Ionov Y, Peinado MA, Malkhosyan S, Shibata D, Perucho M. Ubiquitous somatic mutations in simple repeated sequences reveal a new mechanism for colonic carcinogenesis. Nature. 1993;363:558–61.
Article
CAS
PubMed
Google Scholar
Aaltonen LA, Peltomaki P, Leach FS, Sistonen P, Pylkkanen L, Mecklin JP, et al. Clues to the pathogenesis of familial colorectal cancer. Science. 1993;260:812–6.
Article
CAS
PubMed
Google Scholar
Thibodeau SN, Bren G, Schaid D. Microsatellite instability in cancer of the proximal colon. Science. 1993;260:816–9.
Article
CAS
PubMed
Google Scholar
Kane MF, Loda M, Gaida GM, Lipman J, Mishra R, Goldman H, et al. Methylation of the hMLH1 promoter correlates with lack of expression of hMLH1 in sporadic colon tumors and mismatch repair-defective human tumor cell lines. Cancer Res. 1997;57:808–11.
CAS
PubMed
Google Scholar
Cunningham JM, Christensen ER, Tester DJ, Kim CY, Roche PC, Burgart LJ, et al. Hypermethylation of the hMLH1 promoter in colon cancer with microsatellite instability. Cancer Res. 1998;58:3455–60.
CAS
PubMed
Google Scholar
Herman JG, Umar A, Polyak K, Graff JR, Ahuja N, Issa JP, et al. Incidence and functional consequences of hMLH1 promoter hypermethylation in colorectal carcinoma. Proc Natl Acad Sci U S A. 1998;95:6870–5.
Article
CAS
PubMed
PubMed Central
Google Scholar
Fishel R, Lescoe MK, Rao MR, Copeland NG, Jenkins NA, Garber J, et al. The human mutator gene homolog MSH2 and its association with hereditary nonpolyposis colon cancer. Cell. 1993;75:1027–38.
Article
CAS
PubMed
Google Scholar
Leach FS, Nicolaides NC, Papadopoulos N, Liu B, Jen J, Parsons R, et al. Mutations of a mutS homolog in hereditary nonpolyposis colorectal cancer. Cell. 1993;75:1215–25.
Article
CAS
PubMed
Google Scholar
Bronner CE, Baker SM, Morrison PT, Warren G, Smith LG, Lescoe MK, et al. Mutation in the DNA mismatch repair gene homologue hMLH1 is associated with hereditary non-polyposis colon cancer. Nature. 1994;368:258–61.
Article
CAS
PubMed
Google Scholar
Papadopoulos N, Nicolaides NC, Wei YF, Ruben SM, Carter KC, Rosen CA, et al. Mutation of a mutL homolog in hereditary colon cancer. Science. 1994;263:1625–9.
Article
CAS
PubMed
Google Scholar
Børresen AL, Lothe RA, Meling GI, Lystad S, Morrison P, Lipford J, et al. Somatic mutations in the hMSH2 gene in microsatellite unstable colorectal carcinomas. Hum Mol Genet. 1995;4:2065–72.
Article
PubMed
Google Scholar
Peltomaki P, Lothe RA, Aaltonen LA, Pylkkanen L, Nystrom-Lahti M, Seruca R, et al. Microsatellite instability is associated with tumors that characterize the hereditary non-polyposis colorectal carcinoma syndrome. Cancer Res. 1993;53:5853–5.
CAS
PubMed
Google Scholar
Wooster R, Cleton-Jansen AM, Collins N, Mangion J, Cornelis RS, Cooper CS, et al. Instability of short tandem repeats (microsatellites) in human cancers. Nat Genet. 1994;6:152–6.
Article
CAS
PubMed
Google Scholar
Lothe RA. Microsatellite instability in human solid tumors. Mol Med Today. 1997;3:61–8.
Article
CAS
PubMed
Google Scholar
Hause RJ, Pritchard CC, Shendure J, Salipante SJ. Classification and characterization of microsatellite instability across 18 cancer types. Nat Med. 2016;22:1342–50.
Article
CAS
PubMed
Google Scholar
The Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature. 2012;487:330–7.
Article
PubMed Central
Google Scholar
Vogelstein B, Papadopoulos N, Velculescu VE, Zhou S, Diaz LA, Kinzler KW. Cancer genome landscapes. Science. 2013;339:1546–58.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rajagopalan H, Bardelli A, Lengauer C, Kinzler KW, Vogelstein B, Velculescu VE. Tumorigenesis: RAF/RAS oncogenes and mismatch-repair status. Nature. 2002;418:934.
Article
CAS
PubMed
Google Scholar
Duval A, Hamelin R. Mutations at coding repeat sequences in mismatch repair-deficient human cancers: toward a new concept of target genes for instability. Cancer Res. 2002;62:2447–54.
CAS
PubMed
Google Scholar
Røyrvik EC, Ahlquist T, Rognes T, Lothe RA. Slip slidin’ away: a duodecennial review of targeted genes in mismatch repair deficient colorectal cancer. Crit Rev Oncog. 2007;13:229–57.
Article
PubMed
Google Scholar
Bruun J, Kolberg M, Ahlquist TC, Royrvik EC, Nome T, Leithe E, et al. Regulator of chromosome condensation 2 identifies high-risk patients within both major phenotypes of colorectal cancer. Clin Cancer Res. 2015;21:3759–70.
Article
CAS
PubMed
Google Scholar
Markowitz S, Wang J, Myeroff L, Parsons R, Sun L, Lutterbaugh J, et al. Inactivation of the type II TGF-beta receptor in colon cancer cells with microsatellite instability. Science. 1995;268:1336–8.
Article
CAS
PubMed
Google Scholar
Myeroff LL, Parsons R, Kim SJ, Hedrick L, Cho KR, Orth K, et al. A transforming growth factor beta receptor type II gene mutation common in colon and gastric but rare in endometrial cancers with microsatellite instability. Cancer Res. 1995;55:5545–7.
CAS
PubMed
Google Scholar
Parsons R, Myeroff LL, Liu B, Willson JK, Markowitz SD, Kinzler KW, et al. Microsatellite instability and mutations of the transforming growth factor beta type II receptor gene in colorectal cancer. Cancer Res. 1995;55:5548–50.
CAS
PubMed
Google Scholar
Mullaney JM, Mills RE, Pittard WS, Devine SE. Small insertions and deletions (INDELs) in human genomes. Hum Mol Genet. 2010;19:R131–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ghoneim DH, Myers JR, Tuttle E, Paciorkowski AR. Comparison of insertion/deletion calling algorithms on human next-generation sequencing data. BMC Res Notes. 2014;7:864.
Article
PubMed
PubMed Central
Google Scholar
Giannakis M, Hodis E, Jasmine MX, Yamauchi M, Rosenbluh J, Cibulskis K, et al. RNF43 is frequently mutated in colorectal and endometrial cancers. Nat Genet. 2014;46:1264–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ferlay J, Soerjomataram I, Dikshit R, Eser S, Mathers C, Rebelo M, et al. Cancer incidence and mortality worldwide: sources, methods and major patterns in GLOBOCAN 2012. Int J Cancer. 2015;136:E359–86.
Article
CAS
PubMed
Google Scholar
Lothe RA, Peltomaki P, Meling GI, Aaltonen LA, Nystrom-Lahti M, Pylkkanen L, et al. Genomic instability in colorectal cancer: relationship to clinicopathological variables and family history. Cancer Res. 1993;53:5849–52.
CAS
PubMed
Google Scholar
Popat S, Hubner R, Houlston RS. Systematic review of microsatellite instability and colorectal cancer prognosis. J Clin Oncol. 2005;23:609–18.
Article
CAS
PubMed
Google Scholar
Guidoboni M, Gafa R, Viel A, Doglioni C, Russo A, Santini A, et al. Microsatellite instability and high content of activated cytotoxic lymphocytes identify colon cancer patients with a favorable prognosis. Am J Pathol. 2001;159:297–304.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mlecnik B, Bindea G, Angell HK, Maby P, Angelova M, Tougeron D, et al. Integrative analyses of colorectal cancer show immunoscore is a stronger predictor of patient survival than microsatellite instability. Immunity. 2016;44:698–711.
Article
CAS
PubMed
Google Scholar
Schumacher TN, Schreiber RD. Neoantigens in cancer immunotherapy. Science. 2015;348:69–74.
Article
CAS
PubMed
Google Scholar
Brown SD, Warren RL, Gibb EA, Martin SD, Spinelli JJ, Nelson BH, et al. Neo-antigens predicted by tumor genome meta-analysis correlate with increased patient survival. Genome Res. 2014;24:743–50.
Article
CAS
PubMed
PubMed Central
Google Scholar
Angelova M, Charoentong P, Hackl H, Fischer ML, Snajder R, Krogsdam AM, et al. Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol. 2015;16:64.
Article
PubMed
PubMed Central
Google Scholar
Sanz-Pamplona R, Gil-Hoyos R, Lopez-Doriga A, Alonso MH, Ausso S, Mollevi DG, et al. Mutanome and expression of immune response genes in microsatelite stable colon cancer. Oncotarget. 2016;7:17711–25.
PubMed
PubMed Central
Google Scholar
Giannakis M, Mu XJ, Shukla SA, Qian ZR, Cohen O, Nishihara R, et al. Genomic correlates of immune-cell infiltrates in colorectal carcinoma. Cell Rep. 2016;15:857–65.
Article
CAS
PubMed Central
Google Scholar
Kim CG, Ahn JB, Jung M, Beom SH, Kim C, Kim JH, et al. Effects of microsatellite instability on recurrence patterns and outcomes in colorectal cancers. Br J Cancer. 2016;115:25–33.
Article
CAS
PubMed
Google Scholar
Le DT, Uram JN, Wang H, Bartlett BR, Kemberling H, Eyring AD, et al. PD-1 blockade in tumors with mismatch-repair deficiency. N Engl J Med. 2015;372:2509–20.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hugo W, Zaretsky JM, Sun L, Song C, Moreno BH, Hu-Lieskovan S, et al. Genomic and transcriptomic features of response to anti-PD-1 therapy in metastatic melanoma. Cell. 2016;165:35–44.
Article
CAS
PubMed
PubMed Central
Google Scholar
Charoentong P, Finotello F, Angelova M, Mayer C, Efremova M, Rieder D, et al. Pan-cancer immunogenomic analyses reveal genotype-immunophenotype relationships and predictors of response to checkpoint blockade. Cell Rep. 2017;18:248–62.
Article
CAS
PubMed
Google Scholar
Guinney J, Dienstmann R, Wang X, de Reynies A, Schlicker A, Soneson C, et al. The consensus molecular subtypes of colorectal cancer. Nat Med. 2015;21:1350–6.
Article
CAS
PubMed
PubMed Central
Google Scholar
Becht E, de Reynies A, Giraldo NA, Pilati C, Buttard B, Lacroix L, et al. Immune and stromal classification of colorectal cancer is associated with molecular subtypes and relevant for precision immunotherapy. Clin Cancer Res. 2016;22:4057–66.
Article
CAS
PubMed
Google Scholar
Kerr DJ, Dunn JA, Langman MJ, Smith JL, Midgley RS, Stanley A, et al. Rofecoxib and cardiovascular adverse events in adjuvant treatment of colorectal cancer. N Engl J Med. 2007;357:360–9.
Article
CAS
PubMed
Google Scholar
Marisa L, de Reynies A, Duval A, Selves J, Gaub MP, Vescovo L, et al. Gene expression classification of colon cancer into molecular subtypes: characterization, validation, and prognostic value. PLoS Med. 2013;10:e1001453.
Article
CAS
PubMed
PubMed Central
Google Scholar
Berg M, Danielsen SA, Ahlquist T, Merok MA, Ågesen TH, Vatn MH, et al. DNA sequence profiles of the colorectal cancer critical gene set KRAS-BRAF-PIK3CA-PTEN-TP53 related to age at disease onset. PLoS One. 2010;5:e13978.
Article
PubMed
PubMed Central
Google Scholar
Andresen K, Boberg KM, Vedeld HM, Honne H, Jebsen P, Hektoen M, et al. Four DNA methylation biomarkers in biliary brush samples accurately identify the presence of cholangiocarcinoma. Hepatology. 2015;61:1651–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler transform. Bioinformatics. 2010;26:589–95.
Article
PubMed
PubMed Central
Google Scholar
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol. 2013;31:213–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Saunders CT, Wong WS, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics. 2012;28:1811–7.
Article
CAS
PubMed
Google Scholar
Wang K, Li M, Hakonarson H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 2010;38:e164.
Article
PubMed
PubMed Central
Google Scholar
Lawrence MS, Stojanov P, Polak P, Kryukov GV, Cibulskis K, Sivachenko A, et al. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature. 2013;499:214–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Niu B, Ye K, Zhang Q, Lu C, Xie M, McLellan MD, et al. MSIsensor: microsatellite instability detection using paired tumor-normal sequence data. Bioinformatics. 2014;30:1015–6.
Article
CAS
PubMed
Google Scholar
Alexandrov LB, Nik-Zainal S, Wedge DC, Aparicio SA, Behjati S, Biankin AV, et al. Signatures of mutational processes in human cancer. Nature. 2013;500:415–21.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gehring JS, Fischer B, Lawrence M, Huber W. SomaticSignatures: inferring mutational signatures from single-nucleotide variants. Bioinformatics. 2015;31:3673–5.
CAS
PubMed
PubMed Central
Google Scholar
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012;40:e115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang K, Li M, Hadley D, Liu R, Glessner J, Grant SF, et al. PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. Genome Res. 2007;17:1665–74.
Article
CAS
PubMed
PubMed Central
Google Scholar
McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nat Genet. 2008;40:1166–74.
Article
CAS
PubMed
Google Scholar
Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, et al. Allele-specific copy number analysis of tumors. Proc Natl Acad Sci U S A. 2010;107:16910–5.
Article
PubMed
PubMed Central
Google Scholar
Miller CA, White BS, Dees ND, Griffith M, Welch JS, Griffith OL, et al. SciClone: inferring clonal architecture and tracking the spatial and temporal patterns of tumor evolution. PLoS Comput Biol. 2014;10:e1003665.
Article
PubMed
PubMed Central
Google Scholar
Andor N, Harness JV, Muller S, Mewes HW, Petritsch C. EXPANDS: expanding ploidy and allele frequency on nested subpopulations. Bioinformatics. 2014;30:50–60.
Article
CAS
PubMed
Google Scholar
Johnson WE, Li C, Rabinovic A. Adjusting batch effects in microarray expression data using empirical Bayes methods. Biostatistics. 2007;8:118–27.
Article
PubMed
Google Scholar
Punt CJ, Buyse M, Kohne CH, Hohenberger P, Labianca R, Schmoll HJ, et al. Endpoints in adjuvant treatment trials: a systematic review of the literature in colon cancer and proposed definitions for future trials. J Natl Cancer Inst. 2007;99:998–1003.
Article
PubMed
Google Scholar
Efron B, Tibshirani R. On testing the significance of sets of genes. Ann Appl Stat. 2007;1:107–29.
Article
Google Scholar
Hanzelmann S, Castelo R, Guinney J. GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinf. 2013;14:7.
Article
Google Scholar
Yoshihara K, Shahmoradgoli M, Martinez E, Vegesna R, Kim H, Torres-Garcia W, et al. Inferring tumour purity and stromal and immune cell admixture from expression data. Nat Commun. 2013;4:2612.
Article
PubMed
PubMed Central
Google Scholar
Shukla SA, Rooney MS, Rajasagi M, Tiao G, Dixon PM, Lawrence MS, et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat Biotechnol. 2015;33:1152–8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Hoof I, Peters B, Sidney J, Pedersen LE, Sette A, Lund O, et al. NetMHCpan, a method for MHC class I binding prediction beyond humans. Immunogenetics. 2009;61:1–13.
Article
CAS
PubMed
Google Scholar
Chen C, Li Z, Huang H, Suzek BE, Wu CH. A fast Peptide Match service for UniProt Knowledgebase. Bioinformatics. 2013;29:2808–9.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nielsen M, Lundegaard C, Lund O, Kesmir C. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics. 2005;57:33–41.
Article
CAS
PubMed
Google Scholar
Rayner E, van Gool IC, Palles C, Kearsey SE, Bosse T, Tomlinson I, et al. A panoply of errors: polymerase proofreading domain mutations in cancer. Nat Rev Cancer. 2016;16:71–81.
Article
CAS
PubMed
Google Scholar
Zaretsky JM, Garcia-Diaz A, Shin DS, Escuin-Ordinas H, Hugo W, Hu-Lieskovan S, et al. Mutations associated with acquired resistance to PD-1 blockade in melanoma. N Engl J Med. 2016;375:819–29.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shin DS, Zaretsky JM, Escuin-Ordinas H, Garcia-Diaz A, Hu-Lieskovan S, Kalbasi A, et al. Primary resistance to PD-1 blockade mediated by JAK1/2 mutations. Cancer Discov. 2017;7:188–201.
Article
CAS
PubMed
Google Scholar
Ren Y, Zhang Y, Liu RZ, Fenstermacher DA, Wright KL, Teer JK, et al. JAK1 truncating mutations in gynecologic cancer define new role of cancer-associated protein tyrosine kinase aberrations. Sci Rep. 2013;3:3042.
Article
PubMed
PubMed Central
Google Scholar
Chow LQM, Mehra R, Haddad RI, Mahipal A, Weiss J, Berger R, et al. Biomarkers and response to pembrolizumab in recurrent/metastatic head and neck squamous cell carcinoma. J Clin Oncol. 2016;34(suppl):abstr 6010.
Google Scholar
Stelloo E, Versluis MA, Nijman HW, de Bruyn M, Plat A, Osse EM, et al. Microsatellite instability derived JAK1 frameshift mutations are associated with tumor immune evasion in endometrioid endometrial cancer. Oncotarget. 2016;7:39885–93.
PubMed
PubMed Central
Google Scholar
Kim TM, Laird PW, Park PJ. The landscape of microsatellite instability in colorectal and endometrial cancer genomes. Cell. 2013;155:858–68.
Article
CAS
PubMed
Google Scholar
Supek F, Lehner B. Differential DNA mismatch repair underlies mutation rate variation across the human genome. Nature. 2015;521:81–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sottoriva A, Kang H, Ma Z, Graham TA, Salomon MP, Zhao J, et al. A Big Bang model of human colorectal tumor growth. Nat Genet. 2015;47:209–16.
Article
CAS
PubMed
PubMed Central
Google Scholar
Andor N, Graham TA, Jansen M, Xia LC, Aktipis CA, Petritsch C, et al. Pan-cancer analysis of the extent and consequences of intratumor heterogeneity. Nat Med. 2016;22:105–13.
Article
CAS
PubMed
Google Scholar
Morris LG, Riaz N, Desrichard A, Senbabaoglu Y, Hakimi AA, Makarov V, et al. Pan-cancer analysis of intratumor heterogeneity as a prognostic determinant of survival. Oncotarget. 2016;7:10051–63.
PubMed
PubMed Central
Google Scholar
Sansone P, Bromberg J. Targeting the interleukin-6/Jak/stat pathway in human malignancies. J Clin Oncol. 2012;30:1005–14.
Article
CAS
PubMed
PubMed Central
Google Scholar
Buchert M, Burns CJ, Ernst M. Targeting JAK kinase in solid tumors: emerging opportunities and challenges. Oncogene. 2016;35:939–51.
Article
CAS
PubMed
Google Scholar