Identification of genome-wide copy number variations and a family-based association study of avellino corneal dystrophy

Joon Seol Bae, Hyun Sub Cheong, Ji Yong Chun, Tae Joon Park, Ji On Kim, Eun Mi Kim, Miey Park, Dong Joon Kim, Eun Ju Lee, Eungkweon Kim, Jong Young Lee, Hyoung Doo Shin

Research output: Contribution to journalArticle

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Abstract

Objective: To determine the association of identified copy number variations (CNVs) in whole genome with the risk of Avellino corneal dystrophy (ACD) in a Korean population. Design: Case-control study. Participants: A total of 146 patients with ACD and 226 control subjects. Methods: A total of 193 trios were genotyped by the Illumina HumanHapCNV370-Duo BeadChip (370 404 markers) (Illumina, Inc., San Diego, CA). The intensity signal (log R ratio) and allelic intensity ratio (B allele frequency) of each marker in all individuals were obtained by Illumina BeadStudio software (Illumina, Inc.). To obtain authentic CNVs in this study, we performed a family-based CNV validation and family-based boundary mapping using the PennCNV algorithm, which incorporates multiple factors, including total log R ratio, B allele frequency, and family information, based on an integrated hidden Markov model. Main Outcome Measures: Statistical comparison and identification of CNVs between case and control using family information. Results: We identified 27 267 individual trio CNVs with a median size of 16.2 kb, aggregated in 2245 CNV regions. Most of the identified trio CNVs in this study showed well-defined CNV boundaries and overlapped with those in the Database of Genomic Variants (DGV) (83.4% in number and 79.2% in length). With the common CNV regions (264 CNV regions >5%), we performed a family-based association test with the risk of ACD. Conclusions: Two CNV regions (chr6:29978470-29987783 and chr14:59896944-59916129) were significantly associated with the risk of ACD (P=0.05∼0.003 and P=0.008, respectively). This study describes the first results of a genome-wide association analysis of individual CNVs with the risk of ACD and shows that 2 novel CNV loci may be involved in the risk of ACD.

Original languageEnglish
JournalOphthalmology
Volume117
Issue number7
DOIs
Publication statusPublished - 2010 Jan 1

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Genome
Gene Frequency
Genome-Wide Association Study
Corneal dystrophy Avellino type
Case-Control Studies
Software
Outcome Assessment (Health Care)
Databases
Population

All Science Journal Classification (ASJC) codes

  • Ophthalmology

Cite this

Bae, Joon Seol ; Cheong, Hyun Sub ; Chun, Ji Yong ; Park, Tae Joon ; Kim, Ji On ; Kim, Eun Mi ; Park, Miey ; Kim, Dong Joon ; Lee, Eun Ju ; Kim, Eungkweon ; Lee, Jong Young ; Shin, Hyoung Doo. / Identification of genome-wide copy number variations and a family-based association study of avellino corneal dystrophy. In: Ophthalmology. 2010 ; Vol. 117, No. 7.
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title = "Identification of genome-wide copy number variations and a family-based association study of avellino corneal dystrophy",
abstract = "Objective: To determine the association of identified copy number variations (CNVs) in whole genome with the risk of Avellino corneal dystrophy (ACD) in a Korean population. Design: Case-control study. Participants: A total of 146 patients with ACD and 226 control subjects. Methods: A total of 193 trios were genotyped by the Illumina HumanHapCNV370-Duo BeadChip (370 404 markers) (Illumina, Inc., San Diego, CA). The intensity signal (log R ratio) and allelic intensity ratio (B allele frequency) of each marker in all individuals were obtained by Illumina BeadStudio software (Illumina, Inc.). To obtain authentic CNVs in this study, we performed a family-based CNV validation and family-based boundary mapping using the PennCNV algorithm, which incorporates multiple factors, including total log R ratio, B allele frequency, and family information, based on an integrated hidden Markov model. Main Outcome Measures: Statistical comparison and identification of CNVs between case and control using family information. Results: We identified 27 267 individual trio CNVs with a median size of 16.2 kb, aggregated in 2245 CNV regions. Most of the identified trio CNVs in this study showed well-defined CNV boundaries and overlapped with those in the Database of Genomic Variants (DGV) (83.4{\%} in number and 79.2{\%} in length). With the common CNV regions (264 CNV regions >5{\%}), we performed a family-based association test with the risk of ACD. Conclusions: Two CNV regions (chr6:29978470-29987783 and chr14:59896944-59916129) were significantly associated with the risk of ACD (P=0.05∼0.003 and P=0.008, respectively). This study describes the first results of a genome-wide association analysis of individual CNVs with the risk of ACD and shows that 2 novel CNV loci may be involved in the risk of ACD.",
author = "Bae, {Joon Seol} and Cheong, {Hyun Sub} and Chun, {Ji Yong} and Park, {Tae Joon} and Kim, {Ji On} and Kim, {Eun Mi} and Miey Park and Kim, {Dong Joon} and Lee, {Eun Ju} and Eungkweon Kim and Lee, {Jong Young} and Shin, {Hyoung Doo}",
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Bae, JS, Cheong, HS, Chun, JY, Park, TJ, Kim, JO, Kim, EM, Park, M, Kim, DJ, Lee, EJ, Kim, E, Lee, JY & Shin, HD 2010, 'Identification of genome-wide copy number variations and a family-based association study of avellino corneal dystrophy', Ophthalmology, vol. 117, no. 7. https://doi.org/10.1016/j.ophtha.2009.11.021

Identification of genome-wide copy number variations and a family-based association study of avellino corneal dystrophy. / Bae, Joon Seol; Cheong, Hyun Sub; Chun, Ji Yong; Park, Tae Joon; Kim, Ji On; Kim, Eun Mi; Park, Miey; Kim, Dong Joon; Lee, Eun Ju; Kim, Eungkweon; Lee, Jong Young; Shin, Hyoung Doo.

In: Ophthalmology, Vol. 117, No. 7, 01.01.2010.

Research output: Contribution to journalArticle

TY - JOUR

T1 - Identification of genome-wide copy number variations and a family-based association study of avellino corneal dystrophy

AU - Bae, Joon Seol

AU - Cheong, Hyun Sub

AU - Chun, Ji Yong

AU - Park, Tae Joon

AU - Kim, Ji On

AU - Kim, Eun Mi

AU - Park, Miey

AU - Kim, Dong Joon

AU - Lee, Eun Ju

AU - Kim, Eungkweon

AU - Lee, Jong Young

AU - Shin, Hyoung Doo

PY - 2010/1/1

Y1 - 2010/1/1

N2 - Objective: To determine the association of identified copy number variations (CNVs) in whole genome with the risk of Avellino corneal dystrophy (ACD) in a Korean population. Design: Case-control study. Participants: A total of 146 patients with ACD and 226 control subjects. Methods: A total of 193 trios were genotyped by the Illumina HumanHapCNV370-Duo BeadChip (370 404 markers) (Illumina, Inc., San Diego, CA). The intensity signal (log R ratio) and allelic intensity ratio (B allele frequency) of each marker in all individuals were obtained by Illumina BeadStudio software (Illumina, Inc.). To obtain authentic CNVs in this study, we performed a family-based CNV validation and family-based boundary mapping using the PennCNV algorithm, which incorporates multiple factors, including total log R ratio, B allele frequency, and family information, based on an integrated hidden Markov model. Main Outcome Measures: Statistical comparison and identification of CNVs between case and control using family information. Results: We identified 27 267 individual trio CNVs with a median size of 16.2 kb, aggregated in 2245 CNV regions. Most of the identified trio CNVs in this study showed well-defined CNV boundaries and overlapped with those in the Database of Genomic Variants (DGV) (83.4% in number and 79.2% in length). With the common CNV regions (264 CNV regions >5%), we performed a family-based association test with the risk of ACD. Conclusions: Two CNV regions (chr6:29978470-29987783 and chr14:59896944-59916129) were significantly associated with the risk of ACD (P=0.05∼0.003 and P=0.008, respectively). This study describes the first results of a genome-wide association analysis of individual CNVs with the risk of ACD and shows that 2 novel CNV loci may be involved in the risk of ACD.

AB - Objective: To determine the association of identified copy number variations (CNVs) in whole genome with the risk of Avellino corneal dystrophy (ACD) in a Korean population. Design: Case-control study. Participants: A total of 146 patients with ACD and 226 control subjects. Methods: A total of 193 trios were genotyped by the Illumina HumanHapCNV370-Duo BeadChip (370 404 markers) (Illumina, Inc., San Diego, CA). The intensity signal (log R ratio) and allelic intensity ratio (B allele frequency) of each marker in all individuals were obtained by Illumina BeadStudio software (Illumina, Inc.). To obtain authentic CNVs in this study, we performed a family-based CNV validation and family-based boundary mapping using the PennCNV algorithm, which incorporates multiple factors, including total log R ratio, B allele frequency, and family information, based on an integrated hidden Markov model. Main Outcome Measures: Statistical comparison and identification of CNVs between case and control using family information. Results: We identified 27 267 individual trio CNVs with a median size of 16.2 kb, aggregated in 2245 CNV regions. Most of the identified trio CNVs in this study showed well-defined CNV boundaries and overlapped with those in the Database of Genomic Variants (DGV) (83.4% in number and 79.2% in length). With the common CNV regions (264 CNV regions >5%), we performed a family-based association test with the risk of ACD. Conclusions: Two CNV regions (chr6:29978470-29987783 and chr14:59896944-59916129) were significantly associated with the risk of ACD (P=0.05∼0.003 and P=0.008, respectively). This study describes the first results of a genome-wide association analysis of individual CNVs with the risk of ACD and shows that 2 novel CNV loci may be involved in the risk of ACD.

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