Cancer genomics WGS Sci Life Lab Human WGS

Cancer genomics, WGS Sci. Life. Lab Human WGS Tool. Box Nov 2015 Björn Nystedt, Sci. Life. Lab Bioinformatics platform

Why are we here today? • Human WGS is becoming routine and will be used both for basic science and for medical discovery and diagnostics • Sci. Life. Lab 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 2

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 genotypephenotype space. Goal 100, 000 genomes sequenced by the end of 2017 (!)

Sci. Life. Lab National service Local scientific center 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. 2010: Strategic research initiative 2013: National resource 2015: New management/chairman www. scilifelab. se

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

Human WGS sequencing Oct 2015: $1150, 70 projects, 2300 + 1000 genomes Capacity 5 -10, 000 genomes/year

What is the Human WGS Tool. Box? Tool. Box • • Community building Guidelines Tools Training • A discussion and coordination forum • The bioinformatics platform contributes ~2 FTE to Tool. Box implementations • Intend to complement current deliveries from the sequencing platform https: //wabi-wiki. scilifelab. se/display/SHGATG/

What we do right now • GATK for hg 38 • 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, 10 X) • Integrative designs • Single-cell genomics