title: Combinatorial approach to estimate copy number genotype using whole-exome sequencing data.
abstract: Copy number variations (CNVs) are known risk factors in complex diseases. Array-based approaches have been widely used to detect CNVs, but limitations of array-based CNV detection methods, such as noisy signal and low resolution, have hindered detection of small CNVs. Recently, the development of next-generation sequencing techniques has increased rapidly owing to declines in cost. Particularly, whole-exome sequencing has proved useful for finding causal genes and variants in complex diseases. Because gene copy number may affect expression, CNV genotyping can be very valuable in disease association studies. However, almost all current CNV detection tools consider only two types of CNV genotypes. In this study, we propose a CNV genotype estimation approach using a combination of existing methods. Our approach was comprehensively compared with the customized Agilent array-comparative genomic hybridization. We found that our genotyping approach proved to be accurate, and reproducible, suggesting that it can complement existing CNV genotyping methods.
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea.
authors.forename: Mi Yeong
authors.initials: MY
authors.lastname: Hwang
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea.
authors.forename: Sanghoon
authors.initials: S
authors.lastname: Moon
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea.
authors.forename: Lyong
authors.initials: L
authors.lastname: Heo
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea.
authors.forename: Young Jin
authors.initials: YJ
authors.lastname: Kim
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea.
authors.forename: Ji Hee
authors.initials: JH
authors.lastname: Oh
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea.
authors.forename: Yeon-Jung
authors.initials: YJ
authors.lastname: Kim
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea.
authors.forename: Yun Kyoung
authors.initials: YK
authors.lastname: Kim
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea.
authors.forename: Juyoung
authors.initials: J
authors.lastname: Lee
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea.
authors.forename: Bok-Ghee
authors.initials: BG
authors.lastname: Han
authors.affiliation: Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Chungcheongbuk-do, 361-951, Republic of Korea. Electronic address: kbj6181@cdc.go.kr.
authors.forename: Bong-Jo
authors.initials: BJ
authors.lastname: Kim
mesh_terms: D056915:DNA Copy Number Variations; D059472:Exome; D005260:Female; D015894:Genome, Human; D060005:Genotyping Techniques / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008297:Male
keywords: CNV discovery; CNV genotyping; Combinatorial approach; Copy number variation; Whole-exome sequencing