Date of Completion

12-16-2012

Embargo Period

12-26-2012

Advisors

Reda A. Ammar , Dong-Guk Shin

Field of Study

Computer Science and Engineering

Degree

Master of Science

Open Access

Open Access

Abstract

Structural Variations (SVs) are genomic rearrangements that include both copy-number variants,such as insertion,deletions, duplications and balanced variants like inversion and translocations. These SVs are getting more attentions for research and investigation because of their role on human phenotype, genetic diseases and genomic rearrangements. Evolution of Next-generation Sequencing has provided golden opportunities to investigate these variants and make their wider and clear spectrum in human genome. This investigation includes identification of type of SVs and their breakpoints at base pair level. For their effective identification and breakpoint resolution, many techniques are devised mainly based on paired end read. With relatively low cost and high efficiency different platforms including ION TORRENT, Illumina can generate high throughput Single End reads. In this thesis we provide a novel approach based on Single End reads to detect genomic inversions in human genome. We also compare our approach with existing methods based on paired end reads and show that our approach is competitive in terms of sensitivity and precision at relatively low coverage for detection of breakpoints of genomic inversion.

Major Advisor

Ion Mandoiu Yufeng Wu

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