دورية أكاديمية
Whole-genome reconstruction and mutational signatures in gastric cancer.
| العنوان: | Whole-genome reconstruction and mutational signatures in gastric cancer. |
|---|---|
| المؤلفون: | Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PÉ, Teo AS, Cutcutache I, Zhang Z, Lee WH, Sia YY, Gao S, Ariyaratne PN, Ho A, Woo XY, Veeravali L, Ong CK, Deng N, Desai KV, Khor CC, Hibberd ML, Shahab A, Rao J, Wu M, Teh M, Zhu F, Chin SY, Pang B, So JB, Bourque G, Soong R, Sung WK, Tean Teh B, Rozen S, Ruan X, Yeoh KG, Tan PB, Ruan Y |
| المصدر: | Genome biology [Genome Biol] 2012 Dec 13; Vol. 13 (12), pp. R115. Date of Electronic Publication: 2012 Dec 13. |
| نوع المنشور: | Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't |
| اللغة: | English |
| بيانات الدورية: | Publisher: BioMed Central Ltd Country of Publication: England NLM ID: 100960660 Publication Model: Electronic Cited Medium: Internet ISSN: 1474-760X (Electronic) Linking ISSN: 14747596 NLM ISO Abbreviation: Genome Biol Subsets: MEDLINE |
| أسماء مطبوعة: | Publication: London, UK : BioMed Central Ltd Original Publication: London : Genome Biology Ltd., c2000- |
| مواضيع طبية MeSH: | DNA Mutational Analysis/*methods , High-Throughput Nucleotide Sequencing/*methods , Stomach Neoplasms/*genetics, Adenocarcinoma/genetics ; Chromosomal Instability ; Deamination ; Exome ; Genomics ; Microsatellite Instability ; Mutation ; Reactive Oxygen Species/metabolism |
| مستخلص: | Background: Gastric cancer is the second highest cause of global cancer mortality. To explore the complete repertoire of somatic alterations in gastric cancer, we combined massively parallel short read and DNA paired-end tag sequencing to present the first whole-genome analysis of two gastric adenocarcinomas, one with chromosomal instability and the other with microsatellite instability. Results: Integrative analysis and de novo assemblies revealed the architecture of a wild-type KRAS amplification, a common driver event in gastric cancer. We discovered three distinct mutational signatures in gastric cancer--against a genome-wide backdrop of oxidative and microsatellite instability-related mutational signatures, we identified the first exome-specific mutational signature. Further characterization of the impact of these signatures by combining sequencing data from 40 complete gastric cancer exomes and targeted screening of an additional 94 independent gastric tumors uncovered ACVR2A, RPL22 and LMAN1 as recurrently mutated genes in microsatellite instability-positive gastric cancer and PAPPA as a recurrently mutated gene in TP53 wild-type gastric cancer. Conclusions: These results highlight how whole-genome cancer sequencing can uncover information relevant to tissue-specific carcinogenesis that would otherwise be missed from exome-sequencing data. |
| References: | Bioinformatics. 2010 Mar 1;26(5):589-95. (PMID: 20080505) Nature. 2010 Jan 14;463(7278):184-90. (PMID: 20016488) Genome Res. 2010 Feb;20(2):265-72. (PMID: 20019144) Nature. 2011 Jun 05;475(7354):101-5. (PMID: 21642962) Cancer Res. 2003 Mar 1;63(5):994-9. (PMID: 12615714) J Comput Biol. 2011 Nov;18(11):1681-91. (PMID: 21929371) Bioinformatics. 2009 Aug 15;25(16):2078-9. (PMID: 19505943) Nat Genet. 2011 Oct 30;43(12):1219-23. (PMID: 22037554) Cell. 2010 Oct 1;143(1):122-33. (PMID: 20887897) Nucleic Acids Res. 2010 Jan;38(Database issue):D682-9. (PMID: 19820113) Genome Res. 2009 Apr;19(4):521-32. (PMID: 19339662) Nature. 2010 May 27;465(7297):473-7. (PMID: 20505728) Nucleic Acids Res. 2003 Jul 1;31(13):3812-4. (PMID: 12824425) Genome Biol. 2009;10(3):R25. (PMID: 19261174) Nucleic Acids Res. 2002 Jan 1;30(1):207-10. (PMID: 11752295) Genome Biol. 2004;5(2):R12. (PMID: 14759262) Nature. 2010 Jan 14;463(7278):191-6. (PMID: 20016485) Trends Genet. 2003 Apr;19(4):207-16. (PMID: 12683974) Eur Rev Med Pharmacol Sci. 2010 Apr;14(4):302-8. (PMID: 20496539) Nat Genet. 2012 May;44(5):570-4. (PMID: 22484628) Genome Res. 2009 Sep;19(9):1586-92. (PMID: 19657104) Curr Opin Obstet Gynecol. 2007 Apr;19(2):176-82. (PMID: 17353686) Pathogenetics. 2008 Nov 03;1(1):4. (PMID: 19014668) Biochem Biophys Res Commun. 2004 Mar 12;315(3):686-91. (PMID: 14975755) Genome Res. 2011 May;21(5):665-75. (PMID: 21467267) Gut. 2012 May;61(5):673-84. (PMID: 22315472) Genes Chromosomes Cancer. 2009 Jul;48(7):552-7. (PMID: 19373783) Nat Rev Cancer. 2002 Feb;2(2):133-42. (PMID: 12635176) Antioxid Redox Signal. 2006 May-Jun;8(5-6):1033-45. (PMID: 16771693) Nature. 1998 Dec 17;396(6712):643-9. (PMID: 9872311) Gastroenterology. 2004 Mar;126(3):654-9. (PMID: 14988818) Oncogene. 2010 Apr 1;29(13):1929-40. (PMID: 20062083) Curr Opin Immunol. 2010 Aug;22(4):442-7. (PMID: 20667704) |
| معلومات مُعتمدة: | 5 R33 CA126996-02 United States CA NCI NIH HHS |
| سلسلة جزيئية: | GEO GSE30833 |
| المشرفين على المادة: | 0 (Reactive Oxygen Species) |
| تواريخ الأحداث: | Date Created: 20121215 Date Completed: 20151217 Latest Revision: 20221109 |
| رمز التحديث: | 20221213 |
| مُعرف محوري في PubMed: | PMC4056366 |
| DOI: | 10.1186/gb-2012-13-12-r115 |
| PMID: | 23237666 |
| قاعدة البيانات: | MEDLINE |
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