Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population
Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these...
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| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Wiley
2015-01-01
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| Series: | International Journal of Genomics |
| Online Access: | http://dx.doi.org/10.1155/2015/421715 |
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| _version_ | 1832556516305010688 |
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| author | Tae-Joon Park Lyong Heo Sanghoon Moon Young Jin Kim Ji Hee Oh Sohee Han Bong-Jo Kim |
| author_facet | Tae-Joon Park Lyong Heo Sanghoon Moon Young Jin Kim Ji Hee Oh Sohee Han Bong-Jo Kim |
| author_sort | Tae-Joon Park |
| collection | DOAJ |
| description | Exome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clustering, we performed manual genotype clustering for the targeted identification of 46,076 variants that were identified using GenomeStudio software. To evaluate the effects of applying custom cluster files, we tested cluster files using 804 independent Korean samples and the same platform. Our study firstly suggests practical guidelines for exome chip quality control in Asian populations and provides valuable insight into an association study using exome chip. |
| format | Article |
| id | doaj-art-332eff33b066454282dca70a714ebc7b |
| institution | Kabale University |
| issn | 2314-436X 2314-4378 |
| language | English |
| publishDate | 2015-01-01 |
| publisher | Wiley |
| record_format | Article |
| series | International Journal of Genomics |
| spelling | doaj-art-332eff33b066454282dca70a714ebc7b2025-02-03T05:45:10ZengWileyInternational Journal of Genomics2314-436X2314-43782015-01-01201510.1155/2015/421715421715Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean PopulationTae-Joon Park0Lyong Heo1Sanghoon Moon2Young Jin Kim3Ji Hee Oh4Sohee Han5Bong-Jo Kim6Division of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of KoreaDivision of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of KoreaDivision of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of KoreaDivision of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of KoreaDivision of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of KoreaDivision of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of KoreaDivision of Structural and Functional Genomics, Center for Genome Science, National Institute of Health, Centers for Disease Control and Prevention, Chungcheongbuk-do 363-700, Republic of KoreaExome-based genotyping arrays are cost-effective and have recently been used as alternative platforms to whole-exome sequencing. However, the automated clustering algorithm in an exome array has a genotype calling problem in accuracy for identifying rare and low-frequency variants. To address these shortcomings, we present a practical approach for accurate genotype calling using the Illumina Infinium HumanExome BeadChip. We present comparison results and a statistical summary of our genotype data sets. Our data set comprises 14,647 Korean samples. To solve the limitation of automated clustering, we performed manual genotype clustering for the targeted identification of 46,076 variants that were identified using GenomeStudio software. To evaluate the effects of applying custom cluster files, we tested cluster files using 804 independent Korean samples and the same platform. Our study firstly suggests practical guidelines for exome chip quality control in Asian populations and provides valuable insight into an association study using exome chip.http://dx.doi.org/10.1155/2015/421715 |
| spellingShingle | Tae-Joon Park Lyong Heo Sanghoon Moon Young Jin Kim Ji Hee Oh Sohee Han Bong-Jo Kim Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population International Journal of Genomics |
| title | Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population |
| title_full | Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population |
| title_fullStr | Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population |
| title_full_unstemmed | Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population |
| title_short | Practical Calling Approach for Exome Array-Based Genome-Wide Association Studies in Korean Population |
| title_sort | practical calling approach for exome array based genome wide association studies in korean population |
| url | http://dx.doi.org/10.1155/2015/421715 |
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