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Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer
Open accessAbstract
We conducted comprehensive integrative molecular analyses of the complete set of tumors in The Cancer Genome Atlas (TCGA), consisting of approximately 10,000 specimens and representing 33 types of cancer. We performed molecular clustering using data on chromosome-arm-level aneuploidy, DNA hypermethylation, mRNA, and miRNA expression levels and reverse-phase protein arrays, of which all, except for aneuploidy, revealed clustering primarily organized by histology, tissue type, or anatomic origin. The influence of cell type was evident in DNA-methylation-based clustering, even after excluding sites with known preexisting tissue-type-specific methylation. Integrative clustering further emphasized the dominant role of cell-of-origin patterns. Molecular similarities among histologically or anatomically related cancer types provide a basis for focused pan-cancer analyses, such as pan-gastrointestinal, pan-gynecological, pan-kidney, and pan-squamous cancers, and those related by stemness features, which in turn may inform strategies for future therapeutic development.
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“The nature of these mutations differs for each cancer [90] and in each individual [90,91,92].”
From The Tumor-on-Chip: Recent Advances in the Development of Microfluidic Systems to Recapitulate the Physiology of Solid Tumors (2019) · cites this paper as [92]
Experimental — accuracy not yet measuredIn the citing paper
“First, although tumors are readily recognized through gene expression signatures, they retain transcriptomic features of the parental tissue so that tumors arising in the same organ are more similar to each other than tumors arising in different organs.”
From Metabolic reprogramming and cancer progression (2020) · cites this paper as [3]
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“A study that classified thousands of human tumors found that tissue of origin was a major factor defining DNA methylation and gene expression patterns (3).”
From Metabolic reprogramming and cancer progression (2020) · cites this paper as [3]
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ResultInfluentialSelf-citationGenomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia
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BackgroundSelf-citationComprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas
The Cancer Genome Atlas Research Network (2015) · New England Journal of Medicine · doi:10.1056/nejmoa1402121 · Cited by 3,148
The Molecular Taxonomy of Primary Prostate Cancer
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BackgroundSelf-citationIntegrated Genomic Characterization of Papillary Thyroid Carcinoma
Agrawal, N., Akbani, R., Aksoy, B. A., Ally, A., Arachchi, H., Asa, S. L., Auman, J. T., Balasundaram, M., Balu, S., Baylin, S. B., et al. (2014) · Cell · doi:10.1016/j.cell.2014.09.050 · Cited by 3,118 · cited 2×
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BackgroundSelf-citationmclust 5: Clustering, Classification and Density Estimation Using Gaussian Finite Mixture Models
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“Clustering of tumor samples scored on these five signatures was performed using model-based clustering, using the mclust R package (Scrucca et al., 2016), with the number of clusters, K, determined by maximization of Bayesian Information Criterion (BIC).”
MethodComprehensive and Integrative Genomic Characterization of Hepatocellular Carcinoma
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Olshen, A. B., Venkatraman, E. S., Lucito, R., & Wigler, M. H. (2004) · Biostatistics · doi:10.1093/biostatistics/kxh008 · Cited by 2,304 · cited 1×
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MethodMachine Learning Identifies Stemness Features Associated with Oncogenic Dedifferentiation
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“Two stemness indices (Malta et al., 2018), based on mRNA expression and on DNA methylation data, revealed aggregation of high stemness tumors across distinct regions of the TumorMap (Figures 5C and 5D).”
BackgroundInfluentialSelf-citationAbsolute quantification of somatic DNA alterations in human cancer
Carter, S. L., Cibulskis, K., Helman, E., McKenna, A., Shen, H., Zack, T. I., Laird, P. W., Onofrio, R. C., Winckler, W., Weir, B. A., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2203 · Cited by 2,031 · cited 3×
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MethodSelf-citationStrelka: accurate somatic small-variant calling from sequenced tumor–normal sample pairs
Saunders, C. T., Wong, W. S. W., Swamy, S., Becq, J., Murray, L. J., & Cheetham, R. K. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts271 · Cited by 1,589 · cited 3×
“As drugs become increasingly clinically available to target such cancer-driving pathway targets as ALK, EGFR, ERBB2, ERα, KIT, BRAF, and ABL1, the traditional system of anatomic cancer classification should be supplemented by a classification system based on molecular alterations shared by tumors across different tiss…”
BackgroundHoadley, K. A., Yau, C. S. F., Wolf, D. M., Cherniack, A. D., Tamborero, D., Ng, S., Leiserson, M. D. M., Niu, B., McLellan, M. D., Uzunangelov, V., et al. (2014) · Cell · doi:10.1016/j.cell.2014.06.049 · Cited by 1,530 · cited 18×
“The 22 Gene Programs (Hoadley et al., 2014) and 20 pathway signatures reflecting drug targets and canonical pathways (found in Table S4 of Hoadley et al. [2014]) were hierarchically clustered using 1-Pearson distance and complete linkage and are shown with samples arranged by iCluster subtypes in numerical order.”
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“In particular, our PARADIGM analysis showed that C3:mesenchymal (immune) and C20:mixed (stromal/immune) tumors shared upregulated JAK2/STAT1,3,6 signaling with C14:LUAD tumors and C10:pan-SCC, pointing to the possibility of treating these diverse iCluster tumors with JAK-STAT agents currently approved to treat rheumat…”
BackgroundGenomic and Molecular Landscape of DNA Damage Repair Deficiency across The Cancer Genome Atlas
Knijnenburg, T., Wang, L., Zimmermann, M. T., Chambwe, N., Gao, G. F., Cherniack, A. D., Fan, H., Shen, H., Way, G. P., Greene, C. S., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.076 · Cited by 1,145
Self-citationGenomic and Functional Approaches to Understanding Cancer Aneuploidy
Taylor, A. M., Shih, J., Ha, G., Gao, G. F., Zhang, X., Berger, A. C., Schumacher, S. E., Wang, C., Hu, H., Liu, J., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.03.007 · Cited by 1,044 · cited 2×
“Chromosome arm-level copy-number calls were determined by clustering breakpoint locations and fraction of arm altered (further detailed in Taylor et al., 2018).”
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“, 2014), and wound healing (Chang et al., 2004), robustly reproduced co-clustering of the immune signature sets, and were selected to perform cluster analysis of all cancer types, with the exception of hematologic neoplasias (acute myeloid leukemia, LAML; diffuse large B cell lymphoma, DLBC; and thymoma, THYM).”
BackgroundMethodIntegrated detection and population-genetic analysis of SNPs and copy number variation
McCarroll, S. A., Kuruvilla, F. G., Korn, J. M., Cawley, S., Nemesh, J., Wysoker, A., Shapero, M. H., de Bakker, P. I. W., Maller, J. B., Kirby, A., et al. (2008) · Nature Genetics · doi:10.1038/ng.238 · Cited by 936 · cited 2×
“Somatic Copy-Number Alterations— Somatic copy-number data were generated on Affymetrix SNP 6.0 arrays using standard protocols from the Genome Analysis Platform of the Broad Institute (McCarroll et al., 2008).”
MethodInfluentialSelf-citationIntegrative Analysis Identifies Four Molecular and Clinical Subsets in Uveal Melanoma
Robertson, A. G., Shih, J., Yau, C. S. F., Gibb, E. A., Oba, J., Mungall, K. L., Hess, J. M., Uzunangelov, V., Walter, V., Danilova, L., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.07.003 · Cited by 908
Self-citationShen, R., Olshen, A. B., & Ladanyi, M. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btp543 · Cited by 849 · cited 2×
“We present a new PanCancer Atlas integrative analysis using iCluster (Shen et al., 2009, 2012) identifying 28 distinct molecular subtypes arising from the 33 different tumor types analyzed across at least four different TCGA platforms.”
MethodSelf-citationThe Somatic Genomic Landscape of Chromophobe Renal Cell Carcinoma
Davis, C., Ricketts, C. J., Wang, M., Yang, L., Cherniack, A. D., Shen, H., Buhay, C., Kang, H.-J., Kim, S. C., Fahey, C. C., et al. (2014) · Cancer Cell · doi:10.1016/j.ccr.2014.07.014 · Cited by 838 · cited 2×
“Pan-kidney mapped almost entirely to C28, except for KICH, which grouped with ACC in C9, characterized by a high frequency of hypodiploid samples (Davis et al., 2014; Zheng et al., 2016).”
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“The PARADIGM algorithm with the interaction-learning update (Chu et al., 2014; Vaske et al., 2010) was used to infer protein activities in the context of gene regulatory pathways, based on gene expression and copy-number data.”
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“Somatic Copy-Number Alterations— Somatic copy-number data were generated on Affymetrix SNP 6.0 arrays using standard protocols from the Genome Analysis Platform of the Broad Institute (McCarroll et al., 2008).”
MethodInfluentialSelf-citationThe Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
Ricketts, C. J., de Cubas, A. A., Fan, H., Smith, C. C., Lang, M., Reznik, E., Bowlby, R., Gibb, E. A., Akbani, R., Beroukhim, R., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.075 · Cited by 782 · cited 13×
“Consequently, these four major cell-of-origin patterns are the subject of separate in-depth reports detailing their distinguishing genomic and molecular features (Berger et al., 2018; Campbell et al., 2018; Liu et al., 2018; Malta et al., 2018; Ricketts et al., 2018).”
BackgroundInfluentialSelf-citationThe Cancer Genome Atlas Comprehensive Molecular Characterization of Renal Cell Carcinoma
Ricketts, C. J., de Cubas, A. A., Fan, H., Smith, C. C., Lang, M., Reznik, E., Bowlby, R., Gibb, E. A., Akbani, R., Beroukhim, R., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.06.032 · Cited by 737
Self-citationComprehensive Pan-Genomic Characterization of Adrenocortical Carcinoma
Zheng, S., Cherniack, A. D., Dewal, N., Moffitt, R. A., Danilova, L., Murray, B. A., Lerario, A. M., Else, T., Knijnenburg, T. A., Ciriello, G., et al. (2016) · Cancer Cell · doi:10.1016/j.ccell.2016.04.002 · Cited by 657 · cited 2×
“Pan-kidney mapped almost entirely to C28, except for KICH, which grouped with ACC in C9, characterized by a high frequency of hypodiploid samples (Davis et al., 2014; Zheng et al., 2016).”
BackgroundSelf-citationA Comprehensive Pan-Cancer Molecular Study of Gynecologic and Breast Cancers
Berger, A. C., Korkut, A., Kanchi, R. S., Hegde, A. M., Lenoir, W. F., Liu, W., Liu, Y., Fan, H., Shen, H., Ravikumar, V., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.03.014 · Cited by 621 · cited 7×
“Consequently, these four major cell-of-origin patterns are the subject of separate in-depth reports detailing their distinguishing genomic and molecular features (Berger et al., 2018; Campbell et al., 2018; Liu et al., 2018; Malta et al., 2018; Ricketts et al., 2018).”
BackgroundInfluentialSelf-citationComparative Molecular Analysis of Gastrointestinal Adenocarcinomas
Liu, Y., Sethi, N. S., Hinoue, T., Schneider, B., Cherniack, A. D., Sánchez-Vega, F., Seoane, J. A., Farshidfar, F., Bowlby, R., Islam, M., et al. (2018) · Cancer Cell · doi:10.1016/j.ccell.2018.03.010 · Cited by 614 · cited 6×
“Consequently, these four major cell-of-origin patterns are the subject of separate in-depth reports detailing their distinguishing genomic and molecular features (Berger et al., 2018; Campbell et al., 2018; Liu et al., 2018; Malta et al., 2018; Ricketts et al., 2018).”
BackgroundInfluentialSelf-citationBanerjee, S., Biehl, A. J., Gadina, M., Hasni, S., & Schwartz, D. M. (2017) · Drugs · doi:10.1007/s40265-017-0736-y · Cited by 592
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Self-citationOncotator: Cancer Variant Annotation Tool
Ramos, A. H., Lichtenstein, L., Gupta, M., Lawrence, M. S., Pugh, T. J., Saksena, G., Meyerson, M. M., & Getz, G. A. (2015) · Human Mutation · doi:10.1002/humu.22771 · Cited by 495 · cited 1×
“This concept has led to the development of so-called basket or umbrella trials, such as the NCI-MATCH study, to investigate the feasibility and validity of this new clinical approach (Ramos et al., 2015).”
BackgroundSelf-citationEpigenetic profiling to classify cancer of unknown primary: a multicentre, retrospective analysis
Morán, S., Martínez‐Cardús, A., Sayols, S., Musulén, E., Balañá, C., Estival-Gonzalez, A., Moutinho, C., Heyn, H., Díaz‐Lagares, Á., de Moura, M. C., et al. (2016) · The Lancet Oncology · doi:10.1016/s1470-2045(16)30297-2 · Cited by 489 · cited 2×
“, 2013) or DNA methylation (Moran et al., 2016) profiling has recently led to improved patient outcomes by better defining the tissues of origin for this diverse group of life-threatening malignancies.”
BackgroundPattern discovery and cancer gene identification in integrated cancer genomic data
Mo, Q., Wang, S., Seshan, V. E., Olshen, A. B., Schultz, N., Sander, C., Powers, R. S., Ladanyi, M., & Shen, R. (2013) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1208949110 · Cited by 474 · cited 3×
“Integrative clustering with iCluster—The iCluster clustering algorithm formulates the problem of subgroup discovery as a joint multivariate regression of multiple data types with reference to a set of common latent variables, which represent the underlying 28 tumor subtypes (Mo et al., 2013; Shen et al., 2009, 2012).”
MethodSelf-citationIntegrated Molecular Characterization of Uterine Carcinosarcoma
Cherniack, A. D., Shen, H., Walter, V., Stewart, C., Murray, B. A., Bowlby, R., Hu, X., Ling, S., Soslow, R. A., Broaddus, R. R., et al. (2017) · Cancer Cell · doi:10.1016/j.ccell.2017.02.010 · Cited by 440 · cited 1×
“These clusters were also enriched for other Pan-gyn tumors, including ovarian, high-copy number endometrial, and uterine carcinosarcoma (Cherniack et al., 2017).”
BackgroundSelf-citationHainsworth, J. D., Rubin, M. S., Spigel, D. R., Boccia, R. V., Raby, S., Quinn, R., & Greco, F. A. (2012) · Journal of Clinical Oncology · doi:10.1200/jco.2012.43.3755 · Cited by 365 · cited 2×
“Using either RNA (Hainsworth et al., 2013) or DNA methylation (Moran et al.”
BackgroundSelf-citationGenomic, Pathway Network, and Immunologic Features Distinguishing Squamous Carcinomas
Campbell, J. D., Yau, C. S. F., Bowlby, R., Liu, Y., Brennan, K., Fan, H., Taylor, A. M., Wang, C., Walter, V., Akbani, R., et al. (2018) · Cell Reports · doi:10.1016/j.celrep.2018.03.063 · Cited by 341 · cited 5×
“Consequently, these four major cell-of-origin patterns are the subject of separate in-depth reports detailing their distinguishing genomic and molecular features (Berger et al., 2018; Campbell et al., 2018; Liu et al., 2018; Malta et al., 2018; Ricketts et al., 2018).”
BackgroundResultInfluentialSelf-citationIntegrative Subtype Discovery in Glioblastoma Using iCluster
Shen, R., Mo, Q., Schultz, N. D., Seshan, V., Olshen, A. B., Huse, J. T., Ladanyi, M., & Sander, C. (2012) · PLoS ONE · doi:10.1371/journal.pone.0035236 · Cited by 261 · cited 2×
“We present a new PanCancer Atlas integrative analysis using iCluster (Shen et al., 2009, 2012) identifying 28 distinct molecular subtypes arising from the 33 different tumor types analyzed across at least four different TCGA platforms.”
MethodSelf-citationThe Macrophage Colony-Stimulating Factor 1 Response Signature in Breast Carcinoma
Beck, A. H., Espinosa, Í., Edris, B., Li, R., Montgomery, K. D., Zhu, S., Varma, S., Marinelli, R. J., van de Rijn, M., & West, R. B. (2009) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-08-1283 · Cited by 211 · cited 1×
“Based on the WGCNA analysis, five immuno-oncology-related immune expression signatures: activation of macrophages/monocytes (Beck et al., 2009), overall lymphocyte infiltration (dominated by T and B cells) (Calabrò et al., 2009), TGF-β response (Teschendorff et al., 2010), IFN-γ response (Wolf et…”
MethodTeschendorff, A. E., Gómez, S., Arenas, À., El‐Ashry, D., Schmidt, M., Gehrmann, M. C., & Caldas, C. (2010) · BMC Cancer · doi:10.1186/1471-2407-10-604 · Cited by 152 · cited 2×
“…of macrophages/monocytes (Beck et al., 2009), overall lymphocyte infiltration (dominated by T and B cells) (Calabrò et al., 2009), TGF-β response (Teschendorff et al., 2010), IFN-γ response (Wolf et al., 2014), and wound healing (Chang et al., 2004), robustly reproduced co-clustering of the…”
BackgroundIntegrated genomic analyses of ovarian carcinoma
The Cancer Genome Atlas Research Network (2011) · Nature · doi:10.1038/nature10166 · Cited by 129 · cited 2×
“…of stemness, attesting to their underlying molecular heterogeneity, as previously reported (Cancer Genome Atlas Network, 2015; Cancer Genome Atlas Research Network, 2011, 2012, 2014a, 2014b, 2015a, 2015b, 2017; Cancer Genome Atlas Research Network et al., 2013a, 2013b; Robertson et al., 2017).”
BackgroundGene Co-Expression Modules as Clinically Relevant Hallmarks of Breast Cancer Diversity
Wolf, D. M., Lenburg, M. E., Yau, C. S. F., Boudreau, A., & Veer, L. V. ‘. (2014) · PLoS ONE · doi:10.1371/journal.pone.0088309 · Cited by 128 · cited 1×
“…overall lymphocyte infiltration (dominated by T and B cells) (Calabrò et al., 2009), TGF-β response (Teschendorff et al., 2010), IFN-γ response (Wolf et al., 2014), and wound healing (Chang et al., 2004), robustly reproduced co-clustering of the immune signature sets, and were selected to…”
BackgroundSelf-citationCalabrò, A., Beißbarth, T., Kuner, R., Stojanov, M., Benner, A., Asslaber, M., Ploner, F., Zatloukal, K., Samonigg, H., Poustka, A., et al. (2008) · Breast Cancer Research and Treatment · doi:10.1007/s10549-008-0105-3 · Cited by 127 · cited 2×
“…immune expression signatures: activation of macrophages/monocytes (Beck et al., 2009), overall lymphocyte infiltration (dominated by T and B cells) (Calabrò et al., 2009), TGF-β response (Teschendorff et al., 2010), IFN-γ response (Wolf et al., 2014), and wound healing (Chang et al., 2004),…”
BackgroundChu, J., Sadeghi, S., Raymond, A., Jackman, S. D., Nip, K. M., Mar, R., Mohamadi, H., Butterfield, Y. S. N., Robertson, A. G., & Birol, İ. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu558 · Cited by 123 · cited 2×
“The PARADIGM algorithm with the interaction-learning update (Chu et al., 2014; Vaske et al., 2010) was used to infer protein activities in the context of gene regulatory pathways, based on gene expression and copy-number data.”
MethodSelf-citationCancer stem cells and differentiation therapy
Jin, X. J., Jin, X., & Kim, H. (2017) · Tumor Biology · doi:10.1177/1010428317729933 · Cited by 105
Cluster stability and the use of noise in interpretation of clustering
Davidson, G. S., Wylie, B., & Boyack, K. W. (2005) · IEEE Symposium on Information Visualization · doi:10.1109/infvis.2001.963275 · Cited by 77 · cited 1×
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Metadata
- Authors
- Hoadley, K. A., Yau, C., Hinoue, T., Wolf, D. M., Lazar, A. J., Drill, E., Shen, R., Taylor, A. M., Cherniack, A. D., Thorsson, V., Akbani, R., Bowlby, R., Wong, C. K., Wiznerowicz, M., Sanchez-Vega, F., Robertson, A. G., Schneider, B. G., Lawrence, M. S., Noushmehr, H., Malta, T. M., Caesar-Johnson, S. J., Demchok, J. A., Felau, I., Kasapi, M., Ferguson, M. L., Hutter, C. M., Sofia, H. J., Tarnuzzer, R., Wang, Z., Yang, L., Zenklusen, J. C., Zhang, J. (., Chudamani, S., Liu, J., Lolla, L., Naresh, R., Pihl, T., Sun, Q., Wan, Y., Wu, Y., Cho, J., DeFreitas, T., Frazer, S., Gehlenborg, N., Getz, G., Heiman, D. I., Kim, J., Lawrence, M. S., Lin, P., Meier, S., Noble, M. S., Saksena, G., Voet, D., Zhang, H., Bernard, B., Chambwe, N., Dhankani, V., Knijnenburg, T., Kramer, R., Leinonen, K., Liu, Y., Miller, M., Reynolds, S., Shmulevich, I., Thorsson, V., Zhang, W., Akbani, R., Broom, B. M., Hegde, A. M., Ju, Z., Kanchi, R. S., Korkut, A., Li, J., Liang, H., Ling, S., Liu, W., Lu, Y., Mills, G. B., Ng, K.-S., Rao, A., Ryan, M., Wang, J., Weinstein, J. N., Zhang, J., Abeshouse, A., Armenia, J., Chakravarty, D., Chatila, W. K., de Bruijn, I., Gao, J., Gross, B. E., Heins, Z. J., Kundra, R., La, K., Ladanyi, M., Luna, A., Nissan, M. G., Ochoa, A., Phillips, S. M., Reznik, E., Sanchez-Vega, F., Sander, C., Schultz, N., Sheridan, R., Sumer, S. O., Sun, Y., Taylor, B. S., Wang, J., Zhang, H., Anur, P., Peto, M., Spellman, P., Benz, C., Stuart, J. M., Wong, C. K., Yau, C., Hayes, D. N., Parker, J. S., Wilkerson, M. D., Ally, A., Balasundaram, M., Bowlby, R., Brooks, D., Carlsen, R., Chuah, E., Dhalla, N., Holt, R., Jones, S. J. M., Kasaian, K., Lee, D., Ma, Y., Marra, M. A., Mayo, M., Moore, R. A., Mungall, A. J., Mungall, K., Robertson, A. G., Sadeghi, S., Schein, J. E., Sipahimalani, P., Tam, A., Thiessen, N., Tse, K., Wong, T., Berger, A. C., Beroukhim, R., Cherniack, A. D., Cibulskis, C., Gabriel, S. B., Gao, G. F., Ha, G., Meyerson, M., Schumacher, S. E., Shih, J., Kucherlapati, M. H., Kucherlapati, R. S., Baylin, S., Cope, L., Danilova, L., Bootwalla, M. S., Lai, P. H., Maglinte, D. T., Van Den Berg, D. J., Weisenberger, D. J., Auman, J. T., Balu, S., Bodenheimer, T., Fan, C., Hoadley, K. A., Hoyle, A. P., Jefferys, S. R., Jones, C. D., Meng, S., Mieczkowski, P. A., Mose, L. E., Perou, A. H., Perou, C. M., Roach, J., Shi, Y., Simons, J. V., Skelly, T., Soloway, M. G., Tan, D., Veluvolu, U., Fan, H., Hinoue, T., Laird, P. W., Shen, H., Zhou, W., Bellair, M., Chang, K., Covington, K., Creighton, C. J., Dinh, H., Doddapaneni, H., Donehower, L. A., Drummond, J., Gibbs, R. A., Glenn, R., Hale, W., Han, Y., Hu, J., Korchina, V., Lee, S., Lewis, L., Li, W., Liu, X., Morgan, M., Morton, D., Muzny, D., Santibanez, J., Sheth, M., Shinbrot, E., Wang, L., Wang, M., Wheeler, D. A., Xi, L., Zhao, F., Hess, J., Appelbaum, E. L., Bailey, M., Cordes, M. G., Ding, L., Fronick, C. C., Fulton, L. A., Fulton, R. S., Kandoth, C., Mardis, E. R., McLellan, M. D., Miller, C. A., Schmidt, H. K., Wilson, R. K., Crain, D., Curley, E., Gardner, J., Lau, K., Mallery, D., Morris, S., Paulauskis, J., Penny, R., Shelton, C., Shelton, T., Sherman, M., Thompson, E., Yena, P., Bowen, J., Gastier-Foster, J. M., Gerken, M., Leraas, K. M., Lichtenberg, T. M., Ramirez, N. C., Wise, L., Zmuda, E., Corcoran, N., Costello, T., Hovens, C., Carvalho, A. L., de Carvalho, A. C., Fregnani, J. H., Longatto-Filho, A., Reis, R. M., Scapulatempo-Neto, C., Silveira, H. C. S., Vidal, D. O., Burnette, A., Eschbacher, J., Hermes, B., Noss, A., Singh, R., Anderson, M. L., Castro, P. D., Ittmann, M., Huntsman, D., Kohl, B., Le, X., Thorp, R., Andry, C., Duffy, E. R., Lyadov, V., Paklina, O., Setdikova, G., Shabunin, A., Tavobilov, M., McPherson, C., Warnick, R., Berkowitz, R., Cramer, D., Feltmate, C., Horowitz, N., Kibel, A., Muto, M., Raut, C. P., Malykh, A., Barnholtz-Sloan, J. S., Barrett, W., Devine, K., Fulop, J., Ostrom, Q. T., Shimmel, K., Wolinsky, Y., Sloan, A. E., De Rose, A., Giuliante, F., Goodman, M., Karlan, B. Y., Hagedorn, C. H., Eckman, J., Harr, J., Myers, J., Tucker, K., Zach, L. A., Deyarmin, B., Hu, H., Kvecher, L., Larson, C., Mural, R. J., Somiari, S., Vicha, A., Zelinka, T., Bennett, J., Iacocca, M., Rabeno, B., Swanson, P., Latour, M., Lacombe, L., Têtu, B., Bergeron, A., McGraw, M., Staugaitis, S. M., Chabot, J., Hibshoosh, H., Sepulveda, A., Su, T., Wang, T., Potapova, O., Voronina, O., Desjardins, L., Mariani, O., Roman-Roman, S., Sastre, X., Stern, M.-H., Cheng, F., Signoretti, S., Berchuck, A., Bigner, D., Lipp, E., Marks, J., McCall, S., McLendon, R., Secord, A., Sharp, A., Behera, M., Brat, D. J., Chen, A., Delman, K., Force, S., Khuri, F., Magliocca, K., Maithel, S., Olson, J. J., Owonikoko, T., Pickens, A., Ramalingam, S., Shin, D. M., Sica, G., Van Meir, E. G., Zhang, H., Eijckenboom, W., Gillis, A., Korpershoek, E., Looijenga, L., Oosterhuis, W., Stoop, H., van Kessel, K. E., Zwarthoff, E. C., Calatozzolo, C., Cuppini, L., Cuzzubbo, S., DiMeco, F., Finocchiaro, G., Mattei, L., Perin, A., Pollo, B., Chen, C., Houck, J., Lohavanichbutr, P., Hartmann, A., Stoehr, C., Stoehr, R., Taubert, H., Wach, S., Wullich, B., Kycler, W., Murawa, D., Wiznerowicz, M., Chung, K., Edenfield, W. J., Martin, J., Baudin, E., Bubley, G., Bueno, R., De Rienzo, A., Richards, W. G., Kalkanis, S., Mikkelsen, T., Noushmehr, H., Scarpace, L., Girard, N., Aymerich, M., Campo, E., Giné, E., Guillermo, A. L., Van Bang, N., Hanh, P. T., Phu, B. D., Tang, Y., Colman, H., Evason, K., Dottino, P. R., Martignetti, J. A., Gabra, H., Juhl, H., Akeredolu, T., Stepa, S., Hoon, D., Ahn, K., Kang, K. J., Beuschlein, F., Breggia, A., Birrer, M., Bell, D., Borad, M., Bryce, A. H., Castle, E., Chandan, V., Cheville, J., Copland, J. A., Farnell, M., Flotte, T., Giama, N., Ho, T., Kendrick, M., Kocher, J.-P., Kopp, K., Moser, C., Nagorney, D., O’Brien, D., O’Neill, B. P., Patel, T., Petersen, G., Que, F., Rivera, M., Roberts, L., Smallridge, R., Smyrk, T., Stanton, M., Thompson, R. H., Torbenson, M., Yang, J. D., Zhang, L., Brimo, F., Ajani, J. A., Gonzalez, A. M. A., Behrens, C., Bondaruk, O., Broaddus, R., Czerniak, B., Esmaeli, B., Fujimoto, J., Gershenwald, J., Guo, C., Lazar, A. J., Logothetis, C., Meric-Bernstam, F., Moran, C., Ramondetta, L., Rice, D., Sood, A., Tamboli, P., Thompson, T., Troncoso, P., Tsao, A., Wistuba, I., Carter, C., Haydu, L., Hersey, P., Jakrot, V., Kakavand, H., Kefford, R., Lee, K., Long, G., Mann, G., Quinn, M., Saw, R., Scolyer, R., Shannon, K., Spillane, A., Stretch, J., Synott, M., Thompson, J., Wilmott, J., Al-Ahmadie, H., Chan, T. A., Ghossein, R., Gopalan, A., Levine, D. A., Reuter, V., Singer, S., Singh, B., Tien, N. V., Broudy, T., Mirsaidi, C., Nair, P., Drwiega, P., Miller, J., Smith, J., Zaren, H., Park, J.-W., Hung, N. P., Kebebew, E., Linehan, W. M., Metwalli, A. R., Pacak, K., Pinto, P. A., Schiffman, M., Schmidt, L. S., Vocke, C. D., Wentzensen, N., Worrell, R., Yang, H., Moncrieff, M., Goparaju, C., Melamed, J., Pass, H., Botnariuc, N., Caraman, I., Cernat, M., Chemencedji, I., Clipca, A., Doruc, S., Gorincioi, G., Mura, S., Pirtac, M., Stancul, I., Tcaciuc, D., Albert, M., Alexopoulou, I., Arnaout, A., Bartlett, J., Engel, J., Gilbert, S., Parfitt, J., Sekhon, H., Thomas, G., Rassl, D. M., Rintoul, R. C., Bifulco, C., Tamakawa, R., Urba, W., Hayward, N., Timmers, H., Antenucci, A., Facciolo, F., Grazi, G., Marino, M., Merola, R., de Krijger, R., Gimenez-Roqueplo, A.-P., Piché, A., Chevalier, S., McKercher, G., Birsoy, K., Barnett, G., Brewer, C., Farver, C., Naska, T., Pennell, N. A., Raymond, D., Schilero, C., Smolenski, K., Williams, F., Morrison, C., Borgia, J. A., Liptay, M. J., Pool, M., Seder, C. W., Junker, K., Omberg, L., Dinkin, M., Manikhas, G., Alvaro, D., Bragazzi, M. C., Cardinale, V., Carpino, G., Gaudio, E., Chesla, D., Cottingham, S., Dubina, M., Moiseenko, F., Dhanasekaran, R., Becker, K.-F., Janssen, K.-P., Slotta-Huspenina, J., Abdel-Rahman, M. H., Aziz, D., Bell, S., Cebulla, C. M., Davis, A., Duell, R., Elder, J. B., Hilty, J., Kumar, B., Lang, J., Lehman, N. L., Mandt, R., Nguyen, P., Pilarski, R., Rai, K., Schoenfield, L., Senecal, K., Wakely, P., Hansen, P., Lechan, R., Powers, J., Tischler, A., Grizzle, W. E., Sexton, K. C., Kastl, A., Henderson, J., Porten, S., Waldmann, J., Fassnacht, M., Asa, S. L., Schadendorf, D., Couce, M., Graefen, M., Huland, H., Sauter, G., Schlomm, T., Simon, R., Tennstedt, P., Olabode, O., Nelson, M., Bathe, O., Carroll, P. R., Chan, J. M., Disaia, P., Glenn, P., Kelley, R. K., Landen, C. N., Phillips, J., Prados, M., Simko, J., Smith-McCune, K., VandenBerg, S., Roggin, K., Fehrenbach, A., Kendler, A., Sifri, S., Steele, R., Jimeno, A., Carey, F., Forgie, I., Mannelli, M., Carney, M., Hernandez, B., Campos, B., Herold-Mende, C., Jungk, C., Unterberg, A., von Deimling, A., Bossler, A., Galbraith, J., Jacobus, L., Knudson, M., Knutson, T., Ma, D., Milhem, M., Sigmund, R., Godwin, A. K., Madan, R., Rosenthal, H. G., Adebamowo, C., Adebamowo, S. N., Boussioutas, A., Beer, D., Giordano, T., Mes-Masson, A.-M., Saad, F., Bocklage, T., Landrum, L., Mannel, R., Moore, K., Moxley, K., Postier, R., Walker, J., Zuna, R., Feldman, M., Valdivieso, F., Dhir, R., Luketich, J., Pinero, E. M. M., Quintero-Aguilo, M., Carlotti, C. G., Dos Santos, J. S., Kemp, R., Sankarankuty, A., Tirapelli, D., Catto, J., Agnew, K., Swisher, E., Creaney, J., Robinson, B., Shelley, C. S., Godwin, E. M., Kendall, S., Shipman, C., Bradford, C., Carey, T., Haddad, A., Moyer, J., Peterson, L., Prince, M., Rozek, L., Wolf, G., Bowman, R., Fong, K. M., Yang, I., Korst, R., Rathmell, W. K., Fantacone-Campbell, J. L., Hooke, J. A., Kovatich, A. J., Shriver, C. D., DiPersio, J., Drake, B., Govindan, R., Heath, S., Ley, T., Van Tine, B., Westervelt, P., Rubin, M. A., Lee, J. I., Aredes, N. D., Mariamidze, A., Stuart, J. M., Benz, C. C., & Laird, P. W.
- Affiliations
- University of California, San Francisco (US)
- Memorial Sloan Kettering Cancer Center (US)
- Broad Institute (US)
- Vanderbilt University Medical Center (US)
- Henry Ford Health (US)
- Buck Institute for Research on Aging (US)
- Van Andel Institute (US)
- BC Cancer Agency (CA)
- Institute for Systems Biology (US)
- The University of Texas MD Anderson Cancer Center (US)
- University of California, Santa Cruz (US)
- University of North Carolina at Chapel Hill (US)
- Poznan University of Medical Sciences (PL)
- Corresponding author
- Felau, Ina
- Nissan, Moriah G.
- Weisenberger, Daniel J.
- Jones, Corbin D.
- Bellair, Michelle
- Mallery, David
- Oosterhuis, Wolter
- Kefford, Richard
- Vocke, Cathy D.
- Zuna, Rosemary
- Rubin, Mark A.
- Aredes, Natália D.
- ORCID
- Wolf, Denise M.
- Drill, Esther
- Shen, Ronglai
- Taylor, Alison M.
- Schneider, Barbara G.
- Malta, Tathiane M.
- Felau, Ina
- Kasapi, Melpomeni
- Ferguson, Martin L.
- Sofia, Heidi J.
- Tarnuzzer, Roy
- Yang, Liming
- Zenklusen, Jean C.
- Zhang, Jiashan (Julia)
- Liu, Jia
- Pihl, Todd
- Sun, Qiang
- Wu, Ye
- Gehlenborg, Nils
- Getz, Gad
- Heiman, David I.
- Kim, Jaegil
- Lin, Pei
- Noble, Michael S.
- Saksena, Gordon
- Zhang, Hailei
- Bernard, Brady
- Chambwe, Nyasha
- Knijnenburg, Theo
- Liu, Yuexin
- Miller, Michael
- Shmulevich, Ilya
- Zhang, Wei
- Broom, Bradley M.
- Hegde, Apurva M.
- Ju, Zhenlin
- Korkut, Anil
- Li, Jun
- Liang, Han
- Lu, Yiling
- Mills, Gordon B.
- Wang, Jing
- Weinstein, John N.
- Zhang, Jiexin
- Armenia, Joshua
- Chakravarty, Debyani
- Chatila, Walid K.
- Gross, Benjamin E.
- Heins, Zachary J.
- Kundra, Ritika
- Ladanyi, Marc
- Luna, Augustin
- Ochoa, Angelica
- Phillips, Sarah M.
- Reznik, Ed
- Sander, Chris
- Schultz, Nikolaus
- Sun, Yichao
- Taylor, Barry S.
- Zhang, Hongxin
- Spellman, Paul
- Hayes, D. Neil
- Parker, Joel S.
- Wilkerson, Matthew D.
- Holt, Robert
- Jones, Steven J.M.
- Marra, Marco A.
- Moore, Richard A.
- Mungall, Andrew J.
- Sadeghi, Sara
- Tam, Angela
- Wong, Tina
- Berger, Ashton C.
- Beroukhim, Rameen
- Cibulskis, Carrie
- Gabriel, Stacey B.
- Ha, Gavin
- Meyerson, Matthew
- Schumacher, Steven E.
- Shih, Juliann
- Kucherlapati, Melanie H.
- Kucherlapati, Raju S.
- Baylin, Stephen
- Cope, Leslie
- Danilova, Ludmila
- Maglinte, Dennis T.
- Weisenberger, Daniel J.
- Auman, J. Todd
- Hoyle, Alan P.
- Jones, Corbin D.
- Mieczkowski, Piotr A.
- Perou, Charles M.
- Roach, Jeffrey
- Shi, Yan
- Fan, Huihui
- Shen, Hui
- Zhou, Wanding
- Chang, Kyle
- Covington, Kyle
- Creighton, Chad J.
- Dinh, Huyen
- Doddapaneni, HarshaVardhan
- Gibbs, Richard A.
- Han, Yi
- Korchina, Viktoriya
- Liu, Xiuping
- Morgan, Margaret
- Muzny, Donna
- Sheth, Margi
- Shinbrot, Eve
- Wang, Linghua
- Wang, Min
- Wheeler, David A.
- Zhao, Fengmei
- Hess, Julian
- Bailey, Matthew
- Ding, Li
- Fronick, Catrina C.
- Fulton, Robert S.
- Kandoth, Cyriac
- Mardis, Elaine R.
- McLellan, Michael D.
- Miller, Christopher A.
- Wilson, Richard K.
- Sherman, Mark
- Bowen, Jay
- Leraas, Kristen M.
- Lichtenberg, Tara M.
- Ramirez, Nilsa C.
- Zmuda, Erik
- Corcoran, Niall
- Hovens, Christopher
- Fregnani, José H.
- Reis, Rui M.
- Silveira, Henrique C.S.
- Vidal, Daniel O.
- Anderson, Matthew L.
- Ittmann, Michael
- Huntsman, David
- Kohl, Bernard
- Andry, Chris
- Duffy, Elizabeth R.
- Lyadov, Vladimir
- Paklina, Oxana
- Setdikova, Galiya
- Tavobilov, Mikhail
- Warnick, Ronald
- Berkowitz, Ross
- Feltmate, Colleen
- Horowitz, Neil
- Kibel, Adam
- Raut, Chandrajit P.
- Ostrom, Quinn T.
- Sloan, Andrew E.
- Giuliante, Felice
- Goodman, Marc
- Karlan, Beth Y.
- Somiari, Stella
- Bennett, Joseph
- Iacocca, Mary
- Lacombe, Louis
- Têtu, Bernard
- Bergeron, Alain
- McGraw, Mary
- Hibshoosh, Hanina
- Sepulveda, Antonia
- Wang, Timothy
- Potapova, Olga
- Voronina, Olga
- Desjardins, Laurence
- Mariani, Odette
- Stern, Marc-Henri
- Cheng, Feixiong
- Signoretti, Sabina
- Berchuck, Andrew
- Bigner, Darell
- Lipp, Eric
- McCall, Shannon
- McLendon, Roger
- Secord, Angeles
- Behera, Madhusmita
- Brat, Daniel J.
- Chen, Amy
- Delman, Keith
- Force, Seth
- Khuri, Fadlo
- Magliocca, Kelly
- Maithel, Shishir
- Olson, Jeffrey J.
- Owonikoko, Taofeek
- Ramalingam, Suresh
- Shin, Dong M.
- Sica, Gabriel
- Zhang, Hongzheng
- Looijenga, Leendert
- Oosterhuis, Wolter
- Zwarthoff, Ellen C.
- Calatozzolo, Chiara
- Cuzzubbo, Stefania
- DiMeco, Francesco
- Finocchiaro, Gaetano
- Mattei, Luca
- Perin, Alessandro
- Pollo, Bianca
- Taubert, Helge
- Wach, Sven
- Wullich, Bernd
- Kycler, Witold
- Murawa, Dawid
- Martin, Julie
- Bubley, Glenn
- Bueno, Raphael
- Richards, William G.
- Kalkanis, Steven
- Mikkelsen, Tom
- Scarpace, Lisa
- Girard, Nicolas
- Aymerich, Marta
- Giné, Eva
- Tang, Yufang
- Colman, Howard
- Evason, Kimberley
- Gabra, Hani
- Juhl, Hartmut
- Hoon, Dave
- Kang, Koo Jeong
- Beuschlein, Felix
- Breggia, Anne
- Birrer, Michael
- Borad, Mitesh
- Bryce, Alan H.
- Chandan, Vishal
- Cheville, John
- Copland, John A.
- Flotte, Thomas
- Ho, Thai
- Kendrick, Michael
- Kocher, Jean-Pierre
- Nagorney, David
- O’Brien, Daniel
- O’Neill, Brian Patrick
- Patel, Tushar
- Rivera, Michael
- Roberts, Lewis
- Smyrk, Thomas
- Torbenson, Michael
- Yang, Ju Dong
- Zhang, Lizhi
- Brimo, Fadi
- Ajani, Jaffer A.
- Behrens, Carmen
- Broaddus, Russell
- Czerniak, Bogdan
- Esmaeli, Bita
- Fujimoto, Junya
- Guo, Charles
- Logothetis, Christopher
- Ramondetta, Lois
- Sood, Anil
- Troncoso, Patricia
- Tsao, Anne
- Wistuba, Ignacio
- Carter, Candace
- Haydu, Lauren
- Jakrot, Valerie
- Kakavand, Hojabr
- Kefford, Richard
- Lee, Kenneth
- Long, Georgina
- Mann, Graham
- Quinn, Michael
- Saw, Robyn
- Scolyer, Richard
- Shannon, Kerwin
- Spillane, Andrew
- Stretch, Jonathan
- Thompson, John
- Wilmott, James
- Chan, Timothy A.
- Ghossein, Ronald
- Gopalan, Anuradha
- Levine, Douglas A.
- Singer, Samuel
- Singh, Bhuvanesh
- Broudy, Thomas
- Nair, Praveen
- Zaren, Howard
- Park, Joong-Won
- Kebebew, Electron
- Linehan, W. Marston
- Metwalli, Adam R.
- Pinto, Peter A.
- Schiffman, Mark
- Schmidt, Laura S.
- Vocke, Cathy D.
- Wentzensen, Nicolas
- Yang, Hannah
- Moncrieff, Marc
- Goparaju, Chandra
- Melamed, Jonathan
- Pass, Harvey
- Cernat, Mircea
- Arnaout, Angel
- Bartlett, John
- Thomas, George
- Rassl, Doris M.
- Rintoul, Robert C.
- Bifulco, Carlo
- Urba, Walter
- Hayward, Nicholas
- Timmers, Henri
- Facciolo, Francesco
- Marino, Mirella
- Piché, Alain
- Chevalier, Simone
- McKercher, Ginette
- Barnett, Gene
- Farver, Carol
- Pennell, Nathan A.
- Borgia, Jeffrey A.
- Seder, Christopher W.
- Junker, Kerstin
- Omberg, Larsson
- Manikhas, George
- Alvaro, Domenico
- Bragazzi, Maria Consiglia
- Cardinale, Vincenzo
- Carpino, Guido
- Gaudio, Eugenio
- Dubina, Michael
- Moiseenko, Fedor
- Dhanasekaran, Renumathy
- Becker, Karl-Friedrich
- Janssen, Klaus-Peter
- Cebulla, Colleen M.
- Elder, J. Bradley
- Lehman, Norman L.
- Nguyen, Phuong
- Pilarski, Robert
- Rai, Karan
- Schoenfield, Lynn
- Wakely, Paul
- Lechan, Ronald
- Tischler, Arthur
- Grizzle, William E.
- Henderson, Joel
- Porten, Sima
- Fassnacht, Martin
- Asa, Sylvia L.
- Schadendorf, Dirk
- Couce, Marta
- Graefen, Markus
- Huland, Hartwig
- Sauter, Guido
- Schlomm, Thorsten
- Simon, Ronald
- Tennstedt, Pierre
- Nelson, Mark
- Bathe, Oliver
- Carroll, Peter R.
- Chan, June M.
- Kelley, Robin K.
- Landen, Charles N.
- Prados, Michael
- VandenBerg, Scott
- Roggin, Kevin
- Kendler, Ady
- Steele, Ruth
- Jimeno, Antonio
- Forgie, Ian
- Mannelli, Massimo
- Carney, Michael
- Campos, Benito
- Unterberg, Andreas
- Bossler, Aaron
- Ma, Deqin
- Milhem, Mohammed
- Godwin, Andrew K.
- Madan, Rashna
- Adebamowo, Clement
- Adebamowo, Sally N.
- Boussioutas, Alex
- Beer, David
- Giordano, Thomas
- Bocklage, Therese
- Landrum, Lisa
- Moore, Kathleen
- Moxley, Katherine
- Zuna, Rosemary
- Feldman, Michael
- Luketich, James
- Carlotti, Carlos Gilberto
- Kemp, Rafael
- Tirapelli, Daniela
- Catto, James
- Swisher, Elizabeth
- Creaney, Jenette
- Robinson, Bruce
- Shelley, Carl Simon
- Bradford, Carol
- Carey, Thomas
- Prince, Mark
- Rozek, Laura
- Wolf, Gregory
- Fong, Kwun M.
- Yang, Ian
- Rathmell, W. Kimryn
- Kovatich, Albert J.
- Shriver, Craig D.
- DiPersio, John
- Drake, Bettina
- Govindan, Ramaswamy
- Heath, Sharon
- Ley, Timothy
- Rubin, Mark A.
- Lee, Jung Il
- Aredes, Natália D.
- Mariamidze, Armaz
- Venue
- Cell
- Publisher
- Elsevier BV
- Published
- 2018-04
- Volume
- 173
- Issue
- 2
- Pages
- 291-304.e6
- ISSN
- 0092-8674 (ISSN-L)
- PMC
- PMC5957518
- OpenAlex
- W2796153844
- Cited by
- 2,546
- References
- 58
- Citations by year
- 2026: 284 · 2025: 294 · 2024: 296 · 2023: 355 · 2022: 375 · 2021: 374 · 2020: 330 · 2019: 178 · 2018: 56
- FWCI
- 71.94
- Type
- journal article
- Language
- en
- Open access
- hybrid
- doi.org
- Licence
- Locations
- Cell (publishedVersion, cc-by-nc-nd)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion, cc-by-nc-nd)
- PubMed Central (acceptedVersion, cc-by-nc-nd)
- Minerva Access (University of Melbourne) (submittedVersion, cc-by-nc-nd)
- UWA Profiles and Research Repository (UWA) (submittedVersion, cc-by)
- Archivio Istituzionale della Ricerca (Universita Degli Studi Di Milano) (submittedVersion, other-oa)
- Bern Open Repository and Information System (University of Bern) (submittedVersion, cc-by-nc-nd)
- Archivio istituzionale della ricerca (Alma Mater Studiorum Università di Bologna) (submittedVersion)
- Utrecht University Repository (Utrecht University) (submittedVersion, other-oa)
- eScholarship (California Digital Library) (submittedVersion)
- Florence Research (University of Florence) (submittedVersion)
- IRIS Research product catalog (Sapienza University of Rome) (submittedVersion, cc-by-nc-nd)
- mediaTUM (Technical University of Munich) (submittedVersion, other-oa)
- Institutional Research Information System University of Ferrara (University of Ferrara) (submittedVersion, cc-by-nc-nd)
- Spiral (Imperial College London) (submittedVersion, cc-by-nc-nd)
- Funders
- National Human Genome Research Institute
- National Cancer Institute
- National Institutes of Health (U24 CA143866, U24 CA143843, P30 CA016672, U24 CA143867, U24 CA143840, U24 CA143882, U24 CA143858, U24 CA143835, U54 HG003273, U24 CA143883, U24 CA143848, U24 CA144025, U24 CA143845, U54 HG003079, U24 CA143799, U54 HG003067)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene expression and cancer classification
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
- Keywords
- cell of origin, molecular classification of cancer, pan-cancer analysis, TCGA, aneuploidy, DNA methylation, mRNA expression, microRNA expression, reverse phase protein array, histological subtypes, tissue type, stemness, molecular clustering
- MeSH terms
- Aneuploidy, Chromosomes, Humans, Mutation, Neoplasm Proteins, Neoplasms, RNA, Messenger, Cluster Analysis, Databases, Factual, CpG Islands, DNA Methylation, MicroRNAs
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.
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