Cancer genomics, WGS SciLifeLab Human WGS ToolBox Nov 2015 Björn Nystedt, SciLifeLab Bioinformatics platform.

Slides:

Advertisements

Similar presentations

Translating Science into Improved Health Care: Cancer as a Model William S. Dalton, Ph.D., M.D. Center Director H. Lee Moffitt Cancer Center & Research.

Advertisements

Maryam Nazir. Personal Genomics:  Branch of genomics concerned with the sequencing and analysis of the genome of an individual  Once sequenced, it can.

Senate Education Committee Briefing Russell Ingram, Executive Director March 23, 2011.

10 th October 2013 The delivery of 21 st century services – the implications for the evolution of the Healthcare Science workforce Joan Fletcher.

Presentation to Educational Policy Committee Department of Biology Revised March, 2013 Biology Department: Position Requests.

Wrapup. NHGRI strategic plan What does the NIH think genomics should be for the next 10 years? [Nature, Feb. 2011]

EU RTD + FP Cancer Treatment: A priority for patients in Europe 7 th European Health Forum Bad Gastein 7 October, 2004 Cornelius Schmaltz MD European.

AP Biology Teaching Biology Through Bioinformatics Real world genomics research in your classroom Kim B. Foglia Division Ave. High School Levittown.

Future Trends: Translational Informatics James J. Cimino Chief, Laboratory for Informatics Development Mark O. Hatfield Clinical Research Center National.

National Institute on Aging Richard J. Hodes, M.D. Director,NIA/NIH/DHHS ADC Meeting – NIH Roadmap and Budget October 2003.

Genomics Alexandra Hayes. Genomics is the study of all the genes in a person, as well as the interactions of those genes with each other and a person’s.

European Health Forum Gastein, Bad Hofgastein, Austria, September 2002 Towards the Sixth Framework Programme Parallel Forum V 26 September 2002 Public.

Science, research and developmentEuropean Commission Chile-EC S&T Agreement Brussels, 24 September 2002 Life Sciences, Genomics and Biotechnology for Health.

Building a Roadmap for Research IT John Brussolo Research IT Program Director September 6, 2012 © 2012 The Regents of the University of Michigan.

CceHUB A Knowledge Discovery Environment for Cancer Care Engineering Research Ann Christine Catlin HUBzero Workshop November 7, 2008.

Sage Bionetworks Mission Sage Bionetworks is a non-profit organization with a vision to create a “commons” where integrative bionetworks are evolved by.

Organized Diagnostic Assessment Demonstration Projects Organized Diagnostic Assessment Demonstration Projects Grand River Regional Diagnostic Assessment.

Bioinformatics and medicine: Are we meeting the challenge?

Strategic Research Areas “If I have seen a little further it is by standing on the shoulders of giants”

Assay Development Breakout (red) Who was in the room? About half of attendees are active NGS users N=1 doing whole genome analyses Everyone else doing.

CORPORATE INNOVATION AS AN ENGINE FOR CHANGE: Molecular Diagnostics David Okrongly, Ph.D. SVP Molecular Diagnostics Siemens Healthcare.

Precision Medicine A New Initiative. The Concept of Precision Medicine (PM) The prevention and treatment strategies that take individual variability into.

100k Genomes Project In December 2012 the Prime Minister announced a programme of Whole Genome Sequencing as part of the UK Government’s Life Sciences.

Sage Bionetworks A non-profit organization with a vision to enable networked team approaches to building better models of disease BIOMEDICINE INFORMATION.

Integrated Biomedical Information for Better Health Workprogramme Call 4 IST Conference- Networking Session.

The NIH Roadmap and the Human Microbiome Project Francis S. Collins, M.D., Ph.D. National Human Genome Research Institute April 22, 2007.

Access to Personalised Medicine for PDAC patients STSM of the application of an EU-index for barriers Denis Horgan (EAPM) & Angela Brand (IPHG) on behalf.

”There is nothing so practical as a good theory” Management research in the improvement of health services Mats Brommels Medical Management Centre Karolinska.

Fiancee Lee A. Banzon RPh.RN.  P harmacists practicing today in the Philippines or other developed or developing countries will interact with technology.

Send correspondence to: Bartha Maria Knoppers Chair of Interim Board Centre de recherche en Droit Public Université de Montréal.

Sage Bionetworks A non-profit organization with a vision to enable networked team approaches to building better models of disease BIOMEDICINE INFORMATION.

4/24/2017 Health and Social Care Reform in Greater Manchester Developing a commissioning strategy for Primary Care Rob Bellingham — Director of Commissioning.

A L I M E N T A T I O N A G R I C U L T U R E E N V I R O N N E M E N T 1 G20 – 12th May 2011 An International Research Initiative for Wheat Improvement.

EURORDIS Eurordis Position on Research Priorities for Rare Diseases.

The Importance of a Strategic Plan to Eliminate Health Disparities 2008 eHealth Conference June 9, 2008 Yvonne T. Maddox, PhD Deputy Director Eunice Kennedy.

Histone Methyltransferases: Global Industry Report for Research Tools, Diagnostics and Drug Discovery

Masters Programme in Genomic Medicine Open Day Event Tendering process Anne Gilford, Head of Education and Quality, HEWM 3 rd September.

Yorkshire & the Humber Strategic Clinical Networks Mental Health, Dementia, Acute & Chronic Neurological Conditions David Black Medical Director South.

Why Write A Grant? Elaine M. Hylek, MD, MPH Professor of Medicine Associate Director, Education and Training Division BU CTSI Section of General Internal.

100k Genomes Project Programme of Whole Genome Sequencing, part of UK Life Sciences Strategy Aim to sequence 100,000 genomes from patients with cancer.

EMBL-EBI Data Archives – An Overview. The EMBL-EBI mission Provide freely available data and bioinformatics services to all facets of the scientific community.

An Introduction to NCBI & BLAST National Center for Biotechnology Information Richard Johnston Pasadena City College.

Clinical Research Informatics [CRI]. Informatics, defined generally as the intersection of information and computer science with a health-related discipline,

Ethics in Clinical Genetics and Genomics Key Knowledge Year 4 Medical Ethics and Law Thread Course, The Ethox Centre, University of Oxford.

Advanced User Support in the Swedish National HPC Infrastructure May 13, 2013NeIC Workshop: Center Operations best practices.

Realising MRC’s Vision in Health and Bioinformatics MRC Open Council Meeting July 2014 Janet Valentine Head of Population Health and Informatics.

Center for Nursing Informatics Connie White Delaney, PhD, RN, FAAN, FACMI Dean and Professor Co-Director of the Center for Nursing Informatics September.

Science for Life Laboratory Eva Molin Project coordinator.

100,000 Genomes Project North East and North Cumbria GMC An Introduction Mike Pratt (Genomic Education Development Officer) Susan Goldstein (100,000 Genomes.

1 Finding disease genes: A challenge for Medicine, Mathematics and Computer Science Andrew Collins, Professor of Genetic Epidemiology and Bioinformatics.

1 Population Science SIG: Vision and Goals Paul K. Courtney Pop Sci SIG Lead Dartmouth College/Norris Cotton Cancer Center.

The National Bioinformatics Infrastructure Sweden (NBIS) Björn Nystedt, Head of Bioinformatics Long-term Support.

Moiz Bakhiet, MD, PhD, Professor and Chairman

SciLifeLab mission National technology platforms for life science

To develop the scientific evidence base that will lessen the burden of cancer in the United States and around the world. NCI Mission Key message:

National Healthcare Science Week 2017

Science for Life Laboratory

Science for Life Laboratory

The National Bioinformatics Infrastructure Sweden (NBIS) www

FP6 Priority 1, Life Sciences Genomics and Biotechnology for Health

The National Bioinformatics Infrastructure Sweden (NBIS) www

The National Bioinformatics Infrastructure Sweden (NBIS) www

The National Bioinformatics Infrastructure Sweden (NBIS) www

Björn Nystedt RNAseq Uppsala

Daniela B. Friedman, University of South Carolina

West of England Genomics Medicine Centre Overview

National Cancer Center

FP6 Priority 1, Life Sciences Genomics and Biotechnology for Health

Integration of Genomic Medicine into Pathology Residency Training

Next Generation Sequencing Market. Report Description and Highlights According to Renub Research market research report “Next Generation Sequencing (NGS)

Presentation transcript:

Cancer genomics, WGS SciLifeLab Human WGS ToolBox Nov 2015 Björn Nystedt, SciLifeLab Bioinformatics platform

Why are we here today? 2 Human WGS is becoming routine and will be used both for basic science and for medical discovery and diagnostics SciLifeLab provides multiple resources around Human WGS, which are open to all Swedish researchers The challenges in handling and analyzing Human WGS data calls for collaborations and community knowledge sharing

Genomics England 100,000 genomes Overall aims - Advance genomics medicine (integrate into NHS) - Increase research - Boost the private sector in the field The main focus of the program is cancer and rare disease. Huge efforts into setting up the logistics circle. Long-term to transform clinical diagnostics from using sequencing to try to confirm/reject a specific diagnosis, to make a more general match of the patient’s genotype-phenotype profile to a large curated genotype- phenotype space. Goal 100,000 genomes sequenced by the end of 2017 (!)

SciLifeLab National service Local scientific center SciLifeLab Director: Olli Kallioniemi Co-director: Lena Claesson-Welsh Vision: To be an internationally leading center that develops, uses and provides access to advanced technologies for molecular biosciences with focus on health and environment : Strategic research initiative 2013: National resource 2015: New management/chairman 2010: Strategic research initiative 2013: National resource 2015: New management/chairman

Human WGS at SciLifeLab Call for National Projects Karin Dahlman- Wright Call for National Projects Karin Dahlman- Wright Computer resources Ola Spjuth/Mart in Dahlö Computer resources Ola Spjuth/Mart in Dahlö Bioinformatic s toolbox Björn Nystedt Bioinformatic s toolbox Björn Nystedt Ethics Richard Rosenquist Ethics Richard Rosenquist The Human WGS Steering Committee Data coordination center Johan Rung Data coordination center Johan Rung Reference database Ulf Gyllensten/A dam Ameur Reference database Ulf Gyllensten/A dam Ameur Sequencing and primary analysis Ellen Sherwood Sequencing and primary analysis Ellen Sherwood SciLifeLab management Clinical Diagnostics NGI (Clinical Diagnostics) Bioinformatics + SNIC (Uppmax) Researcher

Human WGS sequencing Oct 2015: $1150, 70 projects, genomes Capacity 5-10,000 genomes/year

What is the Human WGS ToolBox? A discussion and coordination forum The bioinformatics platform contributes ~2 FTE to ToolBox implementations Intend to complement current deliveries from the sequencing platform Community building Guidelines Tools Training ToolBox

What we do right now GATK for hg38 Structural variation: Benchmark, combine tools, compare samples Tumor/Normal/(relapse) somatic variant calling Variant significance tools: Burden tests etc. Some future challenges Epigenetics Time-series designs (Embryo dev, Cell diff, Cell aging) Phased genomes (Imputation, 10X) Integrative designs Single-cell genomics