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Illuminating the Genome Landscape by Deep Sequencing
Speaker:
Dr. Yuan Gao
Assistant Professor
Center for the Study of Biological Complexity and Department of Computer Science
Virginia Commonwealth University
Time: 10:00am-11:00am, Thursday October 25
Location: Room 610, New Life Science Building, Peking University
Abstract:
Technologies to quickly and cost-effectively identify single nucleotide
polymorphisms (SNPs) or other genetic/epigenetic variations at large scale is
critical in understanding the relationship between genotypes and phenotypes.
Application of such technologies will find wide application ranging from medical
genomics, metabolic engineering, to evolutionary study and synthetic biology. DNA
sequencing is regarded as the "Gold Standard" to identify such sequence variations.
The advent of a new generation of sequencing technologies has opened up many
opportunities for the development of such applications.
Conventionally, large scale targeted sequencing and whole genome sequencing have
been done by Sanger sequencing of PCR amplicons, tiling arrays and mass
spectrometry. However, in large-scale studies, PCR has a major limitation in
scalability: it is difficult to perform a high degree of multiplexing in a single
tube reations. Tiling arrays and mass spectrometry require several steps including
re-sequencing of candidate regions and cost more to confirm true positive and
negative.
In this study, we explore the capability of the Illumina Genome Analyzer (Solexa 1G)
to deep sequence eleven laboratory evolved bacteria strains. Using only one out of
eight channels at the cost of only a few hundred dollars, we achieved more than 20X
coverage for each strain and identified previous known single nucleotide changes and
in high confidence possible new ones, and we also identified possible
deletion/insertion regions. To take full advantage of the power of next-generation
DNA sequencing methods, we also developed a new cost effective method for highly
multiplex amplification of arbitrary sets of short sequences from a complex genome.
We demonstrated the feasibility of simultaneously capturing over 10,000 target exons
single tube reactions with ~98% specificity. One current limitation of the current
Genome Analyzer is that it only reads sequences from one end of the constructs.
Developing a pair-end sequencing capability will dramatically expand our ability to
detect insertion, deletion, copy number variation and genome rearrangement.
Bio:
Dr. Yuan Gao is an Assistant Professor in the Center for the Study of Biological
Complexity and Department of Computer Science at Virginia Commonwealth University.
He earned a B.S. degree in Biology from Beijing University, an M.S. degree in
Biochemistry from the University of Tennessee at Memphis, and a Ph.D. in Computer
Science at the University of Memphis. Subsequently, he did his post-doctoral study
in George Church's Lab at Harvard. His research interests include systems biology,
genome sequencing, and algorithm design and analysis. He is currently on the fast
track to analyzing billions of bases.
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