Identification of recurrent and novel mutations by whole‑genome sequencing of colorectal tumors from the Han population in Shanghai, eastern China
Previous studies have identified recurrent oncogenic mutations in colorectal cancer (CRC), but there is limited CRC genomic data from the Chinese Han population. Whole‑genome sequencing was performed on 10 primary CRC tumors and matched adjacent normal tissues from patients from the Han population i...
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| Veröffentlicht in: | Molecular medicine reports 2018-12, Vol.18 (6), p.5361-5370 |
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| creator | Teng, Hongfei Gao, Renyuan Qin, Nan Jiang, Xun Ren, Min Wang, Yu Wu, Shouxin Li, Ning Zhao, Jiangman Qin, Huanlong |
| description | Previous studies have identified recurrent oncogenic mutations in colorectal cancer (CRC), but there is limited CRC genomic data from the Chinese Han population. Whole‑genome sequencing was performed on 10 primary CRC tumors and matched adjacent normal tissues from patients from the Han population in Shanghai, at an average of 27.8x and 27.9x coverage, respectively. In the 10 tumor samples, 32 significant somatic mutated genes were identified, 13 of which were also reported as CRC mutations in The Cancer Genome Atlas Network. All the mutated genes were enriched in functions associated with channel activity, which has rarely been reported in previous studies investigating CRC. Furthermore, 21 chromosomal rearrangements were detected and 4 rearrangements encoded predicted in‑frame fusion proteins, including a fusion of phosphorylase kinase regulatory subunit b and NOTCH2 demonstrated in 2 out of 10 tumors. Chromosome 8 was amplified in 1 tumor and chromosome 20 was amplified in 2 out of 10 CRC patients. The present study produced a genomic mutation profile of CRC, which provides a valuable resource for further insight into the mutations that characterize CRC in patients from the Han population in Shanghai, eastern China. |
| doi_str_mv | 10.3892/mmr.2018.9563 |
| format | Article |
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Whole‑genome sequencing was performed on 10 primary CRC tumors and matched adjacent normal tissues from patients from the Han population in Shanghai, at an average of 27.8x and 27.9x coverage, respectively. In the 10 tumor samples, 32 significant somatic mutated genes were identified, 13 of which were also reported as CRC mutations in The Cancer Genome Atlas Network. All the mutated genes were enriched in functions associated with channel activity, which has rarely been reported in previous studies investigating CRC. Furthermore, 21 chromosomal rearrangements were detected and 4 rearrangements encoded predicted in‑frame fusion proteins, including a fusion of phosphorylase kinase regulatory subunit b and NOTCH2 demonstrated in 2 out of 10 tumors. Chromosome 8 was amplified in 1 tumor and chromosome 20 was amplified in 2 out of 10 CRC patients. The present study produced a genomic mutation profile of CRC, which provides a valuable resource for further insight into the mutations that characterize CRC in patients from the Han population in Shanghai, eastern China.</description><identifier>ISSN: 1791-2997</identifier><identifier>EISSN: 1791-3004</identifier><identifier>DOI: 10.3892/mmr.2018.9563</identifier><identifier>PMID: 30365144</identifier><language>eng</language><publisher>Greece: Spandidos Publications</publisher><subject>Adult ; Aged ; Aged, 80 and over ; Cancer therapies ; Channel gating ; China - epidemiology ; Chromosome 20 ; Chromosome 8 ; Chromosome rearrangements ; Colorectal cancer ; Colorectal carcinoma ; Colorectal Neoplasms - diagnosis ; Colorectal Neoplasms - epidemiology ; Colorectal Neoplasms - genetics ; Computational Biology - methods ; Deoxyribonucleic acid ; DNA ; DNA Copy Number Variations ; DNA Mutational Analysis ; DNA sequencing ; Female ; Gene mutations ; Genes ; Genetic aspects ; Genetic Predisposition to Disease ; Genetic testing ; Genome-Wide Association Study ; Genomes ; Health aspects ; Humans ; Kinases ; Male ; Middle Aged ; Mutation ; Neoplasm Staging ; Nucleotide sequencing ; Patients ; Phosphorylase ; Phosphorylase kinase ; Population Surveillance ; RNA polymerase ; Tumors ; Whole Genome Sequencing</subject><ispartof>Molecular medicine reports, 2018-12, Vol.18 (6), p.5361-5370</ispartof><rights>COPYRIGHT 2018 Spandidos Publications</rights><rights>Copyright Spandidos Publications UK Ltd. 2018</rights><rights>Copyright: © Teng et al. 2018</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c482t-645d2b8373e96da6d5fd819a8135714c61d5f9466205d785e643782dcedf82733</citedby><cites>FETCH-LOGICAL-c482t-645d2b8373e96da6d5fd819a8135714c61d5f9466205d785e643782dcedf82733</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><link.rule.ids>230,315,782,786,887,27931,27932</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/30365144$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Teng, Hongfei</creatorcontrib><creatorcontrib>Gao, Renyuan</creatorcontrib><creatorcontrib>Qin, Nan</creatorcontrib><creatorcontrib>Jiang, Xun</creatorcontrib><creatorcontrib>Ren, Min</creatorcontrib><creatorcontrib>Wang, Yu</creatorcontrib><creatorcontrib>Wu, Shouxin</creatorcontrib><creatorcontrib>Li, Ning</creatorcontrib><creatorcontrib>Zhao, Jiangman</creatorcontrib><creatorcontrib>Qin, Huanlong</creatorcontrib><title>Identification of recurrent and novel mutations by whole‑genome sequencing of colorectal tumors from the Han population in Shanghai, eastern China</title><title>Molecular medicine reports</title><addtitle>Mol Med Rep</addtitle><description>Previous studies have identified recurrent oncogenic mutations in colorectal cancer (CRC), but there is limited CRC genomic data from the Chinese Han population. Whole‑genome sequencing was performed on 10 primary CRC tumors and matched adjacent normal tissues from patients from the Han population in Shanghai, at an average of 27.8x and 27.9x coverage, respectively. In the 10 tumor samples, 32 significant somatic mutated genes were identified, 13 of which were also reported as CRC mutations in The Cancer Genome Atlas Network. All the mutated genes were enriched in functions associated with channel activity, which has rarely been reported in previous studies investigating CRC. Furthermore, 21 chromosomal rearrangements were detected and 4 rearrangements encoded predicted in‑frame fusion proteins, including a fusion of phosphorylase kinase regulatory subunit b and NOTCH2 demonstrated in 2 out of 10 tumors. Chromosome 8 was amplified in 1 tumor and chromosome 20 was amplified in 2 out of 10 CRC patients. The present study produced a genomic mutation profile of CRC, which provides a valuable resource for further insight into the mutations that characterize CRC in patients from the Han population in Shanghai, eastern China.</description><subject>Adult</subject><subject>Aged</subject><subject>Aged, 80 and over</subject><subject>Cancer therapies</subject><subject>Channel gating</subject><subject>China - epidemiology</subject><subject>Chromosome 20</subject><subject>Chromosome 8</subject><subject>Chromosome rearrangements</subject><subject>Colorectal cancer</subject><subject>Colorectal carcinoma</subject><subject>Colorectal Neoplasms - diagnosis</subject><subject>Colorectal Neoplasms - epidemiology</subject><subject>Colorectal Neoplasms - genetics</subject><subject>Computational Biology - methods</subject><subject>Deoxyribonucleic acid</subject><subject>DNA</subject><subject>DNA Copy Number Variations</subject><subject>DNA Mutational Analysis</subject><subject>DNA sequencing</subject><subject>Female</subject><subject>Gene mutations</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genetic Predisposition to Disease</subject><subject>Genetic testing</subject><subject>Genome-Wide Association Study</subject><subject>Genomes</subject><subject>Health aspects</subject><subject>Humans</subject><subject>Kinases</subject><subject>Male</subject><subject>Middle Aged</subject><subject>Mutation</subject><subject>Neoplasm Staging</subject><subject>Nucleotide sequencing</subject><subject>Patients</subject><subject>Phosphorylase</subject><subject>Phosphorylase kinase</subject><subject>Population Surveillance</subject><subject>RNA polymerase</subject><subject>Tumors</subject><subject>Whole Genome Sequencing</subject><issn>1791-2997</issn><issn>1791-3004</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2018</creationdate><recordtype>article</recordtype><sourceid>EIF</sourceid><sourceid>ABUWG</sourceid><sourceid>AFKRA</sourceid><sourceid>AZQEC</sourceid><sourceid>BENPR</sourceid><sourceid>CCPQU</sourceid><sourceid>DWQXO</sourceid><sourceid>GNUQQ</sourceid><recordid>eNptks-KFDEQxhtR3HX16FUCXjzYY_500p2LsAzqLix4UM8hk1RPZ-lOxiS9y958BcEn9ElMO-PgiuSQUPWrr6jKV1XPCV6xTtI30xRXFJNuJblgD6pT0kpSM4ybh4c3lbI9qZ6kdI2x4JTLx9UJw0xw0jSn1Y9LCz673hmdXfAo9CiCmWMsUaS9RT7cwIimOf_OJ7S5Q7dDGOHnt-9b8GEClODrDN44v12qTRhDUch6RHmeQkyoj2FCeQB0oT3ahd087ls5jz4N2m8H7V4j0ClD9Gg9OK-fVo96PSZ4drjPqi_v331eX9RXHz9crs-vatN0NNei4ZZuOtYykMJqYXlvOyJ1RxhvSWMEKRHZCEExt23HQTSs7ag1YPuOtoydVW_3urt5M0GJ-xz1qHbRTTreqaCdup_xblDbcKMEZYLKtgi8OgjEUJaQsppcMjCO2kOYk6KECokZ5rSgL_9Br8McfRmvUIwxIkj5wCO11SMo5_tQ-ppFVJ2XNONFTRZq9R-qHAuTM8FD70r8XkG9LzAxpBShP85IsFpspIqN1GIjtdio8C_-XsyR_uMb9gufY8Wz</recordid><startdate>20181201</startdate><enddate>20181201</enddate><creator>Teng, Hongfei</creator><creator>Gao, Renyuan</creator><creator>Qin, Nan</creator><creator>Jiang, Xun</creator><creator>Ren, Min</creator><creator>Wang, Yu</creator><creator>Wu, Shouxin</creator><creator>Li, Ning</creator><creator>Zhao, Jiangman</creator><creator>Qin, Huanlong</creator><general>Spandidos Publications</general><general>Spandidos Publications UK Ltd</general><general>D.A. 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Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Molecular medicine reports</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Teng, Hongfei</au><au>Gao, Renyuan</au><au>Qin, Nan</au><au>Jiang, Xun</au><au>Ren, Min</au><au>Wang, Yu</au><au>Wu, Shouxin</au><au>Li, Ning</au><au>Zhao, Jiangman</au><au>Qin, Huanlong</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Identification of recurrent and novel mutations by whole‑genome sequencing of colorectal tumors from the Han population in Shanghai, eastern China</atitle><jtitle>Molecular medicine reports</jtitle><addtitle>Mol Med Rep</addtitle><date>2018-12-01</date><risdate>2018</risdate><volume>18</volume><issue>6</issue><spage>5361</spage><epage>5370</epage><pages>5361-5370</pages><issn>1791-2997</issn><eissn>1791-3004</eissn><abstract>Previous studies have identified recurrent oncogenic mutations in colorectal cancer (CRC), but there is limited CRC genomic data from the Chinese Han population. Whole‑genome sequencing was performed on 10 primary CRC tumors and matched adjacent normal tissues from patients from the Han population in Shanghai, at an average of 27.8x and 27.9x coverage, respectively. In the 10 tumor samples, 32 significant somatic mutated genes were identified, 13 of which were also reported as CRC mutations in The Cancer Genome Atlas Network. All the mutated genes were enriched in functions associated with channel activity, which has rarely been reported in previous studies investigating CRC. Furthermore, 21 chromosomal rearrangements were detected and 4 rearrangements encoded predicted in‑frame fusion proteins, including a fusion of phosphorylase kinase regulatory subunit b and NOTCH2 demonstrated in 2 out of 10 tumors. Chromosome 8 was amplified in 1 tumor and chromosome 20 was amplified in 2 out of 10 CRC patients. The present study produced a genomic mutation profile of CRC, which provides a valuable resource for further insight into the mutations that characterize CRC in patients from the Han population in Shanghai, eastern China.</abstract><cop>Greece</cop><pub>Spandidos Publications</pub><pmid>30365144</pmid><doi>10.3892/mmr.2018.9563</doi><tpages>10</tpages><oa>free_for_read</oa></addata></record> |
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| subjects | Adult Aged Aged, 80 and over Cancer therapies Channel gating China - epidemiology Chromosome 20 Chromosome 8 Chromosome rearrangements Colorectal cancer Colorectal carcinoma Colorectal Neoplasms - diagnosis Colorectal Neoplasms - epidemiology Colorectal Neoplasms - genetics Computational Biology - methods Deoxyribonucleic acid DNA DNA Copy Number Variations DNA Mutational Analysis DNA sequencing Female Gene mutations Genes Genetic aspects Genetic Predisposition to Disease Genetic testing Genome-Wide Association Study Genomes Health aspects Humans Kinases Male Middle Aged Mutation Neoplasm Staging Nucleotide sequencing Patients Phosphorylase Phosphorylase kinase Population Surveillance RNA polymerase Tumors Whole Genome Sequencing |
| title | Identification of recurrent and novel mutations by whole‑genome sequencing of colorectal tumors from the Han population in Shanghai, eastern China |
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