Bioinformatics Interpretation of Exome Sequencing: Blood Cancer
We had analyzed 10 exome sequencing data and single nucleotide polymorphism chips for blood cancer provided by the PGM21 (The National Project for Personalized Genomic Medicine) Award program. We had removed sample G06 because the pair is not correct and G10 because of possible contamination. In-hou...
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| Format: | Article |
| Language: | English |
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BioMed Central
2013-03-01
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| Series: | Genomics & Informatics |
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| Online Access: | http://genominfo.org/upload/pdf/gni-11-24.pdf |
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| _version_ | 1832570187805622272 |
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| author | Jiwoong Kim Yun-Gyeong Lee Namshin Kim |
| author_facet | Jiwoong Kim Yun-Gyeong Lee Namshin Kim |
| author_sort | Jiwoong Kim |
| collection | DOAJ |
| description | We had analyzed 10 exome sequencing data and single nucleotide polymorphism chips for blood cancer provided by the PGM21 (The National Project for Personalized Genomic Medicine) Award program. We had removed sample G06 because the pair is not correct and G10 because of possible contamination. In-house software somatic copy-number and heterozygosity alteration estimation (SCHALE) was used to detect one loss of heterozygosity region in G05. We had discovered 27 functionally important mutations. Network and pathway analyses gave us clues that NPM1, GATA2, and CEBPA were major driver genes. By comparing with previous somatic mutation profiles, we had concluded that the provided data originated from acute myeloid leukemia. Protein structure modeling showed that somatic mutations in IDH2, RASGEF1B, and MSH4 can affect protein structures. |
| format | Article |
| id | doaj-art-1ba45eecbff94842ad5cc6d3431d7810 |
| institution | Kabale University |
| issn | 1598-866X 2234-0742 |
| language | English |
| publishDate | 2013-03-01 |
| publisher | BioMed Central |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj-art-1ba45eecbff94842ad5cc6d3431d78102025-02-02T16:04:57ZengBioMed CentralGenomics & Informatics1598-866X2234-07422013-03-01111243310.5808/GI.2013.11.1.2469Bioinformatics Interpretation of Exome Sequencing: Blood CancerJiwoong Kim0Yun-Gyeong Lee1Namshin Kim2Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806, Korea.We had analyzed 10 exome sequencing data and single nucleotide polymorphism chips for blood cancer provided by the PGM21 (The National Project for Personalized Genomic Medicine) Award program. We had removed sample G06 because the pair is not correct and G10 because of possible contamination. In-house software somatic copy-number and heterozygosity alteration estimation (SCHALE) was used to detect one loss of heterozygosity region in G05. We had discovered 27 functionally important mutations. Network and pathway analyses gave us clues that NPM1, GATA2, and CEBPA were major driver genes. By comparing with previous somatic mutation profiles, we had concluded that the provided data originated from acute myeloid leukemia. Protein structure modeling showed that somatic mutations in IDH2, RASGEF1B, and MSH4 can affect protein structures.http://genominfo.org/upload/pdf/gni-11-24.pdfacute myeloid leukemiacomputational biologyexomemutation |
| spellingShingle | Jiwoong Kim Yun-Gyeong Lee Namshin Kim Bioinformatics Interpretation of Exome Sequencing: Blood Cancer Genomics & Informatics acute myeloid leukemia computational biology exome mutation |
| title | Bioinformatics Interpretation of Exome Sequencing: Blood Cancer |
| title_full | Bioinformatics Interpretation of Exome Sequencing: Blood Cancer |
| title_fullStr | Bioinformatics Interpretation of Exome Sequencing: Blood Cancer |
| title_full_unstemmed | Bioinformatics Interpretation of Exome Sequencing: Blood Cancer |
| title_short | Bioinformatics Interpretation of Exome Sequencing: Blood Cancer |
| title_sort | bioinformatics interpretation of exome sequencing blood cancer |
| topic | acute myeloid leukemia computational biology exome mutation |
| url | http://genominfo.org/upload/pdf/gni-11-24.pdf |
| work_keys_str_mv | AT jiwoongkim bioinformaticsinterpretationofexomesequencingbloodcancer AT yungyeonglee bioinformaticsinterpretationofexomesequencingbloodcancer AT namshinkim bioinformaticsinterpretationofexomesequencingbloodcancer |