Computational Analysis of the Genome Variation and issues
Speaker: Shamil Sunyaev, Ph.D , Brigham and Women
Date: April 5 2004
Time: 11:30AM to 12:45PM
Location: 2-338
Host: Peter Clote/ BC & Bonnie Berger/ MIT & CSAIL
Contact: Kathleen Dickey, 617 253 3037, kvdickey@mit.edu
Relevant URL: http://www-math.mit.edu/compbiosem/Abstract:
New massive data on genomic sequences and DNA polymorphism are
now available for large-scale analysis. We analyzed both coding and
non-coding regions of the genome and quantified the effect of genetic
variation on molecular function and organism fitness. We developed a
computational method for predicting the effect of coding single
nucleotide polymorphisms (SNPs) on function and structure of
proteins. Statistical tests of natural selection suggested that most
SNPs in coding regions of functional significance are evolutionarily
deleterious. The distribution of fitness effects of substitutions in
coding and highly conserved non-coding regions was estimated by
comparing sequence divergence in primate and rodent lineages
together with the data on human polymorphism. Applications of this
analysis to studies in medical genetics will be discussed.
We also developed a new method for estimating evolutionary distance
between genomes based on insertions and deletions rather than
substitutions. The method was applied to the human and mouse
genomes.
MIT
Department of Mathematics
& The Theory of
Computation Group
At CSAIL
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