Open data genomics_palermo_2017_ver03
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The document emphasizes the importance of open data in genomics for advancing personalized medicine and scientific research. It discusses the critical role of open data in integrating genomic information with technologies like artificial intelligence and deep learning, highlighting various initiatives, databases, and challenges in making this data accessible and reusable. Ultimately, it advocates for a culture of openness and collaboration to facilitate discoveries in genomics and cancer research.
Open data genomics_palermo_2017_ver03
- 1. Open Data is Essential for Personalized Medicine BF Francis Ouellette https://goo.gl/8U1QJa
- 2. Open Data is Essential for Genomics This presentation is on: https://www.slideshare.net/
- 3. 3Module #: Title of Module
- 4. Open Data is Essential for Genomics
- 5. Open Data is Essential for Genomics @bffo francis@genomequebec.comE-mail
- 6. Open Data is Essential for Genomics Times I’ve been in Italy • Trieste 1996: Last Yeast Genome Meeting • Naples 2005: NETTAB “Workflows management: new abilities for the biological information overflow” • Rome 2017: Elixir • Palermo 2017: NETTAB
- 7. Open Data is Essential for Genomics Outline • What I do • Open Data in genomics • Final thoughts
- 8. Open Data is Essential for Genomics But first, a little about me … … an unfinished story!
- 9. Open Data is Essential for Genomics https://goo.gl/anu933
- 10. Open Data is Essential for Genomics http://goo.gl/dJIur
- 11. Open Data is Essential for Genomics http://goo.gl/LwVOZ
- 12. Open Data is Essential for Genomics http://goo.gl/QI6aL
- 13. Open Data is Essential for Genomics http://goo.gl/mYHFO
- 14. Open Data is Essential for Genomics http://goo.gl/Jc5TK
- 15. Open Data is Essential for Genomics https://goo.gl/3PFr7L 1993-1997
- 16. Open Data is Essential for Genomics from the National Centre for Biotechnology Information
- 17. Open Data is Essential for Genomics from the National Centre for Biotechnology Information
- 18. Open Data is Essential for Genomics from the National Centre for Biotechnology Information PANIC
- 19. Open Data is Essential for Genomics
- 20. Open Data is Essential for Genomics PANIC
- 21. Open Data is Essential for Genomics PANIC
- 22. Open Data is Essential for Genomics
- 23. Open Data is Essential for Genomics https://www.ubc.ca/
- 24. Open Data is Essential for Genomics 1999
- 25. Open Data is Essential for Genomics 2001: Human Genome Project
- 26. Open Data is Essential for Genomics 2003-2007
- 27. Open Data is Essential for Genomics
- 28. Open Data is Essential for Genomics Toronto
- 29. Open Data is Essential for Genomics 2007-2017
- 30. Open Data is Essential for Genomics International Cancer Genome Consortium
- 31. Open Data is Essential for Genomics http://goo.gl/dJIur
- 32. Open Data is Essential for Genomics 2017- …
- 33. Open Data is Essential for Genomics
- 34. Open Data is Essential for Genomics SABs, EBs & projects I’m on:
- 35. Open Data is Essential for Genomics
- 36. Open Data is Essential for Genomics So what unifies all of what I’ve done?
- 37. Open Data is Essential for Genomics So what unifies all of what I’ve done? Helping scientists do science.
- 38. Open Data is Essential for Genomics Open Data https://goo.gl/Z63Wxp
- 39. Open Data is Essential for Genomics Genomics https://goo.gl/MX84KA
- 40. Open Data is Essential for Genomics What am I calling “Genomics”? All “omics” – DNA and RNA, +Epigenomics – Proteomics, +Protein Interactions, +Pathways – Metabolomics – Bioinformatics/Computational Biology – All of the related data and metadata • Phenotype • Clinical • Images – New technologies …
- 41. Open Data is Essential for Genomics Biological scope? • Anything with DNA or RNA or protein
- 42. Open Data is Essential for Genomics
- 43. Open Data is Essential for Genomics Example of one of a challenge for all of us? The integration of genomic data with deep learning and artificial intelligence
- 44. Open Data is Essential for Genomics AI, Big Data, Deep Computing • Artificial Intelligence / Deep Learning and the Big Data Hype? https://goo.gl/WHg36Q
- 45. Open Data is Essential for Genomics What do we need for that? https://goo.gl/JWpXj2
- 46. Open Data is Essential for Genomics What do we need for that? https://goo.gl/JWpXj2
- 47. Open Data is Essential for Genomics What else? • Data has to be FAIR – TO BE FINDABLE – TO BE ACCESSIBLE – TO BE INTEROPERABLE – TO BE RE-USABLE • https://www.force11.org/group/fairgroup/fairprinciples
- 48. Open Data is Essential for Genomics Big data examples • Genomic sequences • Imaging • Population scale collected wearable data
- 49. Open Data is Essential for Genomics Data Center for all in Québec? • Health Care in Canada is governed province by province. • Génome Québec is working with various ministries to set something that could be useful/centralized and make genomic data usable for research (controlled access). • Needs to include clinical data
- 50. Open Data is Essential for Genomics “Building a data centre is like making pancakes, you always need to throw away the 1st one” Robert Grossman Frederick H. Rawson Professor and the Director of the Center for Data Intensive Science (CDIS) at the University of Chicago http://rgrossman.com/
- 51. Open Data is Essential for Genomics Sharing all data types, including clinical data? https://goo.gl/ofEPeX
- 52. Open Data is Essential for Genomics Authors present at the “Toronto meeting” https://goo.gl/ofEPeX
- 53. Open Data is Essential for Genomics 53 Introduction 1.0 Open data critical to progress in Science
- 54. Open Data is Essential for Genomics 54 Introduction 1.0 One example: GenBank GenBank sequence database is an open access, annotated collection of all publicly available nucleotide sequences and their protein translations.
- 55. Open Data is Essential for Genomics 55 Introduction 1.0 Open data critical to progress in Science • Without GenBank and other public sequence databases – There would be no BLAST – There would be no diagnostics DNA testing – There would be no understanding of the human genome (there probably would not have been a human genome to work on in the first place).
- 56. Open Data is Essential for Genomics Adapted from Niko Beerenwinkel ,Chris D. Greenman ,Jens Lagergren ICGC PCAWG Docker Testing Computational Cancer Biology: An Evolutionary Perspective •Published: February 4, 2016. https://doi.org/10.1371/journal.pcbi.1004717
- 57. Open Data is Essential for Genomics Cancer is a Disease of the Genome Challenge in Treating Cancer: Every tumour is different Every cancer patient is different Adapted from Tom Hudsonhttps://www.cancer.gov/research/areas/genomics
- 58. Open Data is Essential for Genomics Analysis Data Types • Simple Somatic Mutations (SSM or SNV) • Copy Number Alterations (CAN or CNV) • Structural Variants (SV) • Germline variants (SNPs) • Gene Expression (micro-arrays and RNASeq) • miRNA Expression (RNASeq) • Epigenomics (Arrays and Methylation) • Splicing Variation (RNASeq) • Protein Expression (Arrays)
- 59. Open Data is Essential for Genomics International Cancer Genome Consortium • Collect ~500 tumour/normal pairs from each of 50 different major cancer types; 25,000 T/N pairs! • Comprehensive genome analysis of each T/N pair: – Genome – Transcriptome – Methylome – Clinical data • Make the data available to the research community & public. Identify genome changes …GATTATTCCAGGTAT… …GATTATTGCAGGTAT… …GATTATTGCAGGTAT… Adapted from Tom Hudson
- 60. ONTARIO INSTITUTE FOR CANCER RESEARC 60
- 61. Open Data is Essential for Genomics International Cancer Genome Consortium: http:/icgc.org
- 62. Open Data is Essential for Genomics ICGC needs to deal with different kinds of users! 62 • Biologists/Clinicians: – Web interface to processed data, providing: • Affected gene lists with consequences • Impact on pathways • Power users: – Application Programing Interface (API) to get to data – Availability and Integration with cloud resources
- 63. Open Data is Essential for Genomics ICGC Data Coordinating Centre: dcc.icgc.org 63
- 64. Open Data is Essential for Genomics https://dcc.icgc.org/ 64
- 65. Open Data is Essential for Genomics 65 https://dcc.icgc.org/icgc-in-the-cloud
- 66. Open Data is Essential for Genomics 66 http://www.cancercollaboratory.org/
- 67. Open Data is Essential for Genomics Some challenges: 67 • So, we have lots of data, is it generated the same way?
- 68. Open Data is Essential for Genomics Every country/group has basically been submitting: 68 – Simple Somatic Mutations (SSM or SNV) – Copy Number Alterations (CAN or CNV) – Structural Variants (SV) – Germline variants (SNPs) – Gene Expression (micro-arrays and RNASeq) – miRNA Expression (RNASeq) – Epigenomics (Arrays and Methylation) – Splicing Variation (RNASeq) – Protein Expression (Arrays)
- 69. Open Data is Essential for Genomics Are they all using the same pipelines? 69 • No
- 70. Open Data is Essential for Genomics 70
- 71. Open Data is Essential for Genomics Steering Committee of PCAWG 71 • Peter Campbell, Sanger Inst. • Gady Getz, Broad • Jan Korbel, EMBL • Lincoln Stein, OICR • Josh Stuart, UCSC
- 72. Open Data is Essential for Genomics PanCancer Analysis of Whole Genomes (PCAWG) • > 2,800 T/N pairs with clinical data from 20 tumour type of whole genome analysis. • Aligned with one standard pipeline. • Genomic Variants determined with 3 pipelines • 17 working groups • > 50 Papers are being written now.
- 73. Open Data is Essential for Genomics https://www.biorxiv.org/search/pcawg
- 74. Open Data is Essential for Genomics Deliverable for PCAWG include: 74 • 1st PANCANCER analysis on > 2,800 cancer tumours from a WGS perspective • RNA, SSM, CNV, Methylation analysis & germline • Published (executable) pipelines – Docker / Dockstore – Mutiple cloud access to data – Multiple portal access to data
- 75. Open Data is Essential for Genomics https://dcc.icgc.org/pcawg 75
- 76. Open Data is Essential for Genomics Working Groups (1/2) 76 1. Novel somatic mutation calling methods 2. Analysis of mutations in regulatory regions 3. Integration of transcriptome and genome 4. Integration of epigenome and genome 5. Consequences of somatic mutations on pathway and network activity 6. Patterns of structural variations, signatures, genomic correlations, retrotransposons, mobile elements 7. Mutation signatures and processes 8. Germline cancer genome
- 77. Open Data is Essential for Genomics Working Groups (2/2) 77 9 Inferring driver mutations and identifying cancer genes and pathways 10 Translating cancer genomes to the clinic 11 Evolution and heterogeneity 12 Exploratory: portals, visualization and software infrastructure 13 Molecular subtypes and classification 14 Analysis of mutations in non-coding RNA 15 Exploratory: mitochondrial 16 Exploratory: pathogens 17 Tech Technical working group
- 78. Open Data is Essential for Genomics https://goo.gl/AMxwSU
- 79. Open Data is Essential for Genomics https://goo.gl/AMxwSU
- 80. Open Data is Essential for Genomics https://goo.gl/AMxwSU
- 81. Open Data is Essential for Genomics https://goo.gl/AMxwSU
- 82. Open Data is Essential for Genomics http://dockstore.org 82
- 83. Open Data is Essential for Genomics Docker Testing Group • Group that to ensure all container workflow work as expected. https://goo.gl/AMxwSU
- 84. Open Data is Essential for Genomics Access to Data? • Human Data • Patients consented to have their DNA looked at so people could understand cancer • Need to have a system to maximize people’s gift to science.
- 85. Open Data is Essential for Genomics
- 86. Open Data is Essential for Genomics Identify yourself Fill out detail form which includes: • Contact and Project Information •Information Technology details and procedures for keeping data secure •Data Access Agreement All of these documents are put into a PDF file that you print and get your institution to sign off on your behalf
- 87. Open Data is Essential for Genomics
- 88. Open Data is Essential for Genomics
- 89. Open Data is Essential for Genomics 89 https://icgc.org/daco/approved-projects 314 groups
- 90. Open Data is Essential for Genomics DACO ICGC dbGaP GDC EGA TCGA BAM Open Open ERA BA M BA M EGA id & password WGS Ger m Line
- 91. Open Data is Essential for Genomics Challenge: • Open Data and controlled access data • Not enough eyeballs on the data • Eyeballs on the data needed to make discoveries. https://goo.gl/ogbWXG
- 92. Open Data is Essential for Genomics Culture of Sharing Openly • Public Funding agencies • Consortiums • Mentors • Peers • New generation (vs my old generation) • Has to become the norm
- 93. Open Data is Essential for Genomics Final thoughts … • Access to data is essential for science • Getting data that is FAIR is hard work • It is essential to share the work you do if you want to be recognized, get tenure, get a job or a promotion. • Human data is more complicated, but don’t let that get in the way! • There is a lot of material out there, learn from it (& cite your sources)!
- 94. Open Data is Essential for Genomics Last message to students and young PDFs and investigators:
- 95. Open Data is Essential for Genomics Last message to students and young PDFs and investigators: Be open so people can see how great you are!
- 96. ONTARIO INSTITUTE FOR CANCER RESEARC 96 915
- 97. Open Data is Essential for Genomics DCC Software Developer Vincent Ferretti Dusan Andric Phuong-My Do Francois Gerthoffert Terry Lin Michael Moncada Vitalii Slobodianyk Bob Tiernay Douglas Wong Linda Xiang Junjun Zhang Acknowledgments ICGC/OICR Project leaders: Tom Hudson John McPherson Lincoln Stein Jared Simpson Paul Boutros Vincent Ferretti Francis Ouellette Jennifer Jennings Ouellette Lab Alysha Moncrieffe Ann Meyer Zhibin Lu Web Dev Joseph Yamada Kaman Wu Kim Cullion Koji Miyauchi Miyuki Fukuma ICGC DCC Biocuration Hardeep Nahal Marc Perry http://oicr.on.ca http://icgc.org … and all the patients and their families that that are putting their hopes into our work! Research IT/Systems David Sutton, Bob Gibson David Magda Rob Naccarato Brian Ott Gino Yearwood EGA Jordi Rambla De Argila Arcadi Navarro Audald Iloret Mauricio Moldes
- 98. | ÉQUIPE DES AFFAIRES SCIENTIFIQUES 9827 mars 2017 B.F. Francis Ouellette Annina Spilker Joël Savard Diana IglesiasDiane Bouchard Cristina CiurliMicheline Ayoub Hélène Fournier
- 99. Open Data is Essential for Genomics 99 Grazie
- 100. Open Data is Essential for Genomics 100