Signatures of mutation and selection in the cancer genome

Stratton, M. R., Campbell, P. J. & Futreal, P. A. The cancer genome. Nature 458, 719–724 (2009)

Pasqualucci, L. et al. Hypermutation of multiple proto-oncogenes in B-cell diffuse large-cell lymphomas. Nature 412, 341–346 (2001)

Liu, M. et al. Two levels of protection for the B cell genome during somatic hypermutation. Nature 451, 841–845 (2008)

Rampino, N. et al. Somatic frameshift mutations in the BAX gene in colon cancers of the microsatellite mutator phenotype. Science 275, 967–969 (1997)

Bader, S. et al. Somatic frameshift mutations in the MBD4 gene of sporadic colon cancers with mismatch repair deficiency. Oncogene 18, 8044–8047 (1999)

Melo, S. A. et al. A TARBP2 mutation in human cancer impairs microRNA processing and DICER1 function. Nature Genet. 41, 365–370 (2009)

Kamb, A. et al. Analysis of the p16 gene (CDKN2) as a candidate for the chromosome 9p melanoma susceptibility locus. Nature Genet. 8, 22–26 (1994)

Fung, Y.-K. T. et al. Structural evidence for the authenticity of the human retinoblastoma gene. Science 236, 1657–1661 (1987)

Thiagalingam, S. et al. Evaluation of candidate tumour suppressor genes on chromosome 18 in colorectal cancers. Nature Genet. 13, 343–346 (1996)

Versteege, I. et al. Truncating mutations of hSNF5/INI1 in aggressive paediatric cancer. Nature 394, 203–206 (1998)

Teng, D. H. F. et al. Human mitogen-activated protein kinase kinase 4 as a candidate tumor suppressor. Cancer Res. 57, 4177–4182 (1997)

Li, J. et al. PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science 275, 1943–1947 (1997)

Lukusa, T. & Fryns, J. P. Human chromosome fragility. Biochim. Biophys. Acta 1779, 3–16 (2008)

Solomon, D. A. et al. Sample type bias in the analysis of cancer genomes. Cancer Res. 69, 5630–5633 (2009)

Krimpenfort, P. et al. p15Ink4b is a critical tumour suppressor in the absence of p16Ink4a . Nature 448, 943–946 (2007)

Markowitz, S. et al. Inactivation of the type II TGF-β receptor in colon cancer cells with microsatellite instability. Science 268, 1336–1338 (1995)

Wiedemeyer, R. et al. Feedback circuit among INK4 tumor suppressors constrains human glioblastoma development. Cancer Cell 13, 355–364 (2008)

Solomon, D. A., Kim, J.-S., Jean, W. & Waldman, T. Conspirators in a capital crime: co-deletion of p18INK4c and p16INK4a/p14ARF/p15INK4b in glioblastoma multiforme. Cancer Res. 68, 8657–8660 (2008)

Ozawa, M., Baribault, H. & Kemler, R. The cytoplasmic domain of the cell adhesion molecule uvomorulin associates with three independent proteins structurally related in different species. EMBO J. 8, 1711–1717 (1989)

Vermeulen, S. J. et al. The αE-catenin gene (CTNNA1) acts as an invasion-suppressor gene in human colon cancer cells. Oncogene 18, 905–915 (1999)

Bullions, L. C., Notterman, D. A., Chung, L. S. & Levine, A. J. Expression of wild-type α-catenin protein in cells with a mutant α-catenin gene restores both growth regulation and tumor suppressor activities. Mol. Cell. Biol. 17, 4501–4508 (1997)

Liu, T. X. et al. Chromosome 5q deletion and epigenetic suppression of the gene encoding α-catenin (CTNNA1) in myeloid cell transformation. Nature Med. 13, 78–83 (2006)

Arlt, M. F. et al. Replication stress induces genome-wide copy number changes in human cells that resemble polymorphic and pathogenic variants. Am. J. Hum. Genet. 84, 339–350 (2009)

Solomon, D. A. et al. Mutational inactivation of PTPRD in glioblastoma multiforme and malignant melanoma. Cancer Res. 68, 10300–10306 (2008)

Ding, L. et al. Somatic mutations affect key pathways in lung adenocarcinoma. Nature 455, 1069–1075 (2008)

Weir, B. A. et al. Characterizing the cancer genome in lung adenocarcinoma. Nature 450, 893–898 (2007)

Sjöblom, T. et al. The consensus coding sequences of human breast and colorectal cancers. Science 314, 268–274 (2006)

Iliopoulos, D. et al. Roles of FHIT and WWOX fragile genes in cancer. Cancer Lett. 232, 27–36 (2006)

Gorgoulis, V. G. et al. Activation of the DNA damage checkpoint and genomic instability in human precancerous lesions. Nature 434, 907–913 (2005)

Ried, K. et al. Common chromosomal fragile site FRA16D sequence: identification of the FOR gene spanning FRA16D and homozygous deletions and translocation breakpoints in cancer cells. Hum. Mol. Genet. 9, 1651–1663 (2000)

Casper, A. M., Nghiem, P., Arlt, M. F. & Glover, T. W. ATR regulates fragile site stability. Cell 111, 779–789 (2002)

Freudenreich, C. H. Chromosome fragility: molecular mechanisms and cellular consequences. Front. Biosci. 12, 4911–4924 (2007)

Schwartz, M. et al. Homologous recombination and nonhomologous end-joining repair pathways regulate fragile site stability. Genes Dev. 19, 2715–2726 (2005)

Greenman, C. D. et al. PICNIC: an algorithm to predict absolute allelic copy number variation with microarray cancer data. Biostatistics 11, 164–175 (2010)

Dicks, E. et al. AutoCSA, an algorithm for high throughput DNA sequence variant detection in cancer genomes. Bioinformatics 23, 1689–1691 (2007)

McCarroll, S. A. et al. Integrated detection and population-genetic analysis of SNPs and copy number variation. Nature Genet. 40, 1166–1174 (2008)

Benjamini, Y. & Hochberg, Y. Controlling the false discovery rate: a practical and powerful approach to multiple testing. J. R. Stat. Soc. B 57, 289–300 (1995)

Sawińska, M. et al. Novel aphidicolin-inducible common fragile site FRA9G maps to 9p22.2, within the C9orf39 gene. Genes Chromosom. Cancer 46, 991–999 (2007)

Freeman, J. L. et al. Definition of the zebrafish genome using flow cytometry and cytogenetic mapping. BMC Genomics 8, 195 (2007)

Perry, G. H. et al. Copy number variation and evolution in humans and chimpanzees. Genome Res. 18, 1698–1710 (2008)