The genomic landscape of 2,023 colorectal cancers.


Journal

Nature
ISSN: 1476-4687
Titre abrégé: Nature
Pays: England
ID NLM: 0410462

Informations de publication

Date de publication:
07 Aug 2024
Historique:
received: 14 11 2022
accepted: 24 06 2024
medline: 8 8 2024
pubmed: 8 8 2024
entrez: 7 8 2024
Statut: aheadofprint

Résumé

Colorectal carcinoma (CRC) is a common cause of mortality

Identifiants

pubmed: 39112709
doi: 10.1038/s41586-024-07747-9
pii: 10.1038/s41586-024-07747-9
doi:

Types de publication

Journal Article

Langues

eng

Sous-ensembles de citation

IM

Informations de copyright

© 2024. The Author(s).

Références

Sung, H. et al. Global Cancer Statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J. Clin. 71, 209–249 (2021).
pubmed: 33538338 doi: 10.3322/caac.21660
Bailey, M. H. et al. Comprehensive characterization of cancer driver genes and mutations. Cell 173, 371–385.e18 (2018).
pubmed: 29625053 pmcid: 6029450 doi: 10.1016/j.cell.2018.02.060
Giannakis, M. et al. Genomic correlates of immune-cell infiltrates in colorectal carcinoma. Cell Rep. 15, 857–865 (2016).
pubmed: 27149842 pmcid: 4850357 doi: 10.1016/j.celrep.2016.03.075
Grasso, C. S. et al. Genetic mechanisms of immune evasion in colorectal cancer. Cancer Discov. 8, 730–749 (2018).
pubmed: 29510987 pmcid: 5984687 doi: 10.1158/2159-8290.CD-17-1327
Liu, Y. et al. Comparative molecular analysis of gastrointestinal adenocarcinomas. Cancer Cell 33, 721–735.e8 (2018).
pubmed: 29622466 pmcid: 5966039 doi: 10.1016/j.ccell.2018.03.010
Martincorena, I. et al. Universal patterns of selection in cancer and somatic tissues. Cell 171, 1029–1041.e21 (2017).
pubmed: 29056346 pmcid: 5720395 doi: 10.1016/j.cell.2017.09.042
TCGA Network. Comprehensive molecular characterization of human colon and rectal cancer. Nature 487, 330–337 (2012).
doi: 10.1038/nature11252
Seshagiri, S. et al. Recurrent R-spondin fusions in colon cancer. Nature 488, 660–664 (2012).
pubmed: 22895193 pmcid: 3690621 doi: 10.1038/nature11282
Yaeger, R. et al. Clinical sequencing defines the genomic landscape of metastatic colorectal cancer. Cancer Cell 33, 125–136.e3 (2018).
pubmed: 29316426 pmcid: 5765991 doi: 10.1016/j.ccell.2017.12.004
Pleguezuelos-Manzano, C. et al. Mutational signature in colorectal cancer caused by genotoxic pks
pubmed: 32106218 pmcid: 8142898 doi: 10.1038/s41586-020-2080-8
Degasperi, A. et al. Substitution mutational signatures in whole-genome-sequenced cancers in the UK population. Science 376, science.abl9283 (2022).
Islam, S. M. A. et al. Uncovering novel mutational signatures by de novo extraction with SigProfilerExtractor. Cell Genom. 2, 100179 (2022).
pubmed: 36388765 pmcid: 9646490 doi: 10.1016/j.xgen.2022.100179
Priestley, P. et al. Pan-cancer whole-genome analyses of metastatic solid tumours. Nature 575, 210–216 (2019).
pubmed: 31645765 pmcid: 6872491 doi: 10.1038/s41586-019-1689-y
Angelova, M. et al. Characterization of the immunophenotypes and antigenomes of colorectal cancers reveals distinct tumor escape mechanisms and novel targets for immunotherapy. Genome Biol. 16, 64 (2015).
pubmed: 25853550 pmcid: 4377852 doi: 10.1186/s13059-015-0620-6
Alexandrov, L. B. et al. The repertoire of mutational signatures in human cancer. Nature 578, 94–101 (2020).
pubmed: 32025018 pmcid: 7054213 doi: 10.1038/s41586-020-1943-3
Li, Y. et al. Patterns of somatic structural variation in human cancer genomes. Nature 578, 112–121 (2020).
pubmed: 32025012 pmcid: 7025897 doi: 10.1038/s41586-019-1913-9
Bergstrom, E. N. et al. SigProfilerMatrixGenerator: a tool for visualizing and exploring patterns of small mutational events. BMC Genomics 20, 685 (2019).
pubmed: 31470794 pmcid: 6717374 doi: 10.1186/s12864-019-6041-2
Martínez-Jiménez, F. et al. A compendium of mutational cancer driver genes. Nat. Rev. Cancer 20, 555–572 (2020).
pubmed: 32778778 doi: 10.1038/s41568-020-0290-x
Guo, Y. J. et al. ERK/MAPK signalling pathway and tumorigenesis. Exp. Ther. Med. 19, 1997–2007 (2020).
pubmed: 32104259 pmcid: 7027163
Maruvka, Y. E. et al. Analysis of somatic microsatellite indels identifies driver events in human tumors. Nat. Biotechnol. 35, 951–959 (2017).
pubmed: 28892075 pmcid: 9123850 doi: 10.1038/nbt.3966
Orlando, G., Kinnersley, B. & Houlston, R. S. Capture Hi-C library generation and analysis to detect chromatin interactions. Curr. Protoc. Hum. Genet. https://doi.org/10.1002/cphg.63 (2018).
Cocco, E. et al. Colorectal carcinomas containing hypermethylated MLH1 promoter and wild-type BRAF/KRAS are enriched for targetable kinase fusions. Cancer Res. 79, 1047–1053 (2019).
pubmed: 30643016 pmcid: 6420871 doi: 10.1158/0008-5472.CAN-18-3126
Giacomini, C. P. et al. Breakpoint analysis of transcriptional and genomic profiles uncovers novel gene fusions spanning multiple human cancer types. PLoS Genet. 9, e1003464 (2013).
pubmed: 23637631 pmcid: 3636093 doi: 10.1371/journal.pgen.1003464
Inaki, K. et al. Transcriptional consequences of genomic structural aberrations in breast cancer. Genome Res. 21, 676–687 (2011).
pubmed: 21467264 pmcid: 3083084 doi: 10.1101/gr.113225.110
Orlando, G. et al. Promoter capture Hi-C-based identification of recurrent noncoding mutations in colorectal cancer. Nat. Genet. 50, 1375–1380 (2018).
pubmed: 30224643 pmcid: 6380472 doi: 10.1038/s41588-018-0211-z
Delhommeau, F. et al. Mutation in TET2 in myeloid cancers. N. Engl. J. Med. 360, 2289–2301 (2009).
pubmed: 19474426 doi: 10.1056/NEJMoa0810069
Böhm, J. et al. Loss of enhancer of zeste homologue 2 (EZH2) at tumor invasion front is correlated with higher aggressiveness in colorectal cancer cells. J. Cancer Res. Clin. Oncol. 145, 2227–2240 (2019).
pubmed: 31317325 pmcid: 6708512 doi: 10.1007/s00432-019-02977-1
Kavanagh, E. & Joseph, B. The hallmarks of CDKN1C (p57, KIP2) in cancer. Biochim. Biophys. Acta 1816, 50–56 (2011).
pubmed: 21447370
Deshpande, V. et al. Exploring the landscape of focal amplifications in cancer using AmpliconArchitect. Nat. Commun. 10, 392 (2019).
pubmed: 30674876 pmcid: 6344493 doi: 10.1038/s41467-018-08200-y
Kim, H. et al. Extrachromosomal DNA is associated with oncogene amplification and poor outcome across multiple cancers. Nat. Genet. 52, 891–897 (2020).
pubmed: 32807987 pmcid: 7484012 doi: 10.1038/s41588-020-0678-2
Gerstung, M. et al. The evolutionary history of 2,658 cancers. Nature 578, 122–128 (2020).
pubmed: 32025013 pmcid: 7054212 doi: 10.1038/s41586-019-1907-7
Bielski, C. M. et al. Genome doubling shapes the evolution and prognosis of advanced cancers. Nat. Genet. 50, 1189–1195 (2018).
pubmed: 30013179 pmcid: 6072608 doi: 10.1038/s41588-018-0165-1
Sztupinszki, Z. et al. Migrating the SNP array-based homologous recombination deficiency measures to next generation sequencing data of breast cancer. NPJ Breast Cancer 4, 16 (2018).
pubmed: 29978035 pmcid: 6028448 doi: 10.1038/s41523-018-0066-6
Mermel, C. H. et al. GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol. 12, R41 (2011).
pubmed: 21527027 pmcid: 3218867 doi: 10.1186/gb-2011-12-4-r41
Palmqvist, R. et al. hTERT gene copy number is not associated with hTERT RNA expression or telomerase activity in colorectal cancer. Int. J. Cancer 116, 395–400 (2005).
pubmed: 15818616 doi: 10.1002/ijc.21020
Chen, E. Y. et al. Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool. BMC Bioinformatics 14, 128 (2013).
pubmed: 23586463 pmcid: 3637064 doi: 10.1186/1471-2105-14-128
Domingo, E. et al. Somatic POLE proofreading domain mutation, immune response, and prognosis in colorectal cancer: a retrospective, pooled biomarker study. Lancet Gastroenterol. Hepatol. 1, 207–216 (2016).
pubmed: 28404093 doi: 10.1016/S2468-1253(16)30014-0
Wallis, C. J. et al. Second malignancies after radiotherapy for prostate cancer: systematic review and meta-analysis. BMJ 352, i851 (2016).
pubmed: 26936410 pmcid: 4775870 doi: 10.1136/bmj.i851
Schumacher, T. N. & Schreiber, R. D. Neoantigens in cancer immunotherapy. Science 348, 69–74 (2015).
pubmed: 25838375 doi: 10.1126/science.aaa4971
Marty, R. et al. MHC-I genotype restricts the oncogenic mutational landscape. Cell 171, 1272–1283.e15 (2017).
pubmed: 29107334 pmcid: 5711564 doi: 10.1016/j.cell.2017.09.050
Xie, T. et al. A comprehensive characterization of genome-wide copy number aberrations in colorectal cancer reveals novel oncogenes and patterns of alterations. PLoS ONE 7, e42001 (2012).
pubmed: 22860045 pmcid: 3409212 doi: 10.1371/journal.pone.0042001
Lakatos, E. et al. Evolutionary dynamics of neoantigens in growing tumors. Nat. Genet. 52, 1057–1066 (2020).
pubmed: 32929288 pmcid: 7610467 doi: 10.1038/s41588-020-0687-1
Li, F. Y. & Lai, M. D. Colorectal cancer, one entity or three. J. Zhejiang Univ. Sci. B 10, 219–229 (2009).
pubmed: 19283877 pmcid: 2650032 doi: 10.1631/jzus.B0820273
Lee-Six, H. et al. The landscape of somatic mutation in normal colorectal epithelial cells. Nature 574, 532–537 (2019).
pubmed: 31645730 doi: 10.1038/s41586-019-1672-7
Jackstadt, R. et al. Epithelial NOTCH signaling rewires the tumor microenvironment of colorectal cancer to drive poor-prognosis subtypes and metastasis. Cancer Cell 36, 319–336.e7 (2019).
pubmed: 31526760 pmcid: 6853173 doi: 10.1016/j.ccell.2019.08.003
Ugai, T. et al. Is early-onset cancer an emerging global epidemic? Current evidence and future implications. Nat. Rev. Clin. Oncol. 19, 656–673 (2022).
pubmed: 36068272 pmcid: 9509459 doi: 10.1038/s41571-022-00672-8
Vuik, F. E. et al. Increasing incidence of colorectal cancer in young adults in Europe over the last 25 years. Gut 68, 1820–1826 (2019).
pubmed: 31097539 doi: 10.1136/gutjnl-2018-317592
Alexandrov, L. B. et al. Clock-like mutational processes in human somatic cells. Nat. Genet. 47, 1402–1407 (2015).
pubmed: 26551669 pmcid: 4783858 doi: 10.1038/ng.3441
Turnbull, C. Introducing whole-genome sequencing into routine cancer care: the Genomics England 100000 Genomes Project. Ann. Oncol. 29, 784–787 (2018).
pubmed: 29462260 doi: 10.1093/annonc/mdy054
Turnbull, C. et al. The 100 000 Genomes Project: bringing whole genome sequencing to the NHS. BMJ 361, k1687 (2018).
pubmed: 29691228 doi: 10.1136/bmj.k1687
Robbe, P. et al. Whole genome landscape of chronic lymphocytic leukaemia and its association with clinical outcome. Nat. Genet. 54, 1675–1689 (2022).
pubmed: 36333502 pmcid: 9649442 doi: 10.1038/s41588-022-01211-y
Raczy, C. et al. Isaac: ultra-fast whole-genome secondary analysis on Illumina sequencing platforms. Bioinformatics 29, 2041–2043 (2013).
pubmed: 23736529 doi: 10.1093/bioinformatics/btt314
Karczewski, K. J. et al. The mutational constraint spectrum quantified from variation in 141,456 humans. Nature 581, 434–443 (2020).
pubmed: 32461654 pmcid: 7334197 doi: 10.1038/s41586-020-2308-7
Tate, J. G. et al. COSMIC: the Catalogue Of Somatic Mutations In Cancer. Nucleic Acids Res. 47, D941–D947 (2019).
pubmed: 30371878 doi: 10.1093/nar/gky1015
Benson, G. Tandem repeats finder: a program to analyze DNA sequences. Nucleic Acids Res. 27, 573–580 (1999).
pubmed: 9862982 pmcid: 148217 doi: 10.1093/nar/27.2.573
Jamal-Hanjani, M. et al. Tracking genomic cancer evolution for precision medicine: the lung TRACERx study. PLoS Biol. 12, e1001906 (2014).
pubmed: 25003521 pmcid: 4086714 doi: 10.1371/journal.pbio.1001906
Cornish, A. J. et al. Reference bias in the Illumina Isaac aligner. Bioinformatics 36, 4671–4672 (2020).
pubmed: 32437525 pmcid: 7653636 doi: 10.1093/bioinformatics/btaa514
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).
pubmed: 24987110 doi: 10.1373/clinchem.2014.223677
Beier, S., Thiel, T., Münch, T., Scholz, U. & Mascher, M. MISA-web: a web server for microsatellite prediction. Bioinformatics 33, 2583–2585 (2017).
pubmed: 28398459 pmcid: 5870701 doi: 10.1093/bioinformatics/btx198
Rayner, E. et al. A panoply of errors: polymerase proofreading domain mutations in cancer. Nat. Rev. Cancer 16, 71–81 (2016).
pubmed: 26822575 doi: 10.1038/nrc.2015.12
Nik-Zainal, S. et al. The life history of 21 breast cancers. Cell 149, 994–1007 (2012).
pubmed: 22608083 pmcid: 3428864 doi: 10.1016/j.cell.2012.04.023
Antonello, A. et al. Computational validation of clonal and subclonal copy number alterations from bulk tumor sequencing using CNAqc. Genome Biol. 25, 38 (2024).
pubmed: 38297376 pmcid: 10832148 doi: 10.1186/s13059-024-03170-5
Cmero, M. et al. Inferring structural variant cancer cell fraction. Nat. Commun. 11, 730 (2020).
pubmed: 32024845 pmcid: 7002525 doi: 10.1038/s41467-020-14351-8
Rausch, T. et al. DELLY: structural variant discovery by integrated paired-end and split-read analysis. Bioinformatics 28, i333–i339 (2012).
pubmed: 22962449 pmcid: 3436805 doi: 10.1093/bioinformatics/bts378
Layer, R. M., Chiang, C., Quinlan, A. R. & Hall, I. M. LUMPY: a probabilistic framework for structural variant discovery. Genome Biol. 15, R84 (2014).
pubmed: 24970577 pmcid: 4197822 doi: 10.1186/gb-2014-15-6-r84
Bignell, G. R. et al. Signatures of mutation and selection in the cancer genome. Nature 463, 893–898 (2010).
pubmed: 20164919 pmcid: 3145113 doi: 10.1038/nature08768
Chu, C. et al. Comprehensive identification of transposable element insertions using multiple sequencing technologies. Nat. Commun. 12, 3836 (2021).
pubmed: 34158502 pmcid: 8219666 doi: 10.1038/s41467-021-24041-8
Rodriguez-Martin, B. et al. Pan-cancer analysis of whole genomes identifies driver rearrangements promoted by LINE-1 retrotransposition. Nat. Genet. 52, 306–319 (2020).
pubmed: 32024998 pmcid: 7058536 doi: 10.1038/s41588-019-0562-0
Tubio, J. M. C. et al. Mobile DNA in cancer. Extensive transduction of nonrepetitive DNA mediated by L1 retrotransposition in cancer genomes. Science 345, 1251343 (2014).
pubmed: 25082706 pmcid: 4380235 doi: 10.1126/science.1251343
Saunders, C. T. et al. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 28, 1811–1817 (2012).
pubmed: 22581179 doi: 10.1093/bioinformatics/bts271
Jun, G. et al. Detecting and estimating contamination of human DNA samples in sequencing and array-based genotype data. Am. J. Hum. Genet. 91, 839–848 (2012).
pubmed: 23103226 pmcid: 3487130 doi: 10.1016/j.ajhg.2012.09.004
Dentro, S. C., Wedge, D. C. & Van Loo, P. Principles of reconstructing the subclonal architecture of cancers. Cold Spring Harb. Perspect. Med. https://doi.org/10.1101/cshperspect.a026625 (2017).
Nik-Zainal, S. et al. Landscape of somatic mutations in 560 breast cancer whole-genome sequences. Nature 534, 47–54 (2016).
pubmed: 27135926 pmcid: 4910866 doi: 10.1038/nature17676
Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet. 46, 310–315 (2014).
pubmed: 24487276 pmcid: 3992975 doi: 10.1038/ng.2892
Rentzsch, P., Witten, D., Cooper, G. M., Shendure, J. & Kircher, M. CADD: predicting the deleteriousness of variants throughout the human genome. Nucleic Acids Res. 47, D886–d894 (2019).
pubmed: 30371827 doi: 10.1093/nar/gky1016
Rentzsch, P., Schubach, M., Shendure, J. & Kircher, M. CADD-Splice—improving genome-wide variant effect prediction using deep learning-derived splice scores. Genome Med. 13, 31 (2021).
pubmed: 33618777 pmcid: 7901104 doi: 10.1186/s13073-021-00835-9
Christensen, S. et al. 5-Fluorouracil treatment induces characteristic T>G mutations in human cancer. Nat. Commun. 10, 4571 (2019).
pubmed: 31594944 pmcid: 6783534 doi: 10.1038/s41467-019-12594-8
Mularoni, L., Sabarinathan, R., Deu-Pons, J., Gonzalez-Perez, A. & López-Bigas, N. OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations. Genome Biol. 17, 128 (2016).
pubmed: 27311963 pmcid: 4910259 doi: 10.1186/s13059-016-0994-0
Arnedo-Pac, C., Mularoni, L., Muiños, F., Gonzalez-Perez, A. & Lopez-Bigas, N. OncodriveCLUSTL: a sequence-based clustering method to identify cancer drivers. Bioinformatics 35, 4788–4790 (2019).
pubmed: 31228182 pmcid: 6853674 doi: 10.1093/bioinformatics/btz501
Weghorn, D. & Sunyaev, S. Bayesian inference of negative and positive selection in human cancers. Nat. Genet. 49, 1785–1788 (2017).
pubmed: 29106416 doi: 10.1038/ng.3987
Dietlein, F. et al. Identification of cancer driver genes based on nucleotide context. Nat. Genet. 52, 208–218 (2020).
pubmed: 32015527 pmcid: 7031046 doi: 10.1038/s41588-019-0572-y
Tokheim, C. et al. Exome-scale discovery of hotspot mutation regions in human cancer using 3D protein structure. Cancer Res. 76, 3719–3731 (2016).
pubmed: 27197156 pmcid: 4930736 doi: 10.1158/0008-5472.CAN-15-3190
Burley, S. K. et al. RCSB Protein Data Bank: celebrating 50 years of the PDB with new tools for understanding and visualizing biological macromolecules in 3D. Protein Sci. 31, 187–208 (2022).
pubmed: 34676613 doi: 10.1002/pro.4213
Porta-Pardo, E. & Godzik, A. e-Driver: a novel method to identify protein regions driving cancer. Bioinformatics 30, 3109–3114 (2014).
pubmed: 25064568 pmcid: 4609017 doi: 10.1093/bioinformatics/btu499
Lever, J., Zhao, E. Y., Grewal, J., Jones, M. R. & Jones, S. J. M. CancerMine: a literature-mined resource for drivers, oncogenes and tumor suppressors in cancer. Nat. Methods 16, 505–507 (2019).
pubmed: 31110280 doi: 10.1038/s41592-019-0422-y
Neph, S. et al. BEDOPS: high-performance genomic feature operations. Bioinformatics 28, 1919–1920 (2012).
pubmed: 22576172 pmcid: 3389768 doi: 10.1093/bioinformatics/bts277
Chakravarty, D. et al. OncoKB: a precision oncology knowledge base. JCO Precis. Oncol. https://doi.org/10.1200/po.17.00011 (2017).
Zack, T. I. et al. Pan-cancer patterns of somatic copy number alteration. Nat. Genet. 45, 1134–1140 (2013).
pubmed: 24071852 pmcid: 3966983 doi: 10.1038/ng.2760
Dale, R. K., Pedersen, B. S. & Quinlan, A. R. Pybedtools: a flexible Python library for manipulating genomic datasets and annotations. Bioinformatics 27, 3423–3424 (2011).
pubmed: 21949271 pmcid: 3232365 doi: 10.1093/bioinformatics/btr539
Quinlan, A. R. & Hall, I. M. BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26, 841–842 (2010).
pubmed: 20110278 pmcid: 2832824 doi: 10.1093/bioinformatics/btq033
Feuerbach, L. et al. TelomereHunter—in silico estimation of telomere content and composition from cancer genomes. BMC Bioinformatics 20, 272 (2019).
pubmed: 31138115 pmcid: 6540518 doi: 10.1186/s12859-019-2851-0
Farmery, J. H. R., Smith, M. L. & Lynch, A. G. Telomerecat: a ploidy-agnostic method for estimating telomere length from whole genome sequencing data. Sci. Rep. 8, 1300 (2018).
pubmed: 29358629 pmcid: 5778012 doi: 10.1038/s41598-017-14403-y
Akdemir, K. C. et al. Disruption of chromatin folding domains by somatic genomic rearrangements in human cancer. Nat. Genet. 52, 294–305 (2020).
pubmed: 32024999 pmcid: 7058537 doi: 10.1038/s41588-019-0564-y
Cortés-Ciriano, I. et al. Comprehensive analysis of chromothripsis in 2,658 human cancers using whole-genome sequencing. Nat. Genet. 52, 331–341 (2020).
pubmed: 32025003 pmcid: 7058534 doi: 10.1038/s41588-019-0576-7
Korbel, J. O. & Campbell, P. J. Criteria for inference of chromothripsis in cancer genomes. Cell 152, 1226–1236 (2013).
pubmed: 23498933 doi: 10.1016/j.cell.2013.02.023
Csardi, G. & Nepusz, T. The Igraph software package for complex network research. InterJournal Complex Syst. 1695 (2005).
Glodzik, D. et al. A somatic-mutational process recurrently duplicates germline susceptibility loci and tissue-specific super-enhancers in breast cancers. Nat. Genet. 49, 341–348 (2017).
pubmed: 28112740 pmcid: 5988034 doi: 10.1038/ng.3771
Haeussler, M. et al. The UCSC Genome Browser database: 2019 update. Nucleic Acids Res. 47, D853–d858 (2019).
pubmed: 30407534 doi: 10.1093/nar/gky1095
She, X. et al. Shotgun sequence assembly and recent segmental duplications within the human genome. Nature 431, 927–930 (2004).
pubmed: 15496912 doi: 10.1038/nature03062
Weddington, N. et al. ReplicationDomain: a visualization tool and comparative database for genome-wide replication timing data. BMC Bioinformatics 9, 530 (2008).
pubmed: 19077204 pmcid: 2636809 doi: 10.1186/1471-2105-9-530
Moore, J. E. et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature 583, 699–710 (2020).
pubmed: 32728249 pmcid: 7410828 doi: 10.1038/s41586-020-2493-4
PCAWG Consortium. Pan-cancer analysis of whole genomes. Nature 578, 82–93 (2020).
doi: 10.1038/s41586-020-1969-6
Barlow, J. H. et al. Identification of early replicating fragile sites that contribute to genome instability. Cell 152, 620–632 (2013).
pubmed: 23352430 pmcid: 3629730 doi: 10.1016/j.cell.2013.01.006
Beroukhim, R. et al. The landscape of somatic copy-number alteration across human cancers. Nature 463, 899–905 (2010).
pubmed: 20164920 pmcid: 2826709 doi: 10.1038/nature08822
Le Tallec, B. et al. Common fragile site profiling in epithelial and erythroid cells reveals that most recurrent cancer deletions lie in fragile sites hosting large genes. Cell Rep. 4, 420–428 (2013).
pubmed: 23911288 doi: 10.1016/j.celrep.2013.07.003
Krijgsman, O., Benner, C., Meijer, G. A., van de Wiel, M. A. & Ylstra, B. FocalCall: an R package for the annotation of focal copy number aberrations. Cancer Inform. 13, 153–156 (2014).
pubmed: 25506197 pmcid: 4251178 doi: 10.4137/CIN.S19519
Iacocca, M. A. et al. ClinVar database of global familial hypercholesterolemia-associated DNA variants. Human Mutat. 39, 1631–1640 (2018).
doi: 10.1002/humu.23634
Ghosh, P. K. Box–Cox power transformation unconditional quantile regressions with an application on wage inequality. J. Appl. Stat. 48, 3086–3101 (2021).
pubmed: 35707252 doi: 10.1080/02664763.2020.1795817
Davies, H. et al. HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures. Nat. Med. 23, 517–525 (2017).
pubmed: 28288110 pmcid: 5833945 doi: 10.1038/nm.4292
Paczkowska, M. et al. Integrative pathway enrichment analysis of multivariate omics data. Nat. Commun. 11, 735 (2020).
pubmed: 32024846 pmcid: 7002665 doi: 10.1038/s41467-019-13983-9
Jassal, B. et al. The reactome pathway knowledgebase. Nucleic Acids Res. 48, D498–d503 (2020).
pubmed: 31691815
Canisius, S., Martens, J. W. & Wessels, L. F. A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence. Genome Biol. 17, 261 (2016).
pubmed: 27986087 pmcid: 5162102 doi: 10.1186/s13059-016-1114-x
Chiu, D. S. & Talhouk, A. diceR: an R package for class discovery using an ensemble driven approach. BMC Bioinformatics 19, 11 (2018).
pubmed: 29334888 pmcid: 5769335 doi: 10.1186/s12859-017-1996-y
Monti, S., Tamayo, P., Mesirov, J. & Golub, T. R. Consensus Clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach. Learn. 52, 91–118 (2003).
doi: 10.1023/A:1023949509487
Ward, J. H. Jr. Hierarchical grouping to optimize an objective function. J. Amer. Stat. Soc. Assoc. 58, 236–244 (1963).
doi: 10.1080/01621459.1963.10500845
Murtagh, F. & Legendre, P. Ward’s hierarchical agglomerative clustering method: which algorithms implement Ward’s criterion? J. Classif. 31, 274–295 (2014).
doi: 10.1007/s00357-014-9161-z
Shukla, S. A. et al. Comprehensive analysis of cancer-associated somatic mutations in class I HLA genes. Nat. Biotechnol. 33, 1152–1158 (2015).
pubmed: 26372948 pmcid: 4747795 doi: 10.1038/nbt.3344
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol. 31, 213–219 (2013).
pubmed: 23396013 pmcid: 3833702 doi: 10.1038/nbt.2514
McGranahan, N. et al. Allele-specific HLA loss and immune escape in lung cancer evolution. Cell 171, 1259–1271.e11 (2017).
pubmed: 29107330 pmcid: 5720478 doi: 10.1016/j.cell.2017.10.001
Rosenthal, R. et al. Neoantigen-directed immune escape in lung cancer evolution. Nature 567, 479–485 (2019).
pubmed: 30894752 pmcid: 6954100 doi: 10.1038/s41586-019-1032-7
Wang, H. et al. PCBP1 suppresses the translation of metastasis-associated PRL-3 phosphatase. Cancer Cell 18, 52–62 (2010).
pubmed: 20609352 doi: 10.1016/j.ccr.2010.04.028
Reynisson, B. et al. Improved prediction of MHC II antigen presentation through integration and motif deconvolution of mass spectrometry MHC eluted ligand data. J. Proteome Res. 19, 2304–2315 (2020).
pubmed: 32308001 doi: 10.1021/acs.jproteome.9b00874
Schenck, R. O., Lakatos, E., Gatenbee, C., Graham, T. A. & Anderson, A. R. A. NeoPredPipe: high-throughput neoantigen prediction and recognition potential pipeline. BMC Bioinformatics 20, 264 (2019).
pubmed: 31117948 pmcid: 6532147 doi: 10.1186/s12859-019-2876-4
Wang, K., Li, M. & Hakonarson, H. ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res. 38, e164 (2010).
pubmed: 20601685 pmcid: 2938201 doi: 10.1093/nar/gkq603
Benjamin, D. et al. Calling somatic SNVs and indels with Mutect2. Preprint at bioRxiv https://doi.org/10.1101/861054 (2019).
Yu, J. et al. Metagenomic analysis of faecal microbiome as a tool towards targeted non-invasive biomarkers for colorectal cancer. Gut 66, 70–78 (2017).
pubmed: 26408641 doi: 10.1136/gutjnl-2015-309800
Walker, M. A. et al. GATK PathSeq: a customizable computational tool for the discovery and identification of microbial sequences in libraries from eukaryotic hosts. Bioinformatics 34, 4287–4289 (2018).
pubmed: 29982281 pmcid: 6289130 doi: 10.1093/bioinformatics/bty501
Nougayrède, J. P. et al. Escherichia coli induces DNA double-strand breaks in eukaryotic cells. Science 313, 848–851 (2006).
pubmed: 16902142 doi: 10.1126/science.1127059
Dohlman, A. B. et al. The cancer microbiome atlas: a pan-cancer comparative analysis to distinguish tissue-resident microbiota from contaminants. Cell Host Microbe 29, 281–298.e5 (2021).
pubmed: 33382980 pmcid: 7878430 doi: 10.1016/j.chom.2020.12.001
Salter, S. J. et al. Reagent and laboratory contamination can critically impact sequence-based microbiome analyses. BMC Biol. 12, 87 (2014).
pubmed: 25387460 pmcid: 4228153 doi: 10.1186/s12915-014-0087-z
Thomas, A. M. et al. Metagenomic analysis of colorectal cancer datasets identifies cross-cohort microbial diagnostic signatures and a link with choline degradation. Nat. Med. 25, 667–678 (2019).
pubmed: 30936548 pmcid: 9533319 doi: 10.1038/s41591-019-0405-7
Gupta, A. et al. Association of Flavonifractor plautii, a flavonoid-degrading bacterium, with the gut microbiome of colorectal cancer patients in India. mSystems 4, e00438-19 (2019).
pubmed: 31719139 pmcid: 7407896 doi: 10.1128/mSystems.00438-19
Feng, Q. et al. Gut microbiome development along the colorectal adenoma-carcinoma sequence. Nat. Commun. 6, 6528 (2015).
pubmed: 25758642 doi: 10.1038/ncomms7528
Vogtmann, E. et al. Colorectal cancer and the human gut microbiome: reproducibility with whole-genome shotgun sequencing. PLoS ONE 11, e0155362 (2016).
pubmed: 27171425 pmcid: 4865240 doi: 10.1371/journal.pone.0155362
Segata, N. et al. Metagenomic biomarker discovery and explanation. Genome Biol. 12, R60 (2011).
pubmed: 21702898 pmcid: 3218848 doi: 10.1186/gb-2011-12-6-r60
Escapa, I. F. et al. New insights into human nostril microbiome from the expanded Human Oral Microbiome Database (eHOMD): a resource for the microbiome of the human aerodigestive tract. mSystems https://doi.org/10.1128/mSystems.00187-18 (2018).
Hu, Y. J. & Satten, G. A. A rarefaction-without-resampling extension of PERMANOVA for testing presence-absence associations in the microbiome. Bioinformatics https://doi.org/10.1093/bioinformatics/btac399 (2022).
Mallick, H. et al. Multivariable association discovery in population-scale meta-omics studies. PLoS Comput. Biol. 17, e1009442 (2021).
pubmed: 34784344 pmcid: 8714082 doi: 10.1371/journal.pcbi.1009442
Joanito, I. et al. Single-cell and bulk transcriptome sequencing identifies two epithelial tumor cell states and refines the consensus molecular classification of colorectal cancer. Nat. Genet. 54, 963–975 (2022).
pubmed: 35773407 pmcid: 9279158 doi: 10.1038/s41588-022-01100-4

Auteurs

Alex J Cornish (AJ)

Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.

Andreas J Gruber (AJ)

Department of Biology, University of Konstanz, Konstanz, Germany.
Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK.

Ben Kinnersley (B)

Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.
University College London Cancer Institute, London, UK.

Daniel Chubb (D)

Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.

Anna Frangou (A)

Big Data Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
Max Planck Institute for Molecular Cell Biology and Genetics, Dresden, Germany.

Giulio Caravagna (G)

Department of Mathematics and Geosciences, University of Trieste, Trieste, Italy.
Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.

Boris Noyvert (B)

Cancer Research UK Centre and Centre for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK.

Eszter Lakatos (E)

Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.

Henry M Wood (HM)

Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.

Steve Thorn (S)

Department of Oncology, University of Oxford, Oxford, UK.

Richard Culliford (R)

Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.

Claudia Arnedo-Pac (C)

Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.
Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

Jacob Househam (J)

Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.

William Cross (W)

Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
Research Department of Pathology, University College London, UCL Cancer Institute, London, UK.

Amit Sud (A)

Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.

Philip Law (P)

Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.

Maire Ni Leathlobhair (MN)

Trinity College, Dublin, Ireland.

Aliah Hawari (A)

Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK.

Connor Woolley (C)

Department of Oncology, University of Oxford, Oxford, UK.

Kitty Sherwood (K)

Department of Oncology, University of Oxford, Oxford, UK.
Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.

Nathalie Feeley (N)

Department of Oncology, University of Oxford, Oxford, UK.
Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.

Güler Gül (G)

Edinburgh Cancer Research, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.

Juan Fernandez-Tajes (J)

Department of Oncology, University of Oxford, Oxford, UK.

Luis Zapata (L)

Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.

Ludmil B Alexandrov (LB)

Department of Cellular and Molecular Medicine, UC San Diego, La Jolla, CA, USA.
Department of Bioengineering, UC San Diego, La Jolla, CA, USA.
Moores Cancer Center, UC San Diego, La Jolla, CA, USA.

Nirupa Murugaesu (N)

Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK.

Alona Sosinsky (A)

Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK.

Jonathan Mitchell (J)

Genomics England, William Harvey Research Institute, Queen Mary University of London, London, UK.

Nuria Lopez-Bigas (N)

Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.
Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Barcelona, Spain.
Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.

Philip Quirke (P)

Pathology and Data Analytics, Leeds Institute of Medical Research at St James's, University of Leeds, Leeds, UK.

David N Church (DN)

Wellcome Centre for Human Genetics, University of Oxford, Oxford, UK.
Oxford NIHR Comprehensive Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK.

Ian P M Tomlinson (IPM)

Department of Oncology, University of Oxford, Oxford, UK. ian.tomlinson@oncology.ox.ac.uk.

Andrea Sottoriva (A)

Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.
Computational Biology Research Centre, Human Technopole, Milan, Italy.

Trevor A Graham (TA)

Centre for Evolution and Cancer, Institute of Cancer Research, London, UK.

David C Wedge (DC)

Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, UK.

Richard S Houlston (RS)

Division of Genetics and Epidemiology, Institute of Cancer Research, London, UK.

Classifications MeSH