Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets
The Wellcome Trust Case Control Consortium (WTCCC) study was a large genome-wide association study that aimed to identify common variants associated with seven diseases. That study combined two control datasets (58C and UK Blood Services) as shared controls. Prior to using the combined controls, the...
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| Language: | English |
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BioMed Central
2019-09-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2019-17-3-e29.pdf |
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| author | Chloe Soohyun Jang Wanson Choi Seungho Cook Buhm Han |
| author_facet | Chloe Soohyun Jang Wanson Choi Seungho Cook Buhm Han |
| author_sort | Chloe Soohyun Jang |
| collection | DOAJ |
| description | The Wellcome Trust Case Control Consortium (WTCCC) study was a large genome-wide association study that aimed to identify common variants associated with seven diseases. That study combined two control datasets (58C and UK Blood Services) as shared controls. Prior to using the combined controls, the WTCCC performed analyses to show that the genomic content of the control datasets was not significantly different. Recently, the analysis of human leukocyte antigen (HLA) genes has become prevalent due to the development of HLA imputation technology. In this project, we extended the between-control homogeneity analysis of the WTCCC to HLA. We imputed HLA information in the WTCCC control dataset and showed that the HLA content was not significantly different between the two control datasets, suggesting that the combined controls can be used as controls for HLA fine-mapping analysis based on HLA imputation. |
| format | Article |
| id | doaj-art-bb6c32622ae448f1b3f058d906a35892 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2019-09-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-bb6c32622ae448f1b3f058d906a358922025-02-02T18:57:07ZengBioMed CentralGenomics & Informatics2234-07422019-09-0117310.5808/GI.2019.17.3.e29572Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasetsChloe Soohyun JangWanson ChoiSeungho CookBuhm HanThe Wellcome Trust Case Control Consortium (WTCCC) study was a large genome-wide association study that aimed to identify common variants associated with seven diseases. That study combined two control datasets (58C and UK Blood Services) as shared controls. Prior to using the combined controls, the WTCCC performed analyses to show that the genomic content of the control datasets was not significantly different. Recently, the analysis of human leukocyte antigen (HLA) genes has become prevalent due to the development of HLA imputation technology. In this project, we extended the between-control homogeneity analysis of the WTCCC to HLA. We imputed HLA information in the WTCCC control dataset and showed that the HLA content was not significantly different between the two control datasets, suggesting that the combined controls can be used as controls for HLA fine-mapping analysis based on HLA imputation.http://genominfo.org/upload/pdf/gi-2019-17-3-e29.pdfgenome-wide association studyhuman leukocyte antigenshared control |
| spellingShingle | Chloe Soohyun Jang Wanson Choi Seungho Cook Buhm Han Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets Genomics & Informatics genome-wide association study human leukocyte antigen shared control |
| title | Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets |
| title_full | Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets |
| title_fullStr | Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets |
| title_full_unstemmed | Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets |
| title_short | Analysis of differences in human leukocyte antigen between the two Wellcome Trust Case Control Consortium control datasets |
| title_sort | analysis of differences in human leukocyte antigen between the two wellcome trust case control consortium control datasets |
| topic | genome-wide association study human leukocyte antigen shared control |
| url | http://genominfo.org/upload/pdf/gi-2019-17-3-e29.pdf |
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