The DOI matches its Crossref record; 42 of the 43 references it cites were found in a registry or an index.
A comprehensive catalogue of somatic mutations from a human cancer genome
Open accessAbstract
All cancers carry somatic mutations. A subset of these somatic alterations, termed driver mutations, confer selective growth advantage and are implicated in cancer development, whereas the remainder are passengers. Here we have sequenced the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The catalogue provides remarkable insights into the forces that have shaped this cancer genome. The dominant mutational signature reflects DNA damage due to ultraviolet light exposure, a known risk factor for malignant melanoma, whereas the uneven distribution of mutations across the genome, with a lower prevalence in gene footprints, indicates that DNA repair has been preferentially deployed towards transcribed regions. The results illustrate the power of a cancer genome sequence to reveal traces of the DNA damage, repair, mutation and selection processes that were operative years before the cancer became symptomatic. The two cancer genome sequences presented in this issue demonstrate how next-generation sequencing technologies can inform us about mutational processes, repair pathways and gene networks associated with cancer development. First, the genome of a cell line derived from a bone marrow metastasis in a patient who had small-cell lung cancer. This cancer is typical of the type induced by smoking, and the sequence contains mutation signatures characteristic of some of the more than 60 carcinogens present in tobacco smoke. The second paper compares the whole genome sequence of a melanoma cell line to a lymphoblastoid cell line from the same individual. This, the first complete mutational analysis of a solid tumour, reveals a dominant mutational signature reflecting DNA damage due to exposure to ultraviolet light. Here, the genomes of a malignant melanoma and a lymphoblastoid cell line from the same person are sequenced, providing the first comprehensive catalogue of somatic mutations from an individual cancer. The data provide insight into the causes of tumour formation and the development of the cancer genome, with the dominant mutational signature reflecting DNA damage due to ultraviolet light exposure.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
In the citing paper
“Melanoma somatic mutations consist almost entirely of C → T transitions, 28% of which are TCC → T mutations (19,31).”
From Evidence for recent, population-specific evolution of the human mutation rate (2015) · cites this paper as [31]
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Fast and accurate short read alignment with Burrows-Wheeler transform
Li, H., & Durbin, R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp324 · Cited by 58,607
Circos: An information aesthetic for comparative genomicsPreprint
Krzywinski, M. I., Schein, J. E., Birol, İ., Connors, J. M., Gascoyne, R. D., Horsman, D. E., Jones, S. J. M., & Marra, M. A. (2009) · Genome Research · doi:10.1101/gr.092759.109 · Cited by 11,029
Velvet: Algorithms for de novo short read assembly using de Bruijn graphsPreprint
Zerbino, D. R., & Birney, E. (2008) · Genome Research · doi:10.1101/gr.074492.107 · Cited by 9,575
Comprehensive genomic characterization defines human glioblastoma genes and core pathways
The Cancer Genome Atlas Research Network (2008) · Nature · doi:10.1038/nature07385 · Cited by 7,735
Genome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693
An Integrated Genomic Analysis of Human Glioblastoma Multiforme
Parsons, D. W., Jones, S., Zhang, X., Lin, J. C.-H., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Siu, I.-M., Gallia, G. L., et al. (2008) · Science · doi:10.1126/science.1164382 · Cited by 5,857
Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses
Jones, S., Zhang, X., Parsons, D. W., Lin, J. C.-H., Leary, R. J., Angenendt, P., Mankoo, P., Carter, H., Kamiyama, H., Jimeno, A., et al. (2008) · Science · doi:10.1126/science.1164368 · Cited by 3,969
Self-citationAccurate whole human genome sequencing using reversible terminator chemistry
Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684
Self-citationStratton, M. R., Campbell, P. J., & Futreal, P. A. (2009) · Nature · doi:10.1038/nature07943 · Cited by 3,625
Self-citationA census of human cancer genes
Futreal, P. A., Coin, L., Marshall, M., Down, T., Hubbard, T., Wooster, R., Rahman, N., & Stratton, M. R. (2004) · Nature Reviews Cancer · doi:10.1038/nrc1299 · Cited by 3,184
Self-citation
Flagged first, then by citations
1 of the 43 references couldn’t be matched to a known paper.
Cited by
Sorted by citations
Items 101–200 of 1,001
What can exome sequencing do for you?
Majewski, J., Schwartzentruber, J., Lalonde, E., Montpetit, A., & Jabado, N. (2011) · Journal of Medical Genetics · doi:10.1136/jmedgenet-2011-100223 · Cited by 417
Mutational and structural analysis of diffuse large B-cell lymphoma using whole-genome sequencing
Morin, R. D., Mungall, K., Pleasance, E., Mungall, A. J. J., Goya, R., Huff, R. D., Scott, D. W., Ding, J., Roth, A. J. L., Chiu, R., et al. (2013) · Blood · doi:10.1182/blood-2013-02-483727 · Cited by 407
Self-citationStanding the test of time: targeting thymidylate biosynthesis in cancer therapy
Wilson, P. M., Danenberg, P. V., Johnston, P. G., Lenz, H., & Ladner, R. D. (2014) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2014.51 · Cited by 393
Chiba, T., Marusawa, H., & Ushijima, T. (2012) · Gastroenterology · doi:10.1053/j.gastro.2012.07.009 · Cited by 385
The Landscape of Microsatellite Instability in Colorectal and Endometrial Cancer Genomes
Kim, T., Laird, P. W., & Park, P. J. (2013) · Cell · doi:10.1016/j.cell.2013.10.015 · Cited by 387
Parallel bacterial evolution within multiple patients identifies candidate pathogenicity genes
Lieberman, T. D., Michel, J.-B., Aingaran, M., Potter-Bynoe, G., Roux, D., Davis, M. R., Skurnik, D., Leiby, N., LiPuma, J. J., Goldberg, J. B., et al. (2011) · Nature Genetics · doi:10.1038/ng.997 · Cited by 367
Lewis, N. E., Liu, X., Li, Y., Nagarajan, H., Yerganian, G., O'Brien, E., Bordbar, A., Roth, A. M., Rosenbloom, J., Bian, C., et al. (2013) · Nature Biotechnology · doi:10.1038/nbt.2624 · Cited by 380
Ren, S., Peng, Z., Mao, J., Yu, Y., Yin, C., Gao, X., Cui, Z., Zhang, J., Kang, Y., Xu, W., et al. (2012) · Cell Research · doi:10.1038/cr.2012.30 · Cited by 362
Driver and Passenger Mutations in Cancer
Pon, J. R., & Marra, M. A. (2014) · Annual Review of Pathology Mechanisms of Disease · doi:10.1146/annurev-pathol-012414-040312 · Cited by 381
Next-generation sequencing for cancer diagnostics: a practical perspective.
Meldrum, C. J., Doyle, M., & Tothill, R. W. (2011) · Europe PMC (PubMed Central) · Cited by 356
Klein, I. A., Resch, W., Janković, M., Oliveira, T. Y., Yamane, A., Nakahashi, H., Virgilio, M. D., Bothmer, A., Nussenzweig, A., Robbiani, D. F., et al. (2011) · Cell · doi:10.1016/j.cell.2011.07.048 · Cited by 353
Differential DNA mismatch repair underlies mutation rate variation across the human genome
Supek, F., & Lehner, B. (2015) · Nature · doi:10.1038/nature14173 · Cited by 359
The Genetic Basis for Cancer Treatment Decisions
Dancey, J. E., Bedard, P. L., Onetto-Pothier, N., & Hudson, T. J. (2012) · Cell · doi:10.1016/j.cell.2012.01.014 · Cited by 345
Melanoma induction by ultraviolet A but not ultraviolet B radiation requires melanin pigment
Noonan, F. P., Zaidi, M. R., Wolnicka-Glubisz, A., Anver, M. R., Bahn, J., Wielgus, A., Cadet, J., Douki, T., Mouret, S., Tucker, M. A., et al. (2012) · Nature Communications · doi:10.1038/ncomms1893 · Cited by 331
Ultraviolet radiation and the skin: Photobiology and sunscreen photoprotection
Young, A. R., Claveau, J., & Rossi, A. B. (2017) · Journal of the American Academy of Dermatology · doi:10.1016/j.jaad.2016.09.038 · Cited by 339
Diverse Mechanisms of Somatic Structural Variations in Human Cancer Genomes
Yang, L., Luquette, L. J., Gehlenborg, N., Xi, R., Haseley, P. S., Hsieh, C.-H., Zhang, C., Ren, X., Protopopov, A. I., Chin, L., et al. (2013) · Cell · doi:10.1016/j.cell.2013.04.010 · Cited by 329
Self-citationMaking sense of cancer genomic dataPreprint
Chin, L., Hahn, W. C., Getz, G. A., & Meyerson, M. M. (2011) · Genes & Development · doi:10.1101/gad.2017311 · Cited by 344
Self-citationZhang, L., Zhou, Y., Cheng, C., Cui, H., Cheng, L., Kong, P., Wang, J., Li, Y., Chen, W., Song, B., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.02.017 · Cited by 331
Self-citationGenome Sequencing and Analysis of the Tasmanian Devil and Its Transmissible Cancer
Murchison, E. P., Schulz-Trieglaff, O. B., Ning, Z., Alexandrov, L. B., Bauer, M. J., Fu, B., Hims, M. M., Ding, Z., Ivakhno, S., Stewart, C. M., et al. (2012) · Cell · doi:10.1016/j.cell.2011.11.065 · Cited by 323
Self-citationThe effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patientsPreprint
Jiang, Z., Jhunjhunwala, S., Liu, J., Haverty, P. M., Kennemer, M. I., Guan, Y., Lee, W., Carnevali, P., Stinson, J., Johnson, S. L., et al. (2012) · Genome Research · doi:10.1101/gr.133926.111 · Cited by 330
Promise of personalized omics to precision medicine
Chen, R., & Snyder, M. P. (2012) · WIREs Systems Biology and Medicine · doi:10.1002/wsbm.1198 · Cited by 338
Schuh, A., Becq, J., Humphray, S., Alexa, A., Burns, A., Clifford, R. M., Feller, S. M., Grocock, R., Henderson, S. J., Khrebtukova, I., et al. (2012) · Blood · doi:10.1182/blood-2012-05-433540 · Cited by 321
Self-citationLandscape of somatic single-nucleotide and copy-number mutations in uterine serous carcinoma
Zhao, S., Choi, M., Overton, J. D., Bellone, S., Roque, D. M., Cocco, E., Guzzo, F., English, D. P.-G., Varughese, J., Gasparrini, S., et al. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1222577110 · Cited by 323
Analysis of error profiles in deep next-generation sequencing data
Ma, X., Shao, Y., Tian, L., Flasch, D. A., Mulder, H. L., Edmonson, M. N., Liu, Y., Chen, X. '., Newman, S., Nakitandwe, J., et al. (2019) · Genome biology · doi:10.1186/s13059-019-1659-6 · Cited by 323
Impact of deleterious passenger mutations on cancer progression
McFarland, C. D., Korolev, K. S., Kryukov, G. V., Sunyaev, S. R., & Mirny, L. A. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1213968110 · Cited by 319
Exhaustion-associated regulatory regions in CD8 + tumor-infiltrating T cells
Mognol, G. P., Spreafico, R., Wong, V., Scott-Browne, J. P., Togher, S., Hoffmann, A., Hogan, P. G., Rao, A., & Trifari, S. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1620498114 · Cited by 324
The Long and Short of Circulating Cell-Free DNA and the Ins and Outs of Molecular Diagnostics
Jiang, P., & Lo, Y. M. D. (2016) · Trends in Genetics · doi:10.1016/j.tig.2016.03.009 · Cited by 316
Oxygen as a friend and enemy: How to combat the mutational potential of 8-oxo-guanine
van Loon, B., Markkanen, E., & Hübscher, U. (2010) · DNA repair · doi:10.1016/j.dnarep.2010.03.004 · Cited by 321
Genomic sequencing of colorectal adenocarcinomas identifies a recurrent VTI1A-TCF7L2 fusion
Bass, A. J., Lawrence, M. S., Brace, L. E., Ramos, A. H., Drier, Y., Cibulskis, K., Sougnez, C. L., Voet, D., Saksena, G., Sivachenko, A., et al. (2011) · Nature Genetics · doi:10.1038/ng.936 · Cited by 312
Self-citationYip, S. S. F., Butterfield, Y. S. N., Morozova, O., Chittaranjan, S., Blough, M. D., An, J., Birol, İ., Chesnelong, C., Chiu, R., Chuah, E., et al. (2011) · The Journal of Pathology · doi:10.1002/path.2995 · Cited by 315
Essential Gene Profiles in Breast, Pancreatic, and Ovarian Cancer Cells
Marcotte, R., Brown, K. R., Suárez, F., Sayad, A., Karamboulas, K., Krzyzanowski, P. M., Sircoulomb, F., Medrano, M., Fedyshyn, Y., Koh, J. L. Y., et al. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0224 · Cited by 303
Determinants of Mutation Rate Variation in the Human Germline
Ségurel, L., Wyman, M. J., & Przeworski, M. (2014) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-031714-125740 · Cited by 289
Genomics and the Continuum of Cancer Care
McDermott, U., Downing, J. R., & Stratton, M. R. (2011) · New England Journal of Medicine · doi:10.1056/nejmra0907178 · Cited by 299
Self-citationRates, distribution and implications of postzygotic mosaic mutations in autism spectrum disorder
Lim, E. T., Uddin, M., De Rubeis, S., Chan, Y., Kamumbu, A. S., Zhang, X., D'Gama, A. M., Kim, S. N., Hill, R. S., Goldberg, A. P., et al. (2017) · Nature Neuroscience · doi:10.1038/nn.4598 · Cited by 299
Genomic Characterization of Upper Tract Urothelial Carcinoma
Sfakianos, J. P., Cha, E. K., Iyer, G., Scott, S. N., Zabor, E. C., Shah, R. H., Ren, Q., Bagrodia, A., Kim, P. H., Hakimi, A. A., et al. (2015) · European Urology · doi:10.1016/j.eururo.2015.07.039 · Cited by 288
Mutational Signature of Aristolochic Acid Exposure as Revealed by Whole-Exome Sequencing
Hoang, M. L., Chen, C., Sidorenko, V. S., He, J., Dickman, K. G., Yun, B. H., Moriya, M., Niknafs, N., Douville, C. B., Karchin, R., et al. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3006200 · Cited by 285
Translesion DNA Synthesis and Mutagenesis in Eukaryotes
Sale, J. E. (2013) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a012708 · Cited by 282
High-resolution characterization of a hepatocellular carcinoma genome
Totoki, Y., Tatsuno, K., Yamamoto, S., Arai, Y., Hosoda, F., Ishikawa, S., Tsutsumi, S., Sonoda, K., Totsuka, H., Shirakihara, T., et al. (2011) · Nature Genetics · doi:10.1038/ng.804 · Cited by 284
Turning ecology and evolution against cancer
Korolev, K. S., Xavier, J. B., & Gore, J. (2014) · Nature reviews. Cancer · doi:10.1038/nrc3712 · Cited by 277
The molecular pathology of cancer
Harris, T., & McCormick, F. P. (2010) · Nature Reviews Clinical Oncology · doi:10.1038/nrclinonc.2010.41 · Cited by 286
Flockhart, R. J., Webster, D. E., Qu, K., Mascarenhas, N., Kovalski, J., Kretz, M., & Khavari, P. A. (2012) · Genome Research · doi:10.1101/gr.140061.112 · Cited by 277
Ha, G., Roth, A. J. L., Lai, D., Bashashati, A., Ding, J., Goya, R., Giuliany, R., Rosner, J., Oloumi, A., Shumansky, K., et al. (2012) · Genome Research · doi:10.1101/gr.137570.112 · Cited by 269
Boeva, V., Zinovyev, A. Y., Kevin Bleakley, A., Vert, J., Janoueix‐Lerosey, I., Delattre, O., & Barillot, E. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq635 · Cited by 265
Temporal Dissection of Tumorigenesis in Primary Cancers
Durinck, S., Ho, C., Wang, N. J., Liao, W. J., Jakkula, L. R., Collisson, E. A., Pons, J., Chan, S.-W., Lam, E. T., Chu, C., et al. (2011) · Cancer Discovery · doi:10.1158/2159-8290.cd-11-0028 · Cited by 271
Kumar, A., White, T. A., MacKenzie, A. P., Clegg, N. J., Lee, C., Dumpit, R. F., Coleman, I. M., Ng, S. B. H., Salipante, S. J., Rieder, M. J., et al. (2011) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1108745108 · Cited by 260
Morganti, S., Tarantino, P., Ferraro, E., D’Amico, P., Duso, B. A., & Curigliano, G. (2019) · Advances in Experimental Medicine and Biology · doi:10.1007/978-3-030-24100-1_2 · Cited by 246
Chronic Obstructive Pulmonary Disease and Lung Cancer: New Molecular Insights
Adcock, I. M., Caramori, G., & Barnes, P. J. (2011) · Respiration · doi:10.1159/000324601 · Cited by 257
The topography of mutational processes in breast cancer genomes
Morganella, S., Alexandrov, L. B., Głodzik, D., Zou, X., Davies, H. R., Staaf, J., Sieuwerts, A. M., Brinkman, A. B., Martin, S., Ramakrishna, M., et al. (2016) · Nature Communications · doi:10.1038/ncomms11383 · Cited by 252
Self-citationTERT Promoter Mutation Status as an Independent Prognostic Factor in Cutaneous Melanoma
Griewank, K., Murali, R., Puig‐Butillé, J. A., Schilling, B., Livingstone, E., Potrony, M., Carrera, C., Schimming, T. T., Möller, I., Schwamborn, M., et al. (2014) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/dju246 · Cited by 251
Somatic Mutations Reveal Lineage Relationships and Age-Related Mutagenesis in Human Hematopoiesis
Osorio, F. G., Huber, A. R., Oka, R., Verheul, M., Patel, S. H., Hasaart, K., de la Fonteijne, L., Varela, I., Camargo, F. D., & van Boxtel, R. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.11.014 · Cited by 246
Self-citationOncogene addiction as a foundational rationale for targeted anti‐cancer therapy: promises and perils
Torti, D., & Trusolino, L. (2011) · EMBO Molecular Medicine · doi:10.1002/emmm.201100176 · Cited by 257
Somatic TP53 Mutations in the Era of Genome SequencingPreprint
Hainaut, P. L., & Pfeifer, G. P. (2016) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a026179 · Cited by 256
Timmermann, B., Kerick, M., Roehr, C., Fischer, A., Isau, M., Boerno, S. T., Wunderlich, A., Barmeyer, C., Seemann, P., Koenig, J., et al. (2010) · PLoS ONE · doi:10.1371/journal.pone.0015661 · Cited by 246
The human health effects of ozone depletion and interactions with climate change
Norval, M., Lucas, R. M., Cullen, A. P., de Gruijl, F. R., Longstreth, J. D., Takizawa, Y., & van der Leun, J. C. (2011) · Photochemical & Photobiological Sciences · doi:10.1039/c0pp90044c · Cited by 251
Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing
Reumers, J., Rijk, P. D., Zhao, H., Liekens, A. M. L., Smeets, D., Cleary, J., Loo, P. V., Bossche, M. J. A. V. D., Catthoor, K., Sabbe, B., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.2053 · Cited by 239
Lung Cancer Cell Lines as Tools for Biomedical Discovery and Research
Gazdar, A. F., Girard, L., Lockwood, W. W., Lam, W. L., & Minna, J. D. (2010) · JNCI Journal of the National Cancer Institute · doi:10.1093/jnci/djq279 · Cited by 240
Key Principles and Clinical Applications of “Next-Generation” DNA Sequencing
Rizzo, J. M., & Buck, M. J. (2012) · Cancer Prevention Research · doi:10.1158/1940-6207.capr-11-0432 · Cited by 251
Cheng, L., Hansen, N. F., Zhao, L., Du, Y., Zou, C., Donovan, F. X., Chou, B.-K., Zhou, G., Li, S., Dowey, S. N., et al. (2012) · Cell stem cell · doi:10.1016/j.stem.2012.01.005 · Cited by 242
Mechanisms of UV-induced mutations and skin cancer
Pfeifer, G. P. (2020) · Genome Instability & Disease · doi:10.1007/s42764-020-00009-8 · Cited by 237
Jiang, P., Sun, K., Tong, Y. K., Cheng, S. H., Cheng, T. H. T., Heung, M. M. S., Wong, J., Wong, V. W., Chan, H. L., Chan, K. C. A., et al. (2018) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1814616115 · Cited by 233
Biomarkers of platinum resistance in ovarian cancer: what can we use to improve treatment
van Zyl, B., Tang, D., & Bowden, N. A. (2018) · Endocrine Related Cancer · doi:10.1530/erc-17-0336 · Cited by 234
Furney, S. J., Turajlic, S., Stamp, G., Nohadani, M., Carlisle, A., Thomas, J. M., Hayes, A. J., Strauß, D., Gore, M. E., van den Oord, J., et al. (2013) · The Journal of Pathology · doi:10.1002/path.4204 · Cited by 233
Clinical Implications of the Cancer Genome
MacConaill, L. E., & Garraway, L. A. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2009.27.4944 · Cited by 234
Heemskerk, B., Kvistborg, P., & Schumacher, T. N. (2012) · The EMBO Journal · doi:10.1038/emboj.2012.333 · Cited by 239
Measuring the exposome: A powerful basis for evaluating environmental exposures and cancer risk
Wild, C. P., Scalbert, A., & Herceg, Z. (2013) · Environmental and Molecular Mutagenesis · doi:10.1002/em.21777 · Cited by 239
Jones, D., Raine, K. M., Davies, H. R., Tarpey, P. S., Butler, A. P., Teague, J. W., Nik‐Zainal, S., & Campbell, P. J. (2016) · Current Protocols in Bioinformatics · doi:10.1002/cpbi.20 · Cited by 207
Self-citationDamsky, W., Rosenbaum, L. E., & Bosenberg, M. (2010) · Cancers · doi:10.3390/cancers3010126 · Cited by 233
Reference standards for next-generation sequencing
Hardwick, S. A., Deveson, I. W., & Mercer, T. R. (2017) · Nature Reviews Genetics · doi:10.1038/nrg.2017.44 · Cited by 227
Tian, Q., Price, N. D., & Hood, L. (2012) · Journal of Internal Medicine · doi:10.1111/j.1365-2796.2011.02498.x · Cited by 224
Kim, I., & He, Y. (2014) · Genes & Diseases · doi:10.1016/j.gendis.2014.08.005 · Cited by 231
Error-prone translesion synthesis mediates acquired chemoresistance
Xie, K., Doles, J. D., Hemann, M. T., & Walker, G. C. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1011412107 · Cited by 228
Translating Tumor Antigens into Cancer Vaccines
Buonaguro, L., Petrizzo, A., Tornesello, M. L., & Buonaguro, L. (2010) · Clinical and Vaccine Immunology · doi:10.1128/cvi.00286-10 · Cited by 229
Evidence of non-random mutation rates suggests an evolutionary risk management strategy
Martincorena, I., Seshasayee, A. S. N., & Luscombe, N. M. (2012) · Nature · doi:10.1038/nature10995 · Cited by 219
The genome as a record of environmental exposure
Nik‐Zainal, S., Kucab, J. E., Morganella, S., Głodzik, D., Alexandrov, L. B., Arlt, V. M., Weninger, A., Hollstein, M. C., Stratton, M. R., & Phillips, D. H. (2015) · Mutagenesis · doi:10.1093/mutage/gev073 · Cited by 209
Self-citationRusch, M., Nakitandwe, J., Shurtleff, S. A., Newman, S., Zhang, Z., Edmonson, M. N., Parker, M. D., Jiao, Y., Ma, X., Liu, Y., et al. (2018) · Nature Communications · doi:10.1038/s41467-018-06485-7 · Cited by 219
Accurate and comprehensive sequencing of personal genomes.Preprint
Ajay, S., Parker, S., Abaan, H., Fuentes-Fajardo, K., & Margulies, E. (2011) · Genome Research · doi:10.1101/gr.123638.111 · Cited by 233
Microsatellite instability: an update
Yamamoto, H., & Imai, K. (2015) · Archives of Toxicology · doi:10.1007/s00204-015-1474-0 · Cited by 247
Chromothripsis: A New Mechanism for Rapid Karyotype Evolution
Leibowitz, M. L., Zhang, C., & Pellman, D. S. (2015) · Annual Review of Genetics · doi:10.1146/annurev-genet-120213-092228 · Cited by 205
Evaluation of the association of chronic inflammation and cancer: Insights and implications
Nigam, M., Mishra, A. P., Deb, V. K., Dimri, D. B., Tiwari, V., BUNGAU, S. G., Bungău, A. F., & Radu, A.-F. (2023) · Biomedicine & Pharmacotherapy · doi:10.1016/j.biopha.2023.115015 · Cited by 224
Comprehensive Genomic Characterization of RNA-Binding Proteins across Human Cancers
Wang, Z., Li, B., Luo, Y.-X., Lin, Q., Liu, S., Zhang, X., Zhou, H., Yang, J., & Qu, L. (2018) · Cell Reports · doi:10.1016/j.celrep.2017.12.035 · Cited by 209
Differential DNA repair underlies mutation hotspots at active promoters in cancer genomes
Perera, D. S., Poulos, R. C., Shah, A., Beck, D., Pimanda, J. E., & Wong, J. W. H. (2016) · Nature · doi:10.1038/nature17437 · Cited by 199
Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing eventsPreprint
Liu, J., Lee, W., Jiang, Z., Chen, Z., Jhunjhunwala, S., Haverty, P. M., Gnad, F., Guan, Y., Gilbert, H., Stinson, J., et al. (2012) · Genome Research · doi:10.1101/gr.140988.112 · Cited by 208
Nathanson, K. L., Martin, A., Wubbenhorst, B. S., Greshock, J. D., Letrero, R., D'Andrea, K. P., O'Day, S. J., Infante, J. R., Falchook, G. S., Arkenau, H., et al. (2013) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-13-0827 · Cited by 200
McBride, D. J., Orpana, A., Sotiriou, C. P., Joensuu, H., Stephens, P. J., Mudie, L. J., Hämäläinen, E., Stebbings, L. A., Andersson, L. C., Flanagan, A. M., et al. (2010) · Genes Chromosomes and Cancer · doi:10.1002/gcc.20815 · Cited by 194
Self-citationGenome-wide kinetics of DNA excision repair in relation to chromatin state and mutagenesis
Adar, S., Hu, J., Lieb, J. D., & Sancar, A. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1603388113 · Cited by 195
Meier, B., Cooke, S. L., Weiss, J., Bailly, A., Alexandrov, L. B., Marshall, J., Raine, K. M., Maddison, M., Anderson, E. L., Stratton, M. R., et al. (2014) · Genome Research · doi:10.1101/gr.175547.114 · Cited by 187
Self-citationOlsen, C. M., Wilson, L. F., Green, A. C., Bain, C. J., Fritschi, L., Neale, R. Ε., & Whiteman, D. C. (2015) · Australian and New Zealand Journal of Public Health · doi:10.1111/1753-6405.12470 · Cited by 198
Cancer Genomics: Technology, Discovery, and Translation
Tran, B., Dancey, J. E., Kamel‐Reid, S., McPherson, J. D., Bedard, P. L., Brown, A. M. K., Zhang, T., Shaw, P. H., Onetto-Pothier, N., Stein, L. D., et al. (2012) · Journal of Clinical Oncology · doi:10.1200/jco.2011.39.2316 · Cited by 188
Acquired and intrinsic BRAF inhibitor resistance in BRAF V600E mutant melanoma
Smalley, I., Paraiso, K. H. T., & Smalley, K. S. M. (2011) · Biochemical Pharmacology · doi:10.1016/j.bcp.2011.05.015 · Cited by 194
Meng, B., Hoang, L. N., McIntyre, J. B., Duggan, M. A., Nelson, G. S., Lee, C., & Köbel, M. (2014) · Gynecologic Oncology · doi:10.1016/j.ygyno.2014.05.006 · Cited by 182
Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology
Cottrell, C. E., Al‐Kateb, H., Bredemeyer, A. J., Duncavage, E. J., Spencer, D. H., Abel, H., Lockwood, C. M., Hagemann, I. S., O’Guin, S. M., Burcea, L. C., et al. (2013) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2013.10.002 · Cited by 187
Huang, S. (2013) · Cancer and Metastasis Reviews · doi:10.1007/s10555-013-9435-7 · Cited by 183
Kerick, M., Isau, M., Timmermann, B., Sültmann, H., Herwig, R., Krobitsch, S., Schaefer, G., Verdorfer, I., Bartsch, G. H., Klocker, H., et al. (2011) · BMC Medical Genomics · doi:10.1186/1755-8794-4-68 · Cited by 181
Next-generation sequencing and its applications in molecular diagnostics
Su, Z., Ning, B., Fang, H., Hong, H., Perkins, R., Tong, W., & Shi, L. M. (2011) · Expert Review of Molecular Diagnostics · doi:10.1586/erm.11.3 · Cited by 193
BreakDancer: Identification of Genomic Structural Variation from Paired‐End Read Mapping
Fan, X., Abbott, T. E., Larson, D. E., & Chen, K. (2014) · Current Protocols in Bioinformatics · doi:10.1002/0471250953.bi1506s45 · Cited by 181
Genomic rearrangements in inherited disease and cancer
Chen, J., Cooper, D. N., Férec, C., Kehrer‐Sawatzki, H., & Patrinos, G. P. (2010) · Seminars in Cancer Biology · doi:10.1016/j.semcancer.2010.05.007 · Cited by 181
Antigen Spreading Contributes to MAGE Vaccination-Induced Regression of Melanoma Metastases
Corbière, V., Chapiro, J., Stroobant, V., Ma, W., Lurquin, C., Lethé, B., van Baren, N., den Eynde, B. J. V., Boon, T., & Coulie, P. G. (2011) · Cancer Research · doi:10.1158/0008-5472.can-10-2693 · Cited by 176
Evidence for recent, population-specific evolution of the human mutation rate
Harris, K. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418652112 · Cited by 165
Cancer Stem Cell Immunology: Key to Understanding Tumorigenesis and Tumor Immune Escape?
Bruttel, V. S., & Wischhusen, J. (2014) · Frontiers in Immunology · doi:10.3389/fimmu.2014.00360 · Cited by 177
From complete genome sequence to ‘complete’ understanding?
Galperin, M. Y., & Koonin, E. V. (2010) · Trends in biotechnology · doi:10.1016/j.tibtech.2010.05.006 · Cited by 183
Metadata
- Authors
- Pleasance, E. D., Cheetham, R. K., Stephens, P. J., McBride, D. J., Humphray, S. J., Greenman, C. D., Varela, I., Lin, M.-L., Ordóñez, G. R., Bignell, G. R., Ye, K., Alipaz, J., Bauer, M. J., Beare, D., Butler, A., Carter, R. J., Chen, L., Cox, A. J., Edkins, S., Kokko-Gonzales, P. I., Gormley, N. A., Grocock, R. J., Haudenschild, C. D., Hims, M. M., James, T., Jia, M., Kingsbury, Z., Leroy, C., Marshall, J., Menzies, A., Mudie, L. J., Ning, Z., Royce, T., Schulz-Trieglaff, O. B., Spiridou, A., Stebbings, L. A., Szajkowski, L., Teague, J., Williamson, D., Chin, L., Ross, M. T., Campbell, P. J., Bentley, D. R., Futreal, P. A., & Stratton, M. R.
- Affiliations
- Wellcome Sanger Institute (GB)
- Illumina (United Kingdom) (GB)
- Leiden University Medical Center (NL)
- Illumina (United States) (US)
- Dana-Farber Cancer Institute (US)
- Institute of Cancer Research (GB)
- Corresponding author
- Futreal, P. Andrew
- Stratton, Michael R.
- ORCID
- Pleasance, Erin D.
- McBride, David J.
- Humphray, Sean J.
- Greenman, Chris D.
- Varela, Ignacio
- Lin, Meng-Lay
- Ye, Kai
- Bauer, Markus J.
- Chen, Lina
- Edkins, Sarah
- James, Terena
- Jia, Mingming
- Marshall, John
- Menzies, Andrew
- Ning, Zemin
- Spiridou, Anastassia
- Teague, Jon
- Ross, Mark T.
- Campbell, Peter J.
- Futreal, P. Andrew
- Stratton, Michael R.
- Venue
- Nature
- Published
- 2009-12-16
- Volume
- 463
- Issue
- 7278
- Pages
- 191-196
- ISSN
- 0028-0836 (ISSN-L)
- 1476-4687
- PMC
- PMC3145108
- OpenAlex
- W2150677022
- Cited by
- 1,696
- References
- 43
- Citations by year
- 2026: 23 · 2025: 47 · 2024: 43 · 2023: 49 · 2022: 50 · 2021: 83 · 2020: 76 · 2019: 87 · 2018: 69 · 2017: 94 · 2016: 121 · 2015: 116 · 2014: 144 · 2013: 166 · 2012: 189
- FWCI
- 58.62
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Nature (publishedVersion, cc-by-nc-sa)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Data Archiving and Networked Services (DANS) (submittedVersion)
- RePEc: Research Papers in Economics (submittedVersion)
- Leiden Repository (Leiden University) (submittedVersion)
- UEA Digital Repository (University of East Anglia) (submittedVersion)
- Funders
- Wellcome Trust (077012/Z/05/Z, 077012, 088340, 093867)
- Kay Kendall Leukaemia Fund
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Chromatin Remodeling and Cancer
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › DNA Repair Mechanisms
- Keywords
- somatic mutations, mutational signatures, melanoma, lymphoblastoid cell lines, DNA repair, small cell lung cancer, tobacco smoke carcinogens, driver mutations, passenger mutations, cancer genome evolution
- MeSH terms
- Adult, DNA Damage, DNA Mutational Analysis, DNA Repair, Humans, Male, Melanoma, Mutation, Neoplasms, Ultraviolet Rays, Genome, Human, Mutagenesis, Insertional, Sequence Deletion, Gene Dosage, Loss of Heterozygosity, Polymorphism, Single Nucleotide, MicroRNAs, Cell Line, Tumor, Genes, Neoplasm, Precision Medicine
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
