Open-architectures for Reading, Writing & Computing with Genomes

Thursday, November 20, 2008 - 7:00pm
George Church
George Church

Relative to a reference human genome, your personal genome has about 10,000 DNA variations which affect final protein function and 3 million which do not. While “association studies” of common DNA variations with diseases yield, so far, weak predictive power and few causative mutations, researchers expect that this will be soon remedied by genome-wide sequencing. Second-generation sequencing (multiplex cycles of fluidics and imaging) has brought costs down since 2004 by
10,000-fold $300M to $30K -- and less than $1000 via targeted sequencing including coding variants (~1% of the genome), regulation, microbes and immune response (quantitated by sequencing). is the only of the second-generation that has open architecture for hardware, software, and wetware – and 4-fold less expensive. Similarly is a uniquely open effort to integrate the above genomic data with comprehensive sets of medical and non-medical traits. We are collecting over 20 terabytes of raw genomic data for each of 100,000 research subject volunteers -- which boils down to less than a gigabyte each of differences from the reference genomes and quantitative genomic and trait data. Like DNA sequencing, raw DNA synthesis has come down in cost by 7-logs since 1980, but the next challenge currently being met is applying this to “programming” organism-level functions – by developing computer-aided design, new homologous recombination instruments, lab-scale accelerated evolution and personalized stem cells.

This seminar is a joint presentation of Boston/Central New England Chapter of the IEEE Computer Society and GBC/ACM.

George Church is Professor of Genetics at Harvard Medical School and Director of the Center for Computational Genetics. With degrees from Duke University in Chemistry and Zoology, he co-authored research on 3D-software & RNA structure with Sung-Hou Kim. His PhD from Harvard in Biochemistry & Molecular Biology with Wally Gilbert included the first direct genomic sequencing method in 1984; initiating the Human Genome Project then as a Research Scientist at newly-formed Biogen Inc. and a Monsanto Life Sciences Research Fellow at UCSF with Gail Martin. He invented the broadly-applied concepts of molecular multiplexing and tags, homologous recombination methods, and array DNA synthesizers. Technology transfer of automated sequencing & software to Genome Therapeutics Corp. resulted in the first commercial genome sequence (the human pathogen, H. pylori, 1994). He has served in advisory roles for 12 journals (including Nature Molecular Systems Biology), 5 granting agencies and 24 biotech companies (e.g. recently founding Codon Devices and LS9). Current research focuses on integrating biosystems-modeling with the Personal Genome Project & synthetic biology.