CNVRuler: A copy number variation-based case-control association analysis tool

Ji Hong Kim; Hae Jin Hu; Seon Hee Yim; Joon Seol Bae; Seon Young Kim; Yeun Jun Chung

doi:10.1093/bioinformatics/bts239

CNVRuler: A copy number variation-based case-control association analysis tool

Ji Hong Kim
, Hae Jin Hu
, Seon Hee Yim
, Joon Seol Bae
, Seon Young Kim
, Yeun Jun Chung

Department of Microbiology

The Catholic University of Korea
Sogang University
Korea Research Institute of Bioscience and Biotechnology

Research output: Contribution to journal › Article › peer-review

81 Scopus citations

Abstract

Summary: The method for genome-wide association study (GWAS) based on copy number variation (CNV) is not as well established as that for single nucleotide polymorphism (SNP)-GWAS. Although there are several tools for CNV association studies, most of them do not provide appropriate definitions of CNV regions (CNVRs), which are essential for CNV-association studies. Here we present a user-friendly program called CNVRuler for CNV-association studies. Outputs from the 10 most common CNV defining algorithms can be directly used as input files for determining the three different definitions of CNVRs. Once CNVRs are defined, CNVRuler supports four kinds of statistical association tests and options for population stratification. CNVRuler is based on the open-source programs R and Java from Sun Microsystems.

Original language	English
Article number	bts239
Pages (from-to)	1790-1792
Number of pages	3
Journal	Bioinformatics
Volume	28
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/bts239
State	Published - Jul 2012

Bibliographical note

Funding Information:
Funding: This study was supported by a grant from the Korea Healthcare Technology R&D Project (A092258) and Korea Health 21 R&D Project (A040002), Ministry of Health and Welfare, Republic of Korea.

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10.1093/bioinformatics/bts239

Cite this

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title = "CNVRuler: A copy number variation-based case-control association analysis tool",

abstract = "Summary: The method for genome-wide association study (GWAS) based on copy number variation (CNV) is not as well established as that for single nucleotide polymorphism (SNP)-GWAS. Although there are several tools for CNV association studies, most of them do not provide appropriate definitions of CNV regions (CNVRs), which are essential for CNV-association studies. Here we present a user-friendly program called CNVRuler for CNV-association studies. Outputs from the 10 most common CNV defining algorithms can be directly used as input files for determining the three different definitions of CNVRs. Once CNVRs are defined, CNVRuler supports four kinds of statistical association tests and options for population stratification. CNVRuler is based on the open-source programs R and Java from Sun Microsystems.",

author = "Kim, \{Ji Hong\} and Hu, \{Hae Jin\} and Yim, \{Seon Hee\} and Bae, \{Joon Seol\} and Kim, \{Seon Young\} and Chung, \{Yeun Jun\}",

note = "Funding Information: Funding: This study was supported by a grant from the Korea Healthcare Technology R\&D Project (A092258) and Korea Health 21 R\&D Project (A040002), Ministry of Health and Welfare, Republic of Korea.",

year = "2012",

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doi = "10.1093/bioinformatics/bts239",

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AU - Hu, Hae Jin

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AU - Bae, Joon Seol

AU - Kim, Seon Young

AU - Chung, Yeun Jun

N1 - Funding Information: Funding: This study was supported by a grant from the Korea Healthcare Technology R&D Project (A092258) and Korea Health 21 R&D Project (A040002), Ministry of Health and Welfare, Republic of Korea.

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N2 - Summary: The method for genome-wide association study (GWAS) based on copy number variation (CNV) is not as well established as that for single nucleotide polymorphism (SNP)-GWAS. Although there are several tools for CNV association studies, most of them do not provide appropriate definitions of CNV regions (CNVRs), which are essential for CNV-association studies. Here we present a user-friendly program called CNVRuler for CNV-association studies. Outputs from the 10 most common CNV defining algorithms can be directly used as input files for determining the three different definitions of CNVRs. Once CNVRs are defined, CNVRuler supports four kinds of statistical association tests and options for population stratification. CNVRuler is based on the open-source programs R and Java from Sun Microsystems.

AB - Summary: The method for genome-wide association study (GWAS) based on copy number variation (CNV) is not as well established as that for single nucleotide polymorphism (SNP)-GWAS. Although there are several tools for CNV association studies, most of them do not provide appropriate definitions of CNV regions (CNVRs), which are essential for CNV-association studies. Here we present a user-friendly program called CNVRuler for CNV-association studies. Outputs from the 10 most common CNV defining algorithms can be directly used as input files for determining the three different definitions of CNVRs. Once CNVRs are defined, CNVRuler supports four kinds of statistical association tests and options for population stratification. CNVRuler is based on the open-source programs R and Java from Sun Microsystems.

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ER -

CNVRuler: A copy number variation-based case-control association analysis tool

Abstract

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