cancer genomics, wgs scilifelab human wgs toolbox nov 2015 björn nystedt, scilifelab bioinformatics...
DESCRIPTION
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 (!)TRANSCRIPT
Cancer genomics, WGS
SciLifeLab Human WGS ToolBox Nov 2015Björn Nystedt, SciLifeLab Bioinformatics platform
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Why are we here today?
• 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.
Goal100,000 genomes sequenced by the end of 2017 (!)
SciLifeLab
National service Local scientific center
SciLifeLab
Director: Olli KallioniemiCo-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.
www.scilifelab.se
2010: Strategic research initiative2013: National resource2015: New management/chairman
Human WGS at SciLifeLab
Call for National Projects
Karin Dahlman-
Wright
Computer resources
Ola Spjuth/Mart
in Dahlö
Bioinformatics toolbox
Björn Nystedt
Ethics
Richard Rosenquist
The Human WGS Steering Committee
Data coordination
center
Johan Rung
Reference database
Ulf Gyllensten/Adam Ameur
Sequencing and
primary analysis
Ellen Sherwood
SciLifeLab management
Clinical Diagnostics
NGI (Clinical Diagnostics)
Bioinformatics +SNIC (Uppmax)
Researcher
Human WGS sequencing
Cheap genomes for all ;)
Oct 2015:$1150, 70 projects, 2300 + 1000 genomesCapacity 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
https://wabi-wiki.scilifelab.se/display/SHGATG/
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