Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis Method
The rapid increase in genetic dataset volume has demanded extensive adoption of biological knowledge to reduce the computational complexity, and the biological pathway is one well-known source of such knowledge. In this regard, we have introduced a novel statistical method that enables the pathway-b...
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| Language: | English |
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BioMed Central
2018-12-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gi-2018-16-4-e39.pdf |
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| author | Sungyoung Lee Taesung Park |
| author_facet | Sungyoung Lee Taesung Park |
| author_sort | Sungyoung Lee |
| collection | DOAJ |
| description | The rapid increase in genetic dataset volume has demanded extensive adoption of biological knowledge to reduce the computational complexity, and the biological pathway is one well-known source of such knowledge. In this regard, we have introduced a novel statistical method that enables the pathway-based association study of large-scale genetic dataset—namely, PHARAOH. However, researcher-level application of the PHARAOH method has been limited by a lack of generally used file formats and the absence of various quality control options that are essential to practical analysis. In order to overcome these limitations, we introduce our integration of the PHARAOH method into our recently developed all-in-one workbench. The proposed new PHARAOH program not only supports various de facto standard genetic data formats but also provides many quality control measures and filters based on those measures. We expect that our updated PHARAOH provides advanced accessibility of the pathway-level analysis of large-scale genetic datasets to researchers. |
| format | Article |
| id | doaj-art-2f417d4a84d040e39d93154fe2e49d65 |
| institution | Kabale University |
| issn | 2234-0742 |
| language | English |
| publishDate | 2018-12-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-2f417d4a84d040e39d93154fe2e49d652025-02-02T18:24:25ZengBioMed CentralGenomics & Informatics2234-07422018-12-0116410.5808/GI.2018.16.4.e39541Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis MethodSungyoung Lee0Taesung Park1 Center for Precision Medicine, Seoul National University Hospital, Seoul 03080, Korea Department of Statistics, Seoul National University, Seoul 08826, KoreaThe rapid increase in genetic dataset volume has demanded extensive adoption of biological knowledge to reduce the computational complexity, and the biological pathway is one well-known source of such knowledge. In this regard, we have introduced a novel statistical method that enables the pathway-based association study of large-scale genetic dataset—namely, PHARAOH. However, researcher-level application of the PHARAOH method has been limited by a lack of generally used file formats and the absence of various quality control options that are essential to practical analysis. In order to overcome these limitations, we introduce our integration of the PHARAOH method into our recently developed all-in-one workbench. The proposed new PHARAOH program not only supports various de facto standard genetic data formats but also provides many quality control measures and filters based on those measures. We expect that our updated PHARAOH provides advanced accessibility of the pathway-level analysis of large-scale genetic datasets to researchers.http://genominfo.org/upload/pdf/gi-2018-16-4-e39.pdfgenetic association studiespathway-level analysismultithreadingvariant calling format |
| spellingShingle | Sungyoung Lee Taesung Park Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis Method Genomics & Informatics genetic association studies pathway-level analysis multithreading variant calling format |
| title | Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis Method |
| title_full | Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis Method |
| title_fullStr | Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis Method |
| title_full_unstemmed | Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis Method |
| title_short | Integration of a Large-Scale Genetic Analysis Workbench Increases the Accessibility of a High-Performance Pathway-Based Analysis Method |
| title_sort | integration of a large scale genetic analysis workbench increases the accessibility of a high performance pathway based analysis method |
| topic | genetic association studies pathway-level analysis multithreading variant calling format |
| url | http://genominfo.org/upload/pdf/gi-2018-16-4-e39.pdf |
| work_keys_str_mv | AT sungyounglee integrationofalargescalegeneticanalysisworkbenchincreasestheaccessibilityofahighperformancepathwaybasedanalysismethod AT taesungpark integrationofalargescalegeneticanalysisworkbenchincreasestheaccessibilityofahighperformancepathwaybasedanalysismethod |