Technology to Enable the Genomics Revolution · LIMS (genomic sequencing data) Clinician Knowledge...
Transcript of Technology to Enable the Genomics Revolution · LIMS (genomic sequencing data) Clinician Knowledge...
Technology to Enable the Genomics Revolution
Kate Birch
Data & Technology Program Manager
How Melbourne Genomics is Delivering for Patient Care
Topics for discussion
• Delivering a shared platform for bioinformatic collaboration as part of GenoVic
• Storage of clinical genomic data as part of GenoVic
Melbourne Genomics Health Alliance | Document Name Here 2
From genetics to genomics
• Genetics scrutinizes the functioning and composition of the single gene where as
• Genomics addresses all genes and their inter relationships in order to identify their combined influence on the growth and development of the organism
World Health Organisation
Melbourne Genomics Health Alliance | Document Name Here 3
From genetics to genomics
Melbourne Genomics Health Alliance | Document Name Here 4
Integration with microbiome, proteomics, metaboloimics...
Whole genome
Whole exome
Large panels
Small panels
Single gene
From genetics to genomics
Melbourne Genomics Health Alliance | Document Name Here 5
Integration with microbiome, proteomics, metaboloimics...
Whole genome
Whole exome
Large panels
Small panels
Single gene
Melbourne Genomics Health Alliance 6
An analogy…..
1000 copies of War and
Peace = a single
genome
An analogy…..
1000 copies of War and
Peace = a single
genome
Shred them. Read each piece and
reconstruct the story. Find the typos.
An analogy…..
1000 copies of War and
Peace = a single
genome
Shred them. Read each piece and
reconstruct the story. Find the typos.
Do they change the meaning of the
sentence?
Research Clinical care
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Only 2% of US genomic data is used for clinical careErik Jylling - Executive Vice President Health Politics, Danish Regions
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The Melbourne Genomic Health Alliance set out to make Victoria a world leader in the translation and use of clinical genomics in healthcare
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Challenge: Create whole of system change
Melbourne Genomics Health Alliance
Melbourne Genomics Health Alliance | Document Name Here 14
Melbourne Genomics Health Alliance 15
Melbourne Genomics Health Alliance
Approach
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Evaluate the place of genomics in health care
practice, by:
(1) evaluating the process and outcomes of
genomic tests in practice, and
(2) establishing and applying a platform for
health service research, program evaluation,
economic evaluation and translational research
in the use of genomics in health care.
.
Establish active relationships and participation in
national and international initiatives with the aim
of disseminating, communicating and
collaborating on the work of the Alliance and its
implications.
STREAM 5: NATIONAL AND
INTERNATIONAL IMPACT
STREAM 3: INNOVATION AND RAPID ADOPTION
Develop and deploy systems to ensure patients
have access to cutting-edge, high quality genomic
testing that is cost-effective.
STREAM 1:
WORKFORCE DEVELOPMENT
Build the literacy, skills and
confidence of the clinical and
diagnostic workforce in
genomics, as relevant to each
professional role
STREAM 4: ACCESS TO GENOMIC INFORMATION
Develop and implement a single set of standards, policies
and procedures to support a common infrastructure for the
management and use of genomic data by stakeholders in
Victoria.
This stream will be the focus of the workshop.
DISEASE FLAGSHIPS
Flagships are the mechanism through which
genomic sequencing is provided to patients with
defined clinical conditions or indications.
Flagships will also be the means by which the
workforce is developed, innovation is adopted,
outcomes are evaluated and information systems
trialled, and underpin the five streams.
STREAM 2: ASSESSING THE VALUE
OF GENOMICS
Technology to enable clinical genomics
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Access to Genomic Information
Melbourne Genomics Health Alliance 18
Develop and implement a single set of standards, policies and
procedures to support a common infrastructure for the
management and use of genomic data by stakeholders in
Victoria.
Ideal end state in an unconstrained environment
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8. Clinical Tools
13. Genomic Data Repository
14. Data Integration
5. Staff to
manage the
data
PeoplePolicy & Process Technology
1. Standardised policy and
processes for data
management & access
(data governance)
11. Data Access Tools
12. Master
Patient Index
7. Identity & Access Management
2. Standardised
policy & processes
for patient consent
Electronic
Orders and
Results
EMR
(clinical data)
LIMS
(genomic
sequencing data)
Clinician
Knowledge
Clinical Decision Support
Tools
9. Diagnostic Tools
Curation Tools
Analysis
(Pipeline) Tools
10. Patient Tools
Education
Consent
Results
6. Staff to
manage the
technology
3. Standardised policy and
processes for test ordering
& reporting
4. Change control process Public variant
curation data
Melbourne Genomics Health Alliance
Diagnostic Tools Approach
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Define Requirements Procure
Prototype learnings
Future needs
LOVD
Cpipe
SeqLiner
EOI
Workshops
Pilot
Prototype
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GenoVic
G SGenomic Orchestration Service
A shared platform for bioinformatic collaboration
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GenoVic
G SGenomic Orchestration Service
Bioinformatics Challenges
Pooling of resources, collaboration
Clinically hardened software
Clinical grade compute
Scalable, cost effective compute
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DNAnexus
A platform for developing and running bioinformatics pipelines on AWS
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Bioinformatics Challenges
Pooling of resources, collaboration
Clinically hardened software
Clinical grade compute
Scalable, cost effective compute
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Pipeline Design
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Each app accepts inputs from any number of samples
• Solves code duplication
• Supports batching
Each app uses a Docker image to run the analysis
• This keeps our workflows portable
• Allows us to leverage existing containers such as the miniconda environment
Acceptance criteria outcomes - runtime
Runtime - trio
Runtime for a Ashkenazim Trio child (NA24385) is 12h 29m.
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Framework for testing shared pipelines
The Alliance has implemented a basic framework which the laboratories can build on to implement the comprehensive pipeline testing required for accreditation.
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Bioinformatics Challenges
Pooling of resources, collaboration
Clinically hardened software
Clinical grade compute
Scalable, cost effective compute
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Variant identification
DNAnexus
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Germline Pipeline
Alliance Pipeline V1
Alliance Pipeline V2
Alliance Pipeline V3
Member's Own Pipeline
New
reference
genome?
Routine QC?
CWL/WDL?
Alt aware?
Rapid
exomes?
Long reads?
Bioinformatics Challenges
Pooling of resources, collaboration
Clinically hardened software
Clinical grade compute
Scaleable, cost effective compute
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Storage of clinical genomic data
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Why store clinical genomic data?
Pathology labs need to
Reanalysis leads to new diagnoses
Clinical reference data
Valuable research data
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GenoVic
G SGenomic Orchestration Service
Storage of genomic data
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Store
Catalogue & search
Release
Storage of genomic data
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Store
Catalogue & search
Release
Storage of genomic data
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Store
Catalogue & search
ReleasePolicies and procedures for data sharing
Data Governance Owners, Stewards and Alliance Data Custodians
Patient’s views on data sharing
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We asked patients having genomic testing what they want
Patient accept genomic testing
More than 96% of patients consented
Melbourne Genomics Health Alliance
Common
clinical consent form
Melbourne Genomics Health Alliance
Opt in to share data for activities
related to their condition
Sharing of anonymised data
Majority are informed and not concerned
Patients are informed after genetic counselling • Over 80% of patients correctly answered questions about the types of results they may receive and
storage of their data
Almost everyone agrees to additional use of re-identifiable data
• 99% agree to additional use of re-identifiable genomic data when giving clinical consent
Majority have no remaining concerns about sharing their data
• 97% received enough information about data sharing
• 93% have no remaining concerns about sharing data
• 13 had concerns (privacy, potential for discrimination – employment, insurance)
Melbourne Genomics Health Alliance
Most not worried even if they are identified
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Difficult
&
concerned
Easy
&
concerned
Difficult
&
Unconcerned
Easy
&
Unconcerned
Ease of identification
&
Level of concern if
identified
How broadly should data be shared?
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Patient trust in sharing data
Melbourne Genomics Health Alliance
Alliance Members
Australian not-for-profit
Overseas not-for-profit
Pharmaceutical
Government
Other Industry
High trust
Low trust
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500 active health care professionals
10 organisations
>1000 received genomics CPD
Melbourne Genomics in action
16 disease areas
National and
international influence
Evaluation informing
government policy and
funding
$37.5M research and clinical
funding leveraged
Our model has been adopted by others
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Melbourne Genomics
Health Alliance
2013-2019
Australian Genomics
Health Alliance
2016-2020
Queensland Genomics
Health Alliance
2016-2020
Genome Canada is
considering the model
Genetic Health Alliance
New Zealand
(formed in 2017)
Melbourne Genomics Health Alliance
Melbourne Genomics – 2013-2015
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CEOs/LeadershipGareth Goodier (RMH)
Christine Kilpatrick (RCH)
Stephen Smith (University of Melbourne)
Doug Hilton (WEHI)
Kathryn North (MCRI)
Lynne Cobiac (CSIRO)
Sue Forrest (AGRF)
–Steering GroupJames Angus (Chair)
Julian Clark
Sue Forrest
Clara Gaff (Exec Director)
Trevor Lockett / David Hansen
Andrew Sinclair
Mike South
Paul Waring / Jon Emery
Ingrid Winship
–Advisory Groups
Information Management Advisory
David Hansen (Chair)
Terry Brennan
Ken Doig
Rowan Gronlund
Andrew Lonie
Fernando Martin-Sanchez
Wayne Mather
Emeline Ramos
Brenda White
Community Advisory
Ingrid Winship (Chair)
Louisa Di Pietro
Heather Renton
Margaret Sahhar
Janney Wale
Christine Walker
Liat Watson
Clinical Interpretation& Reporting Advisory
Paul James (Chair)
Damien Bruno
Paul Ekert
Monique Ryan
Charlotte Slade
Alison Trainer
Genomics & Bioinformatics Advisory
Graham Taylor / Alicia Oshlack (Chair)
Melanie Bahlo
Denis Bauer
Paul James
Andrew Lonie
Simon Sadedin
Kirby Siemering
Data Access Advisory
Yousef Kowsar
Kurt Lackovic
Steven Manos
Candice McGregor
Owen O’Neill
Gayle Philip
Bernie Pope
Melissa Southey
Advanced Users Group
–Flagships
AML
Andrew Roberts
Ian Majewski
Seong Lin Khaw
Francoise Merchinaud
Edward Chew
CMT
Monique Ryan
Paul James
Tim Day
Lynette Kiers
Adrienne Sexton
CRC
Alex Boussioutas
Finlay Macrae
Alison Trainer
Ingrid Winship
Michael Bogwitz
CS
Sue White
Zornitza Stark
Tiong Tan
Paul Ekert
Christiane Theda
David Amor
Maie Walsh
Patrick Yap
Epilepsy
Patrick Kwan
Terry O’Brien
Ingrid Scheffer
Piero Perucca
Paul James
–Laboratories
CTP
Paul Waring
Graham Taylor
Tiffany Cowie
Sebastian Lunke
Renata Marquis-Nicholson
Greg Corboy
Michael Christie
Arthur Hsu
VCGS
Graham Taylor
Damien Bruno
Steven Nasioulas
Belinda Chong
Shannon Cowie
Melanie Smith
Clare Love
Chris Guest
AGRF
Sue Forrest
Kirby Siemering
Melanie O’Keefe
Matthew Tinning
Lavinia Gordon
Rust Turakulov
Stephen Wilcox
–
Information SystemsCPIPE / MG LOVD VLSCI
Andrew Lonie
Simon Sadedin
John-Paul Plazzer
Charlotte Anderson
Anthony Marty
Peter Georgeson
Denis Bauer
Harriet Dashnow
Guido Grazioli
Richard Sinnott
Glenn Tesla
Clare Sloggett
Clinical Systems - MCRI & REDCAP
Jane Halliday
Susan Donath
Leanne Mills
Ross Dunn
Luke Stephens
BIOGRID
Maureen Turner
Leon Heffer
Alice Johnstone
–
Working GroupsPatient-entered data tool
Patient survey
Research access
Education symposium
Evaluation
Information requirements
Reporting
Database users
Pipeline platform
–Project TeamClara Gaff (Exec Director)
Tim Bakker (Info Mgmt)
Michele Cook (Admin)
Ivan Macciocca (Clinical)
Karen Meehan (Comms)
Natalie Thorne (Bioinf)
Evaluation Team
Emily Forbes
Melissa Martyn
Nessie Mupfeki
Bill Wilson
Genetic Counsellors
Gemma Brett
Emma Creed
Ella Wilkins
Health Economics
Khurshid Alam
Deborah Schofield
Rupendra Shrestha
Melbourne Genomics – 2016-2019
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Alliance BoardCatherine Walter (Chair)Christine Kilpatrick (RMH)Andrew Stripp (Monash Health)Dale Fisher (PeterMac)Christine Kilpatrick (RCH)Shitij Kapur (UoM)Doug Hilton (WEHI)Kathryn North (MCRI)Rob Grenfell (CSIRO)Irene Kourtis (AGRF)Sue Shilbury (Austin Health)Anna Burgess (DHHS observer)
–Executive Management CommitteeClara Gaff (Chair)David HansenAndrew SinclairRichard KingJulian ClarkFelicity ToppFergus KerrPeter McDougallIngrid WinshipSean GrimmondKirby SiemeringPaul Fennessy (DHHS observer)
–Advisory Groups Clinical Adoption Advisory
Fergus Kerr (Chair)Cate Kelly Sylvia Metcalfe Don CampbellLindsay GraysonMargaret Kelaher Noel CranswickJayesh Desai
Community Advisory
Jane Bell (Chair)Louisa Di PietroHeather RentonMargaret SahharJanney WaleChristine WalkerLiat Watson
Diagnostic Advisory
Richard King (Chair)Kirby SiemeringSebastian Lunke Melanie O’KeefeVivien VasicMichael ChristieAndrew FellowesSuzanne SvobodovaTony Papenfuss Simon SadedinPaul James
Information Management Advisory/GenoVic Project Control Group
David Hansen (Chair)Wayne Mather Rowan GronlundKevin EricksenTony Papenfuss Michael CarolanErminia SchiavoneKris JenkinsMike SouthAngela WattAndrew LonieClara GaffMalcolm Smart
–Flagships 2016-2018Congenital Deafness
David AmorLilian DownieValerie SungLibby SmithBibi GernerMatthew HunterKerryn SaundersNatasha BrownMelissa WakeRachel BurtJane HallidayZeffie PoulakisElizabeth Rose
Complex Care in Children
Sue WhiteZornitza StarkTiong TanAlison YeungMatthew HunterKatrina Harris
Dilated Cardiomyopathy
Paul JamesJay RamchandMatthew WallisDavid HareOmar Farouque
Immunology
Jo DouglassCharlotte SladeVanessa BryantJo SmartSara BarnesSeth MastersMimi TangIngrid WinshipZornitza Stark
Lymphoma
Stephen OpatMiles PrinceGareth GregoryMichael DickinsonEliza HawkesPiers Blombery
Solid Cancers
Jayesh DesaiKortnye SmithSophie BeckDong Anh Khuong QuongHui GanPaul EckertBen SolomonBen Markman
–Flagships 2017-2019Bone marrow failure
Piers BlomberyDavid RitchieFrancoise MechinaudAnthea GreewayAndrew GriggErica WoodPaddy Barbaro
Controlling Superbugs
Lindsay GraysonBen HowdenNorelle SherryJason KwongTony Korman
Caroline MarshallMark ChanMonica SlavinMarcel Leroi
Complex neurological
Patrick KwanSam BerkovicMartin DelatyckiDennis VelakoulisMichael FaheyMelanie BahloRick LeventerAmy Schneider
Genetic kidney disease
Catherine QuinlanSue WhiteZornitza StarkElla WilkinsMathew WallisDavid PowerKathy NichollsPeter Kerr
Perinatal autopsy
George McGillivrayJacqueline CollettIan SimpsonTrishe LeongJan PymanAlison YeungNatasha BrownSue WhiteSue Walker
–LaboratoriesCTP
Paul WaringGraham TaylorTiffany CowieSebastian LunkeRenata Marquis-NicholsonGreg Corboy
Michael ChristieArthur Hsu
VCGS
Graham TaylorDamien BrunoSteven NasioulasBelinda ChongShannon CowieMelanie SmithClare LoveChris Guest
AGRF
Sue ForrestKirby SiemeringMelanie O’KeefeMatthew TinningLavinia GordonRust TurakulovStephen Wilcox
–Information SystemsCPIPE / MG LOVD VLSCI
Andrew LonieSimon SadedinJohn-Paul PlazzerCharlotte AndersonAnthony MartyPeter GeorgesonMichael MiltonJuny KesumadewiGayle PhilipsDenis BauerHarriet DashnowGuido GrazioliRichard SinnottGlenn TeslaClare Sloggett
Clinical Systems - MCRI & REDCAP
Jane HallidaySusan DonathLeanne MillsRoss DunnLuke StephensBIOGRIDMaureen TurnerLeon HefferAlice Johnstone
–Working GroupsPatient-entered data toolPatient surveyResearch accessEducation symposiumEvaluationInformation requirementsReportingDatabase usersPipeline platformCuration tool pilot evaluatorsCuration tool RFQ evaluatorsAnalysis tool user groupCuration tool user groupInformation architecture reference group
–Genetic Counsellors
Gemma BrettEmma CreedAnna JarmolowiczIvan MaccioccaEllie PrawerGiulia ValenteKirsty West
Health Economics
Khurshid AlamDeborah SchofieldRupendra Shrestha
Melbourne Genomics Health Alliance Program Team
Thank you