a pattern growth approach to detect breakpoints of small indels and complex structural variants from next-generation sequence data

Speaker

Kai Ye, Ph.D.
Assistant professor
Leiden University Medical Center
the Netherlands

Time

2-3pm, Thursday, Dec 8

Location

Room 610, New Life Science Building, Peking University

Title

a pattern growth approach to detect breakpoints of small indels and complex structural variants from next-generation sequence data

Abstract

There is a strong demand in the genomic research community to develop effective and efficient algorithm genomic variants from next-generation sequence data, in order to investigate disease-related variants and genetic survey of large populations. Previously we developed a so-called Pindel method to identify breakpoints of large deletions (1bp-10kb) and medium sized insertions (1-20bp) at base level precision from 36 bp paired-end short reads.
Recently we further developed novel procedures to complex structural variants such as inversions and tandem duplications. These novel algorithms and their applications in 1000 Genomes project, cancer genome projects and Genome of the Netherlands will be discussed.