MSIseq: Software for assessing microsatellite instability from catalogs of somatic mutations

Scientific Reports

Volumn 5, Issue , 2015, Pages

  Ni Huang, Mi ^a   McPherson, John R ^a   Cutcutache, Ioana ^a   Teh, Bin Tean ^a,b   Tan, Patrick ^a,c,d,e   Rozen, Steven G ^a  

^a DUKE NUS MEDICAL SCHOOL   (Singapore)

^b DIVISION OF MEDICAL ONCOLOGY   (Singapore)

^c NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

^d INSTITUTE OF MOLECULAR AND CELL BIOLOGY   (Singapore)

^e GENOME INSTITUTE OF SINGAPORE   (Singapore)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; AUTOMATED PATTERN RECOGNITION; DATA MINING; DATABASE MANAGEMENT SYSTEM; DNA MUTATIONAL ANALYSIS; DNA SEQUENCE; GENETIC DATABASE; HUMAN; MACHINE LEARNING; MICROSATELLITE INSTABILITY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PROCEDURES; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; SOFTWARE;

ALGORITHMS; BASE SEQUENCE; DATA MINING; DATABASE MANAGEMENT SYSTEMS; DATABASES, GENETIC; DNA MUTATIONAL ANALYSIS; HUMANS; MACHINE LEARNING; MICROSATELLITE INSTABILITY; MOLECULAR SEQUENCE DATA; PATTERN RECOGNITION, AUTOMATED; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84940421708     PISSN: None     EISSN: 20452322     Source Type: Journal    
DOI: 10.1038/srep13321     Document Type: Article

References (38)

1. Iacopetta, B., Grieu, F. & Amanuel, B. Microsatellite instability in colorectal cancer. Asia-Pac J Clin Onco. 6, 260-269, doi: 10.1111/J.1743-7563.2010.01335.X (2010
2. Boland, C. R., et al. A National Cancer Institute workshop on microsatellite mnstability for cancer detection and familial predisposition: development of international criteria for the determination of microsatellite instability in colorectal cancer. Cancer Res. 58, 5248-5257 (1998
3. Eshleman, J. R. & Markowitz, S. D. Mismatch repair defects in human carcinogenesis. Hum Mol Genet. 5, 1489-1494 (1996
4. Greenman, C., et al. Patterns of somatic mutation in human cancer genomes. Nature. 446, 153-158, doi: 10.1038/nature05610 (2007
5. Veigl, M. L., et al. Biallelic inactivation of hMLH1 by epigenetic gene silencing, a novel mechanism causing human MSI cancers. P Natl Acad Sci USA. 95, 8698-8702, doi: 10.1073/Pnas.95.15.8698 (1998
6. Cunningham, J. M., et al. Hypermethylation of the hMLH1 promoter in colon cancer with microsatellite instability. Cancer Res. 58, 3455-3460 (1998
7. Ionov, Y., Peinado, M. A., Malkhosyan, S., Shibata, D. & Perucho, M. Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic carcinogenesis. Nature. 363, 558-561, doi: 10.1038/363558a0 (1993
8. Lothe, R. A., et al. Genomic instability in colorectal-cancer - relationship to clinicopathological variables and family history. Cancer Res. 53, 5849-5852 (1993
9. Zaanan, A., Meunier, K., Sangar, F., Flejou, J. F. & Praz, F. Microsatellite instability in colorectal cancer: from molecular oncogenic mechanisms to clinical implications. Cell Oncol. 34, 155-176, doi: 10.1007/S13402-011-0024-X (2011
10. Merok, M. A., et al. Microsatellite instability has a positive prognostic impact on stage II colorectal cancer after complete resection: results from a large, consecutive Norwegian series. Ann Oncol. 24, 1274-1282, doi: 10.1093/annonc/mds614 (2013
11. Akkiz, H., et al. Tumor microsatellite instability and clinical outcome in patients with colorectal cancer. Ann Oncol. 17, 248-248 (2006
12. Schofield, L., et al. Population-based detection of Lynch syndrome in young colorectal cancer patients using microsatellite instability as the initial test. Int J Cancer. 124, 1097-1102, doi: 10.1002/Ijc.23863 (2009
13. Vilar, E. & Gruber, S. B. Microsatellite instability in colorectal cancer-The stable evidence. Nat Rev Clin Oncol. 7, 153-162, doi: 10.1038/Nrclinonc.2009.237 (2010
14. Promega. MSI Analysis System, Version 1.2, Technical Manual. (2014). http://www.promega.sg/resources/protocols/technicalmanuals/.0/msi-Analysis-system-version-12-protocol. (Accessed: 1st July 2015
15. National Cancer Institute. NCI Wiki - Microsatellite data. (2012). https://wiki.nci.nih.gov/display/TCGA/Microsatellite+ data. (Accessed: 19th June 2014
16. The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 487, 330-337, doi: 10.1038/nature11252 (2012
17. Getz, G., et al. Integrated genomic characterization of endometrial carcinoma. Nature. 497, 67-73, doi: 10.1038/Nature12113 (2013
18. Wang, K., et al. Exome sequencing identifies frequent mutation of ARID1A in molecular subtypes of gastric cancer. Nat Genet. 43, 1219-1223, doi: 10.1038/ng.982 (2011
19. Murphy, K. M., et al. Comparison of the microsatellite instability analysis system and the Bethesda panel for the determination of microsatellite instability in colorectal cancers. J Mol Diagn. 8, 305-311, doi: 10.2353/Jmoldx.2006.050092 (2006
20. Metzker, M. L. Sequencing technologies-The next generation. Nat Rev Genet. 11, 31-46, doi: 10.1038/nrg2626 (2009
21. Voelkerding, K. V., Dames, S. A. & Durtschi, J. D. Next-generation sequencing: from basic research to diagnostics. Clin Chem. 55, 641-658, doi: 10.1373/Clinchem.2008.112789 (2009
22. Roychowdhury, S., et al. Personalized oncology through integrative high-Throughput sequencing: a pilot study. Sci Transl Med. 3, 111ra121-111ra121 (2011
23. Niu, B., et al. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics. 30, 1015-1016, doi: 10.1093/bioinformatics/btt755 (2014
24. Salipante, S. J., Scroggins, S. M., Hampel, H. L., Turner, E. H. & Pritchard, C. C. Microsatellite Instability Detection by Next Generation Sequencing. Clin Chem. 60, 1192-1199 (2014
25. Lu, Y., Soong, T. D. & Elemento, O. A novel approach for characterizing microsatellite instability in cancer cells. PloS one. 8, e63056, doi: 10.1371/journal.pone.0063056 (2013
26. Zang, Z. J., et al. Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet. 44, 570-574, doi: 10.1038/ng.2246 (2012
27. Poon, S., et al. Mutation signatures implicate aristolochic acid in bladder cancer development. Genome Medicine. 7, 38 (2015
28. Wang, K., et al. Whole-genome sequencing and comprehensive molecular profiling identify new driver mutations in gastric cancer. Nat Genet. 46, 573-582, doi: 10.1038/ng.2983 (2014
29. Saunders, C. T., et al. Strelka: Accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics, doi: 10.1093/bioinformatics/bts271 (2012
30. Nagarajan, N., et al. Whole-genome reconstruction and mutational signatures in gastric cancer. Genome Biology. 13, R115 (2012
31. Ribic, C. M., et al. Tumor microsatellite-instability status as a predictor of benefit from fluorouracil-based adjuvant chemotherapy for colon cancer. New Engl J Med. 349, 247-257, doi: 10.1056/Nejmoa022289 (2003
32. Tomlinson, I., Halford, S., Aaltonen, L., Hawkins, N. & Ward, R. Does MSI-low exist? J Pathol. 197, 6-13, doi: 10.1002/Path.1071 (2002
33. Laiho, P., et al. Low-level microsatellite instability in most colorectal carcinomas. Cancer Res. 62, 1166-1170 (2002
34. Hall, M., et al. The WEKA data mining software: an update. SIGKDD Explorations. 11, 10-18 (2009
35. Hornik, K., Buchta, C. & Zeileis, A. Open-source machine learning: R meets Weka. Computational Statistics. 24, 225-232 (2009
36. Quinlan, J. R. C4.5: programs for machine learning. (Morgan Kaufmann Publishers Inc., 1993
37. Alexandrov, L. B., et al. Signatures of mutational processes in human cancer. Nature. 500, 415-421, doi: 10.1038/nature12477 (2013
38. R: A language and environment for statistical computing (R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria, 2012