Identifying recurrent mutations in cancer reveals widespread lineage diversity and mutational specificity

Nature Biotechnology

Volumn 34, Issue 2, 2016, Pages 155-163

  Chang, Matthew T ^a,b   Asthana, Saurabh ^c   Gao, Sizhi Paul ^a   Lee, Byron H ^a   Chapman, Jocelyn S ^c   Kandoth, Cyriac ^a   Gao, JianJiong ^a   Socci, Nicholas D ^a   Solit, David B ^a,d   Olshen, Adam B ^c,e   Schultz, Nikolaus ^a   Taylor, Barry S ^a  

^a MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d WEILL CORNELL MEDICAL COLLEGE   (United States)

^e UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DISEASES; TUMORS;

BROAD SPECTRUM; MOLECULAR FUNCTION; MUTANT ALLELES; MUTATED GENES; RECURRENT MUTATION; SELECTIVE PRESSURE; STATISTICAL ALGORITHM; TUMOR SAMPLES;

GENES;

ARHGAP28 PROTEIN; ATM PROTEIN; BRG1 PROTEIN; CYCLIN D1; CYCLIN DEPENDENT KINASE 4; CYCLIN DEPENDENT KINASE INHIBITOR 2A; DNA; E1A ASSOCIATED P300 PROTEIN; EPIDERMAL GROWTH FACTOR RECEPTOR 3; HEPATOCYTE NUCLEAR FACTOR 3ALPHA; ING1 PROTEIN; K RAS PROTEIN; MAX PROTEIN; MITOGEN ACTIVATED PROTEIN KINASE 7; MYC PROTEIN; MYOCYTE ENHANCER FACTOR 2A; ONCOPROTEIN; PHOSPHATIDYLINOSITOL 3,4,5 TRISPHOSPHATE 3 PHOSPHATASE; PHOSPHATIDYLINOSITOL 4,5 BISPHOSPHATE 3 KINASE; PIK3R1 PROTEIN; PROTEIN; PROTEIN TYROSINE PHOSPHATASE SHP 2; RAC1 PROTEIN; RETINOBLASTOMA BINDING PROTEIN 2; RNA; RRAS2 PROTEIN; SMAD2 PROTEIN; SMAD4 PROTEIN; TRANSCRIPTION FACTOR NFE2L2; TRANSFORMING GROWTH FACTOR BETA RECEPTOR 2; UNCLASSIFIED DRUG;

ARTICLE; CANCER CELL; CANCER GENETICS; CARCINOGENESIS; CARCINOSARCOMA; CELL LINEAGE; CELL SPECIFICITY; CHRONIC LYMPHATIC LEUKEMIA; COMPARATIVE STUDY; CONTROLLED STUDY; CUTANEOUS MELANOMA; ENDOMETRIUM CANCER; GENE DOSAGE; GENE FREQUENCY; GENETIC VARIABILITY; GLIOBLASTOMA; GLIOMA; HUMAN; KIDNEY CARCINOMA; LUNG ADENOCARCINOMA; MAJOR CLINICAL STUDY; MANTLE CELL LYMPHOMA; MOLECULAR PATHOLOGY; MULTIPLE MYELOMA; MUTATION RATE; NONHODGKIN LYMPHOMA; PAPILLARY CARCINOMA; PILOCYTIC ASTROCYTOMA; PONTINE GLIOMA; PRIMARY TUMOR; PRIORITY JOURNAL; RENAL PAPILLARY CELL CARCINOMA; RNA SEQUENCE; SOMATIC MUTATION; SQUAMOUS CELL CARCINOMA; SQUAMOUS CELL LUNG CARCINOMA; STATISTICAL MODEL; TRANSITIONAL CELL CARCINOMA; TUMOR GENE; TUMOR GROWTH; UTERINE CARCINOSARCOMA; UTERUS CARCINOMA; UTERUS SARCOMA; WNT SIGNALING PATHWAY; ALGORITHM; BIOLOGY; DNA MUTATIONAL ANALYSIS; GENETICS; MUTATION; NEOPLASM; PROCEDURES;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA MUTATIONAL ANALYSIS; HUMANS; MUTATION; NEOPLASMS;

EID: 84957550528     PISSN: 10870156     EISSN: 15461696     Source Type: Journal    
DOI: 10.1038/nbt.3391     Document Type: Article

References (52)

1. Vogelstein B., et a.l. Cancer genome landscapes. Science 339, 1546-1558 (2013
2. Garraway L.A., & Lander E.S. Lessons from the cancer genome. Cell 153, 17-37 (2013
3. Tamborero D., et a.l. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Sci. Rep. 3, 2650 (2013
4. Lawrence M.S., et a.l. Mutational heterogeneity in cancer and the search for new cancer-associated genes. Nature 499, 214-218 (2013
5. Kandoth C., et a.l. Mutational landscape and significance across 12 major cancer types. Nature 502, 333-339 (2013
6. Gonzalez-Perez A., et a.l. IntOGen-mutations identifies cancer drivers across tumor types. Nat. Methods 10, 1081-1082 (2013
7. Santarius T., Shipley J., Brewer D., Stratton M.R., & Cooper C.S. A census of amplified and overexpressed human cancer genes. Nat. Rev. Cancer 10, 59-64 (2010
8. Burd C.E., et a.l. Mutation-specific RAS oncogenicity explains NRAS codon 61 selection in melanoma. Cancer Discov. 4, 1418-1429 (2014
9. Menzies A.M., et a.l. Distinguishing clinicopathologic features of patients with V600E and V600K BRAF-mutant metastatic melanoma. Clin. Cancer Res. 18, 3242-3249 (2012
10. Vivanco I., et a.l. Differential sensitivity of glioma-versus lung cancer-specific EGFR mutations to EGFR kinase inhibitors. Cancer Discov. 2, 458-471 (2012
11. Westcott P.M., et a.l. The mutational landscapes of genetic and chemical models of Kras-driven lung cancer. Nature 517, 489-492 (2015
12. Krauthammer M., et a.l. Exome sequencing identifies recurrent somatic RAC1 mutations in melanoma. Nat. Genet. 44, 1006-1014 (2012
13. Cancer Genome Atlas Research Network. Comprehensive molecular characterization of urothelial bladder carcinoma. Nature 507, 315-322 (2014
14. Lee C.S., et a.l. Recurrent point mutations in the kinetochore gene KNSTRN in cutaneous squamous cell carcinoma. Nat. Genet. 46, 1060-1062 (2014
15. Jaiswal B.S., et a.l. Oncogenic ERBB3 mutations in human cancers. Cancer Cell 23, 603-617 (2013
16. Alexandrov L.B., et a.l. Signatures of mutational processes in human cancer. Nature 500, 415-421 (2013
17. Mullighan C.G., et a.l. CREBBP mutations in relapsed acute lymphoblastic leukaemia. Nature 471, 235-239 (2011
18. Cheung L.W., et a.l. Naturally occurring neomorphic PIK3R1 mutations activate the MAPK pathway, dictating therapeutic response to MAPK pathway inhibitors. Cancer Cell 26, 479-494 (2014
19. Weng A.P., et a.l. Activating mutations of NOTCH1 in human T cell acute lymphoblastic leukemia. Science 306, 269-271 (2004
20. Hart T., Brown K.R., Sircoulomb F., Rottapel R., & Moffat J. Measuring error rates in genomic perturbation screens: gold standards for human functional genomics. Mol. Syst. Biol. 10, 733 (2014
21. Yu H.A., et a.l. Prognostic impact of KRAS mutation subtypes in 677 patients with metastatic lung adenocarcinomas. J. Thorac. Oncol. 10, 431-437 (2015
22. Ihle N.T., et a.l. Effect of KRAS oncogene substitutions on protein behavior: implications for signaling and clinical outcome. J. Natl. Cancer Inst. 104, 228-239 (2012
23. Garassino M.C., et a.l. Different types of K-Ras mutations could affect drug sensitivity and tumour behaviour in non-small-cell lung cancer. Ann. Oncol. 22, 235-237 (2011
24. de Bruin E.C., et a.l. Spatial and temporal diversity in genomic instability processes defines lung cancer evolution. Science 346, 251-256 (2014
25. Cancer Genome Atlas Research Network. Integrated genomic characterization of endometrial carcinoma. Nature 497, 67-73 (2013
26. Cancer Genome Atlas Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330-337 (2012
27. Whitehall V.L., et a.l. Oncogenic PIK3CA mutations in colorectal cancers and polyps. Int. J. Cancer 131, 813-820 (2012
28. Lawrence M.S., et a.l. Discovery and saturation analysis of cancer genes across 21 tumour types. Nature 505, 495-501 (2014
29. Grabiner B.C., et a.l. A diverse array of cancer-associated MTOR mutations are hyperactivating and can predict rapamycin sensitivity. Cancer Discov. 4, 554-563 (2014
30. Al-Ahmadie H., et a.l. Synthetic lethality in ATM-deficient RAD50-mutant tumors underlies outlier response to cancer therapy. Cancer Discov. 4, 1014-1021 (2014
31. Iyer G., et a.l. Genome sequencing identifies a basis for everolimus sensitivity. Science 338, 221 (2012
32. Forbes S.A., et a.l. COSMIC: exploring the world's knowledge of somatic mutations in human cancer. Nucleic Acids Res. 43, D805-D811 (2015
33. Hodis E., et a.l. A landscape of driver mutations in melanoma. Cell 150, 251-263 (2012
34. Watson I.R., et a.l. The RAC1 P29S hotspot mutation in melanoma confers resistance to pharmacological inhibition of RAF. Cancer Res. 74, 4845-4852 (2014
35. Van Allen E.M., et a.l. The genetic landscape of clinical resistance to RAF inhibition in metastatic melanoma. Cancer Discov. 4, 94-109 (2014
36. Janakiraman M., et a.l. Genomic and biological characterization of exon 4 KRAS mutations in human cancer. Cancer Res. 70, 5901-5911 (2010
37. Ehrhardt A., Ehrhardt G.R., Guo X., & Schrader J.W. Ras and relatives-job sharing and networking keep an old family together. Exp. Hematol. 30, 1089-1106 (2002
38. Barker K.T., & Crompton M.R. Ras-related TC21 is activated by mutation in a breast cancer cell line, but infrequently in breast carcinomas in vivo. Br. J. Cancer 78, 296-300 (1998
39. Clark G.J., Kinch M.S., Gilmer T.M., Burridge K., & Der C.J. Overexpression of the Ras-related TC21/R-Ras2 protein may contribute to the development of human breast cancers. Oncogene 12, 169-176 (1996
40. Huang Y., et a.l. A novel insertional mutation in the TC21 gene activates its transforming activity in a human leiomyosarcoma cell line. Oncogene 11, 1255-1260 (1995
41. Erdogan M., Pozzi A., Bhowmick N., Moses H.L., & Zent R. Signaling pathways regulating TC21-induced tumorigenesis. J. Biol. Chem. 282, 27713-27720 (2007
42. Rosário M., Paterson H.F., & Marshall C.J. Activation of the Ral and phosphatidylinositol 3' kinase signaling pathways by the ras-related protein TC21. Mol. Cell. Biol. 21, 3750-3762 (2001
43. Rong R., He Q., Liu Y., Sheikh M.S., & Huang Y. TC21 mediates transformation and cell survival via activation of phosphatidylinositol 3-kinase/Akt and NF-kappaB signaling pathway. Oncogene 21, 1062-1070 (2002
44. Rosário M., Paterson H.F., & Marshall C.J. Activation of the Raf/MAP kinase cascade by the Ras-related protein TC21 is required for the TC21-mediated transformation of NIH 3T3 cells. EMBO J. 18, 1270-1279 (1999
45. Cerami E., et a.l. The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov. 2, 401-404 (2012
46. Gao J., et a.l. Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci. Signal. 6, pl1 (2013
47. Karolchik D., et a.l. The UCSC Genome Browser database: 2014 update. Nucleic Acids Res. 42, D764-D770 (2014
48. McLaren W., et a.l. Deriving the consequences of genomic variants with the Ensembl API and SNP Effect Predictor. Bioinformatics 26, 2069-2070 (2010
49. Benjamini Y., & Yekutieli D. The control of the false discovery rate in multiple testing under dependency. Ann. Stat. 29, 1165-1188 (2001
50. Cheng D.T., et a.l. MSK-IMPACT: A hybridization capture-based next generation sequencing clinical assay for solit tumor molecular oncology. J. Mol. Diagn. 17, 251-264 (2015
51. Bao L., Pu M., & Messer K. AbsCN-seq: a statistical method to estimate tumor purity, ploidy and absolute copy numbers from next-generation sequencing data. Bioinformatics 30, 1056-1063 (2014
52. Nik-Zainal S., et a.l. The life history of 21 breast cancers. Cell 149, 994-1007 (2012