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High-Performance In-Memory Genome (HIG) Project
- 1. HIG Project Overview August 31, 2012 Matthieu-P. Schapranow Hasso Plattner Institute Chair of Prof. Hasso Plattner
- 2. Vision: Real-time Analysis of Genomic Data to Improve Medical Treatment 2 HIG Project Overview, M. Schapranow, Aug 31, 2012
- 3. Build up the Whole Picture out of Layers 3 ■ Data: □ Combine research findings from int’l scientific databases in single system at HPI ■ Platform: □ Expose information as a service to be consumed by special purpose applications ■ Applications: □ Support genome alignment pipeline processing by □ Massively parallel execute: □ Alignment algorithms, e.g. BWA, BT2, etc. □ Variant calling □ Analyze individual patient results (real-time annotations with combined data) □ Analyze patient cohorts using individual filters HIG Project Overview, M. Schapranow, Aug 31, 2012
- 4. How the Vision Becomes Real 4 ■ Platform: □ Worker Framework: Enables parallel execution of tasks (alignment, variant calling) across node limits □ Updating Framework: Retrieves periodic database updated of international databases and automatically integrates them into local store ■ Applications: □ Alignment Coordinator: Submit alignment tasks and retrieve mutation lists, e.g. CSV □ Genome Browser: Interactive browsing in reference and specific patient genomes HIG Project Overview, M. Schapranow, Aug 31, 2012
- 5. Alignment Coordinator 5 ■ Available Alignment Algorithms (and growing) □ Bowtie2 □ Bowtie □ BWA □ TMAP □ SNAP □ MAQ □ SOAP HIG Project Overview, M. Schapranow, Aug 31, 2012
- 6. Numbers you should know Alignment Execution Time 6 ■ One cell line ~600k reads / 110MB ■ Pipeline: Alignment and variant calling Property Traditional HPI Full Genome No Yes Cores 2 * 6 cores 25 * 40 cores Main Memory 48 GB 25 TB Runtime ~720 ~40s HIG Project Overview, M. Schapranow, Aug 31, 2012
- 7. Numbers you should know History of the Human Genome Project 7 ■ 1984: Idea of a global Human Genome (HG) project discussed at Alta Summit: “DNA available on the Internet” ■ 1990: HG project for 15 years started in the US (3 billion USD funding) ■ 2000: Rough draft of the HG announced ■ 2003: Complete genome sequenced ■ 2006: Last and longest chr1 sequenced ■ … what’s next? HIG Project Overview, M. Schapranow, Aug 31, 2012
- 8. Numbers you should know Human Genome 8 Entity Cardinality Different Bases 4 (A,C,G,T) Base Pairs 3.137 Bbp Chromosomes 23 Distinct Genes 20k-25k Amino Acids 21 (coded as triplets) Proteins 50k-300k Taken from http://de.wikipedia.org/wiki/Code-Sonne HIG Project Overview, M. Schapranow, Aug 31, 2012
- 9. 9 Costs in USD 0,01 0,1 1 10 100 1000 10000 01.01.01 01.05.01 01.09.01 01.01.02 01.05.02 01.09.02 01.01.03 01.05.03 01.09.03 01.01.04 01.05.04 Comparison of Costs 01.09.04 01.01.05 Costs per Megabyte RAM 01.05.05 01.09.05 Numbers you should know HIG Project Overview, M. Schapranow, Aug 31, 2012 01.01.06 01.05.06 01.09.06 01.01.07 01.05.07 01.09.07 01.01.08 01.05.08 01.09.08 01.01.09 Costs per Megabase Sequencing 01.05.09 01.09.09 01.01.10 Comparison of Costs for Main Memory and Genome Analysis 01.05.10 01.09.10 01.01.11 01.05.11 01.09.11 01.01.12
- 10. Hardware Characteristics 10 ■ 1,000 core cluster, 25 TB main memory ■ Consists of 25 identical nodes: □ 80 cores □ 1 TB main memory □ Intel® Xeon® E7- 4870 □ 2.40GHz □ 30 MB Cache HIG Project Overview, M. Schapranow, Aug 31, 2012
- 11. Customer Process as of Today 11 ■ Tissue sequencing in context of cancer treatment ■ Complex, time-consuming, media breaks, manual steps HIG Project Overview, M. Schapranow, Aug 31, 2012
- 12. Project Objectives 12 ■ Alignment of DNA reads (FASTQ) against reference genome (FASTA) è mapped reads ■ Real-time analysis of mapped reads □ Detection of mutations (SNP, INDELs) □ Comparison of multiple tissues □ Detection of similar clusters to identify co-relations ■ Analysis of mutations □ Identify mutations with scientific references (existing knowledge) □ Detection of similar clusters to identify co-relations □ Identify genes and regulators for certain phenotypic characteristics, e.g. “fast running horses” HIG Project Overview, M. Schapranow, Aug 31, 2012
- 13. Thank you for your interest! Keep in contact with us. 13 Matthieu-P. Schapranow, M.Sc. schapranow@hpi.uni-potsdam.de http://j.mp/schapranow Hasso Plattner Institute Enterprise Platform & Integration Concepts Matthieu-P. Schapranow August-Bebel-Str. 88 14482 Potsdam, Germany HIG Project Overview, M. Schapranow, Aug 31, 2012