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[theory-seminar] Algorithms and Friends Lunch, Monday (May 20), in Gates 463A

Shivam Garg shivamgarg at stanford.edu
Sat May 18 10:22:38 PDT 2019


Hi everyone,

Hanlee P. Ji<https://profiles.stanford.edu/hanlee-ji> will be giving a talk on coming Monday (May 20th), at noon, in Gates 463A.

Title: Characterizing structural variation in human genome code

Abstract: Structural variants (SVs) involve complex rearrangements of the human genome code, occur throughout the human genome, and may encompass alterations spanning Megabases of DNA sequences. These rearrangements lead to a variety of genetic disorders that include cancer, congenital malformations, and neurocognitive conditions such as autism. The detection and characterization of germline and somatic rearrangements are critical for determining the genetic pathogenesis of these diseases and provide valuable diagnostic information. The majority of genomic studies characterizing SVs rely on short sequence reads (<several hundred bases) derived from small DNA inserts (~0.5 kb). However, short reads do not provide long range genomic contiguity nor do they provide robust identification of SVs and rearrangements, particularly for ones spanning large DNA segments. Alternatively, whole genome sequencing with long reads provides contiguity of genome sequence but with major limitations: the base calling accuracy of long read sequencers is low, the cost is higher than short read sequencing. Addressing these challenges, we developed a variety of experimental and computational methods to characterize the structural changes with greater accuracy.


Thanks,
Shivam

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