Technology to Enable the Genomics Revolution How Melbourne Genomics - - PowerPoint PPT Presentation

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Technology to Enable the Genomics Revolution How Melbourne Genomics - - PowerPoint PPT Presentation

Jan 19, 2024 676 likes •1.25k views

Technology to Enable the Genomics Revolution How Melbourne Genomics is Delivering for Patient Care Kate Birch Data & Technology Program Manager Topics for discussion Delivering a shared platform for bioinformatic collaboration as part

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Technology to Enable the Genomics Revolution

Kate Birch Data & Technology Program Manager

How Melbourne Genomics is Delivering for Patient Care

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Topics for discussion

  • Delivering a shared platform for bioinformatic collaboration as part
  • f GenoVic
  • Storage of clinical genomic data as part of GenoVic
Melbourne Genomics Health Alliance | Document Name Here 2
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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
  • rder to identify their combined influence on the growth and

development of the organism World Health Organisation

Melbourne Genomics Health Alliance | Document Name Here 3
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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

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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

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SLIDE 6 Melbourne Genomics Health Alliance 6
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An analogy…..

1000 copies of War and Peace = a single genome

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An analogy…..

1000 copies of War and Peace = a single genome Shred them. Read each piece and reconstruct the story. Find the typos.

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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?

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Research Clinical care

Melbourne Genomics Health Alliance | Document Name Here 10
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Only 2% of US genomic data is used for clinical care

Erik 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

  • f clinical genomics in healthcare
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Challenge: Create whole of system change

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Melbourne Genomics Health Alliance

Melbourne Genomics Health Alliance | Document Name Here 14
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SLIDE 15 Melbourne Genomics Health Alliance 15

Melbourne Genomics Health Alliance

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Approach

Melbourne Genomics Health Alliance 16 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
  • f 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. . 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,
  • utcomes are evaluated and information systems
trialled, and underpin the five streams. STREAM 2: ASSESSING THE VALUE OF GENOMICS
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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.

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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 People Policy & 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
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Diagnostic Tools Approach

21 Melbourne Genomics Health Alliance

Define Requirements Procure

Prototype learnings Future needs

LOVD Cpipe SeqLiner

EOI Workshops Pilot

Prototype

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SLIDE 22 22 Melbourne Genomics Health Alliance
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GenoVic

G S

Genomic Orchestration Service
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A shared platform for bioinformatic collaboration

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GenoVic

G S

Genomic Orchestration Service
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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

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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

  • n 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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SLIDE 33 Melbourne Genomics Health Alliance | Document Name Here 33 Variant identification
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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?

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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 S

Genomic Orchestration Service
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Storage of genomic data

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Store Catalogue & search Release

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Storage of genomic data

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Store Catalogue & search Release

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Storage of genomic data

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Store Catalogue & search Release

Policies and procedures for data sharing Data Governance Owners, Stewards and Alliance Data Custodians

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Patient’s views on data sharing

Melbourne Genomics Health Alliance | Document Name Here 42
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We asked patients having genomic testing what they want

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Patient accept genomic testing

More than 96% of patients consented

Melbourne Genomics Health Alliance
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Common clinical consent form

Melbourne Genomics Health Alliance

Opt in to share data for activities related to their condition Sharing of anonymised data

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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
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Most not worried even if they are identified

Melbourne Genomics Health Alliance 49

Difficult & concerned

Easy & concerned Difficult & Unconcerned

Easy & Unconcerned Ease of identification & Level of concern if identified

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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

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Our model has been adopted by others

52 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
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Melbourne Genomics – 2013-2015

Melbourne Genomics Health Alliance | Document Name Here 53 CEOs/Leadership Gareth Goodier (RMH) Christine Kilpatrick (RCH) Stephen Smith (University of Melbourne) Doug Hilton (WEHI) Kathryn North (MCRI) Lynne Cobiac (CSIRO) Sue Forrest (AGRF)

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Steering Group James Angus (Chair) Julian Clark Sue Forrest Clara Gaff (Exec Director) Trevor Lockett / David Hansen Andrew Sinclair Mike South Paul Waring / Jon Emery Ingrid Winship

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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

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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

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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

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Information Systems CPIPE / 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

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Working Groups Patient-entered data tool Patient survey Research access Education symposium Evaluation Information requirements Reporting Database users Pipeline platform

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Project Team Clara 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
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Melbourne Genomics – 2016-2019

Melbourne Genomics Health Alliance | Document Name Here 54 Alliance Board Catherine 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)

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Executive Management Committee Clara Gaff (Chair) David Hansen Andrew Sinclair Richard King Julian Clark Felicity Topp Fergus Kerr Peter McDougall Ingrid Winship Sean Grimmond Kirby Siemering Paul Fennessy (DHHS observer)

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Advisory Groups Clinical Adoption Advisory Fergus Kerr (Chair) Cate Kelly Sylvia Metcalfe Don Campbell Lindsay Grayson Margaret Kelaher Noel Cranswick Jayesh Desai Community Advisory Jane Bell (Chair) Louisa Di Pietro Heather Renton Margaret Sahhar Janney Wale Christine Walker Liat Watson Diagnostic Advisory Richard King (Chair) Kirby Siemering Sebastian Lunke Melanie O’Keefe Vivien Vasic Michael Christie Andrew Fellowes Suzanne Svobodova Tony Papenfuss Simon Sadedin Paul James Information Management Advisory/GenoVic Project Control Group David Hansen (Chair) Wayne Mather Rowan Gronlund Kevin Ericksen Tony Papenfuss Michael Carolan Erminia Schiavone Kris Jenkins Mike South Angela Watt Andrew Lonie Clara Gaff Malcolm Smart

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Flagships 2016-2018 Congenital Deafness David Amor Lilian Downie Valerie Sung Libby Smith Bibi Gerner Matthew Hunter Kerryn Saunders Natasha Brown Melissa Wake Rachel Burt Jane Halliday Zeffie Poulakis Elizabeth Rose Complex Care in Children Sue White Zornitza Stark Tiong Tan Alison Yeung Matthew Hunter Katrina Harris Dilated Cardiomyopathy Paul James Jay Ramchand Matthew Wallis David Hare Omar Farouque Immunology Jo Douglass Charlotte Slade Vanessa Bryant Jo Smart Sara Barnes Seth Masters Mimi Tang Ingrid Winship Zornitza Stark Lymphoma Stephen Opat Miles Prince Gareth Gregory Michael Dickinson Eliza Hawkes Piers Blombery Solid Cancers Jayesh Desai Kortnye Smith Sophie Beck Dong Anh Khuong Quong Hui Gan Paul Eckert Ben Solomon Ben Markman

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Flagships 2017-2019 Bone marrow failure Piers Blombery David Ritchie Francoise Mechinaud Anthea Greeway Andrew Grigg Erica Wood Paddy Barbaro Controlling Superbugs Lindsay Grayson Ben Howden Norelle Sherry Jason Kwong Tony Korman Caroline Marshall Mark Chan Monica Slavin Marcel Leroi Complex neurological Patrick Kwan Sam Berkovic Martin Delatycki Dennis Velakoulis Michael Fahey Melanie Bahlo Rick Leventer Amy Schneider Genetic kidney disease Catherine Quinlan Sue White Zornitza Stark Ella Wilkins Mathew Wallis David Power Kathy Nicholls Peter Kerr Perinatal autopsy George McGillivray Jacqueline Collett Ian Simpson Trishe Leong Jan Pyman Alison Yeung Natasha Brown Sue White Sue Walker

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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

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Information Systems CPIPE / MG LOVD VLSCI Andrew Lonie Simon Sadedin John-Paul Plazzer Charlotte Anderson Anthony Marty Peter Georgeson Michael Milton Juny Kesumadewi Gayle Philips 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

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Working Groups Patient-entered data tool Patient survey Research access Education symposium Evaluation Information requirements Reporting Database users Pipeline platform Curation tool pilot evaluators Curation tool RFQ evaluators Analysis tool user group Curation tool user group Information architecture reference group

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Genetic Counsellors Gemma Brett Emma Creed Anna Jarmolowicz Ivan Macciocca Ellie Prawer Giulia Valente Kirsty West Health Economics Khurshid Alam Deborah Schofield Rupendra Shrestha Melbourne Genomics Health Alliance Program Team
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Thank you