Bilkent University
Department of Computer Engineering


Breakpoint Refinement and quick Genotyping of Genomic Structural Variation


Balanur İçen
MS Student
Computer Engineering Department
Bilkent University

Genomic structural variations (SVs) are changes in DNA that are longer than 50 base pairs. SVs come in many different flavors, such as copy number variants; deletions, duplications, insertions, or balanced rearrangements; inversions and translocations, and many SVs are associated with genetic diseases. Rapid and accurate computational tools are needed to detect and characterize specific classes of structural variants using high throughput sequencing technologies (HTS). Main challenge in SV detection emerge from the fact that most variants are located within or around segmental duplications or long repeat regions. SV detection strategies often provide a confidence interval for breakpoint rather than a precise location due to the nature of the methodology such as read depth and read pair analysis. Other detection strategies like de novo assembly and split read can offer 1 base-pair resolution but they typically require more coverage and longer read length. In this work, our main aim is to incorporate the knowledge of confidence intervals obtained using former methods by applying the latter strategies in a targeted way to achieve higher resolution on SV breakpoints.


DATE: 09 April, 2018, Monday, CS590 & CS690 presentations begin at @ 15:40