Presentations from Subject Matter Experts

Precision Medicine Task Force

August 5, 2015Leslie Kelly Hall, Co-ChairJon White, Co-Chair

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Agenda

• Call to Order/Roll Call• Welcome, Opening Remarks• Presentations from Subject Matter Experts

– Intel Corporation– Intermountain Healthcare– National Library of Medicine (NLM), National Center for

Biotechnology Information (NCBI)

• Q & A• Recap & Next Steps• Public Comment• Adjourn

Precision Medicine Task Force Membership

Member OrganizationCo-ChairsLeslie Kelly Hall HealthwiseJon White ONC / Agency for Healthcare Research and Quality (AHRQ)MembersMary Barton National Committee for Quality Assurance (NCQA)Lisa Gallagher Healthcare Information and Management Systems Society (HIMSS)David McCallie, Jr. Cerner CorporationAndrey Ostrovsky Care at HandEric Rose Intelligent Medical ObjectsAndrew Wiesenthal Deloitte Consulting, LLPFederal Ex OfficioJames Breeling Veterans Health Administration (VHA)Josh Denny National Institutes of Health (NIH)Betsy Humphreys National Library of Medicine (NLM)Mitra Rocca Food and Drug Administration (FDA)Linda Sanches HHS Office for Civil Rights (OCR)Christina Heide HHS Office for Civil Rights (OCR)Invited GuestsMina Hsiang United States Digital Service (USDS) / Office of Management and Budget (OMB)Claudia Williams White House Office of Science & Technology Policy ONC StaffMaya Uppaluru ONC – Federal Staff LeadDebbie Bucci ONC - Technical Advisor

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Task Force Charge

• Identify opportunities for innovative collaboration around pilots and testing of standards that support health IT interoperability for precision medicine

• Recommend existing standards that are currently ready to support PMI

• Identify emerging standards and reference implementations that may require further pilot testing in order to support PMI

• Identify gaps in available data standards related to PMI

2015 Q3 2015 Q4

Jun Jul Aug Sep Oct Nov Dec

FACA Workplan

Kick-off

Joint HITPC/HITSC Meeting

Quality Measure TF (QMTF) - PFS NPRM

Standards Advisory (ISA) Task Force

P&S Big Data Recommendations

ISA Recommendations

Milestone

Interoperability Task Force (ITF)

Precision Medicine Task Force

QMTF - PFS NPRM Feedback

Precision Medicine Recommendations

ITF Recommendations

Meetings Task

July 17, 2015 11:00 am - 1:30 pm ET Kick-off Meeting

• Review charge, work plan• Overview of the Precision Medicine Initiative

o White House Office of Science & Technology Policyo National Institutes of Health

Wednesday July 29, 2015 1:30 - 3:00 pm ET

• Presentations from expertso 23andmeo NIH Precision Medicine Workshopo Genetic Alliance, Institute of Medicine

Wednesday August 5, 2015 12:00 - 1:30 pm ET

• Presentations from expertso Intel Corporationo Intermountain Healthcareo NLM / dbSNP / dbGaPo Written comment: Jonathan Sheldon, MD, Oracle

Wednesday August 19, 2015 12:00 - 1:30 pm ET

• Presentations from expertso Duke Me Tree Projecto Google Baselineo PCORIo ResearchKit / Sageo Written comment from physicians: Joan Elmore , Nancy Keating , Justin Starren

Monday August 31, 2015 12:00 - 1:30 pm ET

• Develop Preliminary Task Force Recommendations• Prep for Sept. HITSC presentation.

Thursday September 10, 2015 1:30 - 3:00 pm ET

• Finalize recommandations to HITSC

September 22, 2015 – HITSC Meeting

• Present final recommendations

Precision Medicine Task Force Workplan7/27/15

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Questions for Presenters

Your Organization

1. What role does your organization provide with regard to precision medicine?2. How do genomics and other “omics” play a part in that work?3. How important is interoperability to your organization?

Standards 1. Will data standards help you?2. What standards, if any, do you currently use? Both HIT and other?

a) Taxonomy or vocabulary standards?b) Data?c) Transport?

3. How committed are you to standards use?4. Are standards you may be using fit for purpose or for regulatory recommendations or both?

Roles 1. What roles should actors play?a) Government?b) Consumers / Patients?

Challenges 1. What are the biggest barriers to interoperability that you have experienced with respect to data and systems?

2. What makes it hard or easy to use the following data for population analytics or research: EHR data, genomics data, mHealth data?

3. What other data, gathered from patients, are needed in order to make genomics data as useful as possible in care?

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Intel Corporation• Ketan Paranjape, Director Healthcare and Life Sciences• Matt Quinn, Managing Director, Life Sciences• Ashley Rees, Marketing & Business Strategist, Intel Corporation• Yentram Huyen, Innovation Leader in Healthcare & Life Sciences Ecosystems

CLINICAL GENOMICS ISSUES AND STANDARDS

PERSONALIZED MEDICINE INITIATIVE

Marc Probst, Stan Huff, Grant WoodAugust 5, 2015

Challenges Implementing Precision Medicine

• Prioritization of HIT resources (MU requirements, EHR implementation, business strategy for an ‘Omic repository and clinical genomics platform, etc.)

• Storing and using family health history and genetic/genomic tests results in the HER

• Infrastructure to support molecular clinical decision making

• Data interfaces with labs, data at the source not in structured format

• Lack of true interoperability, getting there is hard, terminology, information models, process for adopting standards, etc.

Standards for Precision Medicine

• HL7 Clinical Genomics activities - Version 2, Version 3, Clinical Document Architecture, for Family Health History and Clinical Genetics/Genomics

• HL7 moving towards Fast Healthcare Information Resources (FHIR) for genomic information

• SMART on FHIR apps (HSPC)• API’s to access genomic databases (GA4GH, etc.)• IOM Digitize - Genetic results from lab to EHR• WEDI, ASCO HIT WG• NIH multi-center grants - eMerge network, IGNITE

Building from this Foundation

A Few Questions

• IOM Digitize pilot to include Intermountain, Cerner, ARUP, Invitae. Other pilots involve Partners Healthcare and EPIC. Allscripts has been part of discussions. However, how the clinicians will view the data in the EHR is another matter. Clinical genomic interpretation services.

• Is HL7 genomics standards inadequate for PMI? We should have a discussion with the HL7 workgroup – identify if there is a gap in standards that are not finished.

• dbSNP a standard for genomic/proteomic data? If the question is about a database schema to store genomic/proteomic data, we can ask the genomic database vendors.

• What are the challenges with family history data in the EHR? Getting people to collaborate/share data with family members and back to their physician. Looking at issues that support a pedigree in the EHR.

Genomics for PMI Task ForceAugust 5, 2015

James Ostell

National Center for Biotechnology Information US National Institutes of Health, Bethesda, MD, 20894-6513

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DANGER!

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“GenBank” Today

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Trace and SRA are part of GenBank

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Read IDs as stringsOriginal quality & recalibrated quality scoresAdditional analysis tags

Read IDs as integers40-level read qualities using recalibrated quality scores

8 level qualities for all sitesUniform binning of recalibrated quality scores Variant Call

Format (VCF)Genotype likelihoods for all variants

Total Project Size

SRA-40 SRA-8 Analysis Genotypes

Size

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What is the Big Data Problem in Biology?Example: Reducing the 1000 Genome Dataset

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SRAreads

Reads and placement only

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The human reference genome assembly represents multiple individuals

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2007 2008 2009 2010 2011 2012 2013 20140

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Number of Bases Released

Open Acess Controlled Access

The Problem with Human Data

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Secure Hybrid Cloud

User Actions•Obtains security

certificate from dbGaP or other Access Control system

• Launches FUSE with • Security certificate•Encryption Key• Local Disk Area • Local mount point

•Reads and writes data from mount point as if it is a local filesystem

• Shutdowns FUSE when work is completed

FUSE Server Actions•Gets the list of remote

files based on security certificate

•Gets the list of local files from Work Area

•Returns and decrypts already downloaded pages

•Decrypts local files•Requests missing pages

from HTTP• Saves delivered pages to

local disk•Encrypts Writes before

saving them to the disk•After FUSE is shutdown all

data on local disks including newly created is secured

NCB

I dbG

aP

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Volume CVolume B

Volume A

HTTP

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Encrypted at rest

Page1

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Local Disk Cache

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FUSE Server Implementation

Virtual Image of Remote And Local Data

User application

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Rea d

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Using Beacons to Discover Data

Repository Discovery

• Does the data exist?

• Role of Public Beacons

• Query: Do you have any genomes with an “A” at position 100,735 on chromosome 3?

• Reply: ‘Yes’ or ‘No’

Data context

• Does the data have the properties I require?

• Role of Registered Access Beacons

• Shows details of studies with data and provides link for requesting access

Data Preview

• Does the metadata have the properties I require?

• Requires approved access

• Permits users to narrow the search and access the precise sets of data needed.

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Registration example: NIH eRA

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Registered Access Beacon: dbGaP

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Recap & Next Steps