Genetic associations of common deletion polymorphisms in families with Avellino corneal dystrophy

Miey Park, Dong Joon Kim, Kwang Joong Kim, Chang Bum Hong, Young Jin Kim, Hyun Sub Cheong, Hyoung Doo Shin, Eun Ju Lee, Han Na Kim, Hye Won Chung, Eungkweon Kim, Jong Young Lee, Hyung Lae Kim

Research output: Contribution to journalArticle

4 Citations (Scopus)

Abstract

Although the locations of many common deletion variants in the human genome are unknown, such deletions may be causative in rare disorders. Deletions can be mapped through the identification of Mendelian inconsistencies in pedigrees. Data for a total of 341,577 SNPs from an ACD family cohort (n = 551) and 341,039 SNPs from a Korean-Vietnamese family cohort (n = 554) were collected for a genome-wide association study using Illumina 370K-Duo Beadchips ® . In the present study, a Mendelian inconsistency analysis of genotype data identified 1029 deletion variants in Korean and Korean-Vietnam family cohorts of 404 trios comprising 1105 individuals. Small-deletion copy number variations adjacent to 10 deletion variants were then validated by the real-time quantitative polymerase chain reaction. The expected copy numbers of each deletion variant were directly matched to its genotype cluster image. Deletion variants were also in strong linkage disequilibrium with nearby SNPs. To determine the overall contribution of the 1029 deletion variants, we analyzed case-control trio associations with the risk for Avellino corneal dystrophy. One SNP marker (rs885945) neighboring the gene encoding major histocompatibility complex class I F (HLA-F) was significantly associated with the risk of Avellino corneal dystrophy (P = 0.0003). rs885945 showed high LD with SNPs within the HLA-F gene. Therefore, HLA-F may be a potential candidate gene for Avellino corneal dystrophy. Crown

Original languageEnglish
Pages (from-to)688-693
Number of pages6
JournalBiochemical and Biophysical Research Communications
Volume387
Issue number4
DOIs
Publication statusPublished - 2009 Oct 2

Fingerprint

Polymorphism
Single Nucleotide Polymorphism
Genes
Gene encoding
Genotype
Polymerase chain reaction
Vietnam
Genome-Wide Association Study
Linkage Disequilibrium
Human Genome
Pedigree
Major Histocompatibility Complex
Crowns
Real-Time Polymerase Chain Reaction
Corneal dystrophy Avellino type

All Science Journal Classification (ASJC) codes

  • Biophysics
  • Biochemistry
  • Molecular Biology
  • Cell Biology

Cite this

Park, Miey ; Kim, Dong Joon ; Kim, Kwang Joong ; Hong, Chang Bum ; Kim, Young Jin ; Cheong, Hyun Sub ; Shin, Hyoung Doo ; Lee, Eun Ju ; Kim, Han Na ; Chung, Hye Won ; Kim, Eungkweon ; Lee, Jong Young ; Kim, Hyung Lae. / Genetic associations of common deletion polymorphisms in families with Avellino corneal dystrophy. In: Biochemical and Biophysical Research Communications. 2009 ; Vol. 387, No. 4. pp. 688-693.
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abstract = "Although the locations of many common deletion variants in the human genome are unknown, such deletions may be causative in rare disorders. Deletions can be mapped through the identification of Mendelian inconsistencies in pedigrees. Data for a total of 341,577 SNPs from an ACD family cohort (n = 551) and 341,039 SNPs from a Korean-Vietnamese family cohort (n = 554) were collected for a genome-wide association study using Illumina 370K-Duo Beadchips {\circledR} . In the present study, a Mendelian inconsistency analysis of genotype data identified 1029 deletion variants in Korean and Korean-Vietnam family cohorts of 404 trios comprising 1105 individuals. Small-deletion copy number variations adjacent to 10 deletion variants were then validated by the real-time quantitative polymerase chain reaction. The expected copy numbers of each deletion variant were directly matched to its genotype cluster image. Deletion variants were also in strong linkage disequilibrium with nearby SNPs. To determine the overall contribution of the 1029 deletion variants, we analyzed case-control trio associations with the risk for Avellino corneal dystrophy. One SNP marker (rs885945) neighboring the gene encoding major histocompatibility complex class I F (HLA-F) was significantly associated with the risk of Avellino corneal dystrophy (P = 0.0003). rs885945 showed high LD with SNPs within the HLA-F gene. Therefore, HLA-F may be a potential candidate gene for Avellino corneal dystrophy. Crown",
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Park, M, Kim, DJ, Kim, KJ, Hong, CB, Kim, YJ, Cheong, HS, Shin, HD, Lee, EJ, Kim, HN, Chung, HW, Kim, E, Lee, JY & Kim, HL 2009, 'Genetic associations of common deletion polymorphisms in families with Avellino corneal dystrophy', Biochemical and Biophysical Research Communications, vol. 387, no. 4, pp. 688-693. https://doi.org/10.1016/j.bbrc.2009.07.084

Genetic associations of common deletion polymorphisms in families with Avellino corneal dystrophy. / Park, Miey; Kim, Dong Joon; Kim, Kwang Joong; Hong, Chang Bum; Kim, Young Jin; Cheong, Hyun Sub; Shin, Hyoung Doo; Lee, Eun Ju; Kim, Han Na; Chung, Hye Won; Kim, Eungkweon; Lee, Jong Young; Kim, Hyung Lae.

In: Biochemical and Biophysical Research Communications, Vol. 387, No. 4, 02.10.2009, p. 688-693.

Research output: Contribution to journalArticle

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T1 - Genetic associations of common deletion polymorphisms in families with Avellino corneal dystrophy

AU - Park, Miey

AU - Kim, Dong Joon

AU - Kim, Kwang Joong

AU - Hong, Chang Bum

AU - Kim, Young Jin

AU - Cheong, Hyun Sub

AU - Shin, Hyoung Doo

AU - Lee, Eun Ju

AU - Kim, Han Na

AU - Chung, Hye Won

AU - Kim, Eungkweon

AU - Lee, Jong Young

AU - Kim, Hyung Lae

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Y1 - 2009/10/2

N2 - Although the locations of many common deletion variants in the human genome are unknown, such deletions may be causative in rare disorders. Deletions can be mapped through the identification of Mendelian inconsistencies in pedigrees. Data for a total of 341,577 SNPs from an ACD family cohort (n = 551) and 341,039 SNPs from a Korean-Vietnamese family cohort (n = 554) were collected for a genome-wide association study using Illumina 370K-Duo Beadchips ® . In the present study, a Mendelian inconsistency analysis of genotype data identified 1029 deletion variants in Korean and Korean-Vietnam family cohorts of 404 trios comprising 1105 individuals. Small-deletion copy number variations adjacent to 10 deletion variants were then validated by the real-time quantitative polymerase chain reaction. The expected copy numbers of each deletion variant were directly matched to its genotype cluster image. Deletion variants were also in strong linkage disequilibrium with nearby SNPs. To determine the overall contribution of the 1029 deletion variants, we analyzed case-control trio associations with the risk for Avellino corneal dystrophy. One SNP marker (rs885945) neighboring the gene encoding major histocompatibility complex class I F (HLA-F) was significantly associated with the risk of Avellino corneal dystrophy (P = 0.0003). rs885945 showed high LD with SNPs within the HLA-F gene. Therefore, HLA-F may be a potential candidate gene for Avellino corneal dystrophy. Crown

AB - Although the locations of many common deletion variants in the human genome are unknown, such deletions may be causative in rare disorders. Deletions can be mapped through the identification of Mendelian inconsistencies in pedigrees. Data for a total of 341,577 SNPs from an ACD family cohort (n = 551) and 341,039 SNPs from a Korean-Vietnamese family cohort (n = 554) were collected for a genome-wide association study using Illumina 370K-Duo Beadchips ® . In the present study, a Mendelian inconsistency analysis of genotype data identified 1029 deletion variants in Korean and Korean-Vietnam family cohorts of 404 trios comprising 1105 individuals. Small-deletion copy number variations adjacent to 10 deletion variants were then validated by the real-time quantitative polymerase chain reaction. The expected copy numbers of each deletion variant were directly matched to its genotype cluster image. Deletion variants were also in strong linkage disequilibrium with nearby SNPs. To determine the overall contribution of the 1029 deletion variants, we analyzed case-control trio associations with the risk for Avellino corneal dystrophy. One SNP marker (rs885945) neighboring the gene encoding major histocompatibility complex class I F (HLA-F) was significantly associated with the risk of Avellino corneal dystrophy (P = 0.0003). rs885945 showed high LD with SNPs within the HLA-F gene. Therefore, HLA-F may be a potential candidate gene for Avellino corneal dystrophy. Crown

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