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Reference-unbiased copy number variant analysis using CGH microarrays

Cited 20 time in Web of Science Cited 21 time in Scopus
Authors
Ju, Young Seok; Hong, Dongwan; Kim, Sheehyun; Park, Sung-Soo; Lee, Seungbok; Kim, Jong-Il; Seo, Jeong-Sun; Park, Hansoo; Kim, Sujung
Issue Date
2010-08
Publisher
OXFORD UNIV PRESS
Citation
NUCLEIC ACIDS RESEARCH; Vol.38 20; e190
Abstract
Comparative genomic hybridization (CGH) microarrays have been used to determine copy number variations (CNVs) and their effects on complex diseases. Detection of absolute CNVs independent of genomic variants of an arbitrary reference sample has been a critical issue in CGH array experiments. Whole genome analysis using massively parallel sequencing with multiple ultra-high resolution CGH arrays provides an opportunity to catalog highly accurate genomic variants of the reference DNA (NA10851). Using information on variants, we developed a new method, the CGH array reference-free algorithm (CARA), which can determine reference-unbiased absolute CNVs from any CGH array platform. The algorithm enables the removal and rescue of false positive and false negative CNVs, respectively, which appear due to the effects of genomic variants of the reference sample in raw CGH array experiments. We found that the CARA remarkably enhanced the accuracy of CGH array in determining absolute CNVs. Our method thus provides a new approach to interpret CGH array data for personalized medicine.
ISSN
0305-1048
Language
English
URI
http://hdl.handle.net/10371/76839
DOI
https://doi.org/10.1093/nar/gkq730
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College of Medicine/School of Medicine (의과대학/대학원)Dept. of Biochemistry & Molecular Biology (생화학교실)Journal Papers (저널논문_생화학교실)
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