Somatic Mutaome Profile in Human Cancer Tissues
Somatic mutation is a major cause of cancer progression and varied responses of tumors against anticancer agents. Thus, we must obtain and characterize genome-wide mutational profiles in individual cancer subtypes. The Cancer Genome Atlas database includes large amounts of sequencing and omics data...
| Main Authors: | , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
Korea Genome Organization
2013-12-01
|
| Series: | Genomics & Informatics |
| Subjects: | |
| Online Access: | http://genominfo.org/upload/pdf/gni-11-239.pdf |
| _version_ | 1811304874997972992 |
|---|---|
| author | Nayoung Kim Yourae Hong Doyoung Kwon Sukjoon Yoon |
| author_facet | Nayoung Kim Yourae Hong Doyoung Kwon Sukjoon Yoon |
| author_sort | Nayoung Kim |
| collection | DOAJ |
| description | Somatic mutation is a major cause of cancer progression and varied responses of tumors against anticancer agents. Thus, we must obtain and characterize genome-wide mutational profiles in individual cancer subtypes. The Cancer Genome Atlas database includes large amounts of sequencing and omics data generated from diverse human cancer tissues. In the present study, we integrated and analyzed the exome sequencing data from ~3,000 tissue samples and summarized the major mutant genes in each of the diverse cancer subtypes and stages. Mutations were observed in most human genes (~23,000 genes) with low frequency from an analysis of 11 major cancer subtypes. The majority of tissue samples harbored 20-80 different mutant genes, on average. Lung cancer samples showed a greater number of mutations in diverse genes than other cancer subtypes. Only a few genes were mutated with over 5% frequency in tissue samples. Interestingly, mutation frequency was generally similar between non-metastatic and metastastic samples in most cancer subtypes. Among the 12 major mutations, the TP53, USH2A, TTN, and MUC16 genes were found to be frequent in most cancer types, while BRAF, FRG1B, PBRM1, and VHL showed lineage-specific mutation patterns. The present study provides a useful resource to understand the broad spectrum of mutation frequencies in various cancer types. |
| first_indexed | 2024-04-13T08:15:12Z |
| format | Article |
| id | doaj.art-d096db66cc85482bbeafdc8066bb9c9a |
| institution | Directory Open Access Journal |
| issn | 1598-866X 2234-0742 |
| language | English |
| last_indexed | 2024-04-13T08:15:12Z |
| publishDate | 2013-12-01 |
| publisher | Korea Genome Organization |
| record_format | Article |
| series | Genomics & Informatics |
| spelling | doaj.art-d096db66cc85482bbeafdc8066bb9c9a2022-12-22T02:54:50ZengKorea Genome OrganizationGenomics & Informatics1598-866X2234-07422013-12-0111423924410.5808/GI.2013.11.4.23964Somatic Mutaome Profile in Human Cancer TissuesNayoung Kim0Yourae Hong1Doyoung Kwon2Sukjoon Yoon3Department of Biological Sciences, Center for Advanced Bioinformatics and Systems Medicine, Sookmyung Women's University, Seoul 140-742, Korea.Department of Biological Sciences, Center for Advanced Bioinformatics and Systems Medicine, Sookmyung Women's University, Seoul 140-742, Korea.Department of Biological Sciences, Center for Advanced Bioinformatics and Systems Medicine, Sookmyung Women's University, Seoul 140-742, Korea.Department of Biological Sciences, Center for Advanced Bioinformatics and Systems Medicine, Sookmyung Women's University, Seoul 140-742, Korea.Somatic mutation is a major cause of cancer progression and varied responses of tumors against anticancer agents. Thus, we must obtain and characterize genome-wide mutational profiles in individual cancer subtypes. The Cancer Genome Atlas database includes large amounts of sequencing and omics data generated from diverse human cancer tissues. In the present study, we integrated and analyzed the exome sequencing data from ~3,000 tissue samples and summarized the major mutant genes in each of the diverse cancer subtypes and stages. Mutations were observed in most human genes (~23,000 genes) with low frequency from an analysis of 11 major cancer subtypes. The majority of tissue samples harbored 20-80 different mutant genes, on average. Lung cancer samples showed a greater number of mutations in diverse genes than other cancer subtypes. Only a few genes were mutated with over 5% frequency in tissue samples. Interestingly, mutation frequency was generally similar between non-metastatic and metastastic samples in most cancer subtypes. Among the 12 major mutations, the TP53, USH2A, TTN, and MUC16 genes were found to be frequent in most cancer types, while BRAF, FRG1B, PBRM1, and VHL showed lineage-specific mutation patterns. The present study provides a useful resource to understand the broad spectrum of mutation frequencies in various cancer types.http://genominfo.org/upload/pdf/gni-11-239.pdfhuman tissue samplesmetastasismutation frequencyTCGA |
| spellingShingle | Nayoung Kim Yourae Hong Doyoung Kwon Sukjoon Yoon Somatic Mutaome Profile in Human Cancer Tissues Genomics & Informatics human tissue samples metastasis mutation frequency TCGA |
| title | Somatic Mutaome Profile in Human Cancer Tissues |
| title_full | Somatic Mutaome Profile in Human Cancer Tissues |
| title_fullStr | Somatic Mutaome Profile in Human Cancer Tissues |
| title_full_unstemmed | Somatic Mutaome Profile in Human Cancer Tissues |
| title_short | Somatic Mutaome Profile in Human Cancer Tissues |
| title_sort | somatic mutaome profile in human cancer tissues |
| topic | human tissue samples metastasis mutation frequency TCGA |
| url | http://genominfo.org/upload/pdf/gni-11-239.pdf |
| work_keys_str_mv | AT nayoungkim somaticmutaomeprofileinhumancancertissues AT youraehong somaticmutaomeprofileinhumancancertissues AT doyoungkwon somaticmutaomeprofileinhumancancertissues AT sukjoonyoon somaticmutaomeprofileinhumancancertissues |