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CNVR Detection Reflecting the Properties of the Reference Sequence in HLA Region  

Lee, Jong-Keun (한림대학교 컴퓨터공학과)
Hong, Dong-Wan (한림대학교 컴퓨터공학과)
Yoon, Jee-Hee (한림대학교 컴퓨터공학과)
Publication Information
Journal of KIISE:Computing Practices and Letters / v.16, no.6, 2010 , pp. 712-716 More about this Journal
Abstract
In this paper, we propose a novel shape-based approach to detect CNV regions (CNVR) by analyzing the coverage graph obtained by aligning the giga-sequencing data onto the human reference sequence. The proposed algorithm proceeds in two steps: a filtering step and a post-processing step. In the filtering step, it takes several shape parameters as input and extracts candidate CNVRs having various depth and width. In the post-processing step, it revises the candidate regions to make up for errors potentially included in the reference sequence and giga-sequencing data, and filters out regions with high ratio of GC-contents, and returns the final result set from those candidate CNVRs. To verify the superiority of our approach, we performed extensive experiments using giga-sequencing data publicly opened by "1000 genome project" and verified the accuracy by comparing our results with those registered in DGV database. The result revealed that our approach successfully finds the CNVR having various shapes (gains or losses) in HLA (Human Leukocyte Antigen) region.
Keywords
Giga-sequencing; Copy Number Variation; Shape-based extraction;
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Times Cited By KSCI : 1  (Citation Analysis)
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