prioritized representation performance of their
list experiment
•variant call accuracy
•process performance
measures to enable
optimization