Pan-cancer analysis of the extent and consequences of intratumor heterogeneity (original) (raw)
Marusyk, A. & Polyak, K. Tumor heterogeneity: causes and consequences. Biochim. Biophys. Acta1805, 105–117 (2010). CASPubMed Google Scholar
Bonavia, R., Inda, M.-M., Cavenee, W.K. & Furnari, F.B. Heterogeneity maintenance in glioblastoma: a social network. Cancer Res.71, 4055–4060 (2011). ArticleCASPubMedPubMed Central Google Scholar
McGranahan, N. et al. Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Sci. Transl. Med.7, 283ra54 (2015). ArticlePubMedPubMed Central Google Scholar
Mroz, E.A., Tward, A.D., Hammon, R.J., Ren, Y. & Rocco, J.W. Intratumor genetic heterogeneity and mortality in head and neck cancer: analysis of data from the Cancer Genome Atlas. PLoS Med.12, e1001786 (2015). ArticleCASPubMedPubMed Central Google Scholar
Almendro, V. et al. Inference of tumor evolution during chemotherapy by computational modeling and in situ analysis of genetic and phenotypic cellular diversity. Cell Rep.6, 514–527 (2014). ArticleCASPubMedPubMed Central Google Scholar
Gerlinger, M. et al. Intratumor heterogeneity and branched evolution revealed by multiregion sequencing. N. Engl. J. Med.366, 883–892 (2012). ArticleCASPubMedPubMed Central Google Scholar
Oesper, L., Satas, G. & Raphael, B.J. Quantifying tumor heterogeneity in whole-genome and whole-exome sequencing data. Bioinformatics30, 3532–3540 (2014). ArticleCASPubMedPubMed Central Google Scholar
Li, B. & Li, J.Z. A general framework for analyzing tumor subclonality using SNP array and DNA sequencing data. Genome Biol.15, 473 (2014). ArticleCASPubMedPubMed Central Google Scholar
Andor, N., Harness, J.V., Müller, S., Mewes, H.W. & Petritsch, C. EXPANDS: expanding ploidy and allele frequency on nested subpopulations. Bioinformatics30, 50–60 (2014). ArticleCASPubMed Google Scholar
Ha, G. et al. TITAN: inference of copy number architectures in clonal cell populations from tumor whole-genome sequence data. Genome Res.24, 1881–1893 (2014). ArticleCASPubMedPubMed Central Google Scholar
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol.31, 213–219 (2013). ArticleCASPubMedPubMed Central Google Scholar
Sathirapongsasuti, J.F. et al. Exome sequencing–based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics27, 2648–2654 (2011). ArticleCASPubMedPubMed Central Google Scholar
Barber, L.J., Davies, M.N. & Gerlinger, M. Dissecting cancer evolution at the macro-heterogeneity and micro-heterogeneity scale. Curr. Opin. Genet. Dev.30, 1–6 (2015). ArticleCASPubMedPubMed Central Google Scholar
Yadav, V.K. & De, S. An assessment of computational methods for estimating purity and clonality using genomic data derived from heterogeneous tumor tissue samples. Brief. Bioinform.16, 232–241 (2015). ArticleCASPubMed Google Scholar
Yoshihara, K. et al. Inferring tumor purity, and stromal and immune cell admixture from expression data. Nat. Commun.4, 2612 (2013). ArticleCASPubMed Google Scholar
Tajiri, R. et al. Intratumoral heterogeneous amplification of ERBB2 and subclonal genetic diversity in gastric cancers revealed by multiple ligation-dependent probe amplification and fluorescence in situ hybridization. Hum. Pathol.45, 725–734. ArticleCASPubMed Google Scholar
Sakurada, A., Lara-Guerra, H., Liu, N., Shepherd, F.A. & Tsao, M.-S. Tissue heterogeneity of EGFR mutation in lung adenocarcinoma. J. Thorac. Oncol.3, 527–529 (2008). ArticlePubMed Google Scholar
Vitale, M. Intratumor _BRAF_V600E heterogeneity and kinase inhibitors in the treatment of thyroid cancer: a call for participation. Thyroid23, 517–519 (2013). ArticlePubMed Google Scholar
Carpenter, A.E. et al. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biol.7, R100 (2006). ArticleCASPubMedPubMed Central Google Scholar
Wang, W., Ozolek, J.A. & Rohde, G.K. Detection and classification of thyroid follicular lesions based on nuclear structure from histopathology images. Cytometry A77, 485–494 (2010). PubMedPubMed Central Google Scholar
Hartwell, K.A. et al. Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nat. Chem. Biol.9, 840–848 (2013). ArticleCASPubMedPubMed Central Google Scholar
Yamamoto, S. et al. Clinical relevance of Ki67 gene expression analysis using formalin-fixed paraffin-embedded breast cancer specimens. Breast Cancer20, 262–270 (2013). ArticlePubMed Google Scholar
Cazier, J.-B. et al. Whole-genome sequencing of bladder cancers reveals somatic CDKN1A mutations and clinicopathological associations with mutation burden. Nat. Commun.5, 3756 (2014). ArticleCASPubMed Google Scholar
Swanton, C. Cancer evolution constrained by mutation order. N. Engl. J. Med.372, 661–663 (2015). ArticleCASPubMed Google Scholar
Cancer Genome Atlas Research Network. et al. Comprehensive, integrative genomic analysis of diffuse lower-grade gliomas. N. Engl. J. Med.372, 2481–2498 (2015).
Roylance, R. et al. Relationship of extreme chromosomal instability with long-term survival in a retrospective analysis of primary breast cancer. Cancer Epidemiol. Biomarkers Prev.20, 2183–2194 (2011). ArticlePubMedPubMed Central Google Scholar
Birkbak, N.J. et al. Paradoxical relationship between chromosomal instability and survival outcome in cancer. Cancer Res.71, 3447–3452 (2011). ArticleCASPubMedPubMed Central Google Scholar
Bochtler, T. et al. Clonal heterogeneity as detected by metaphase karyotyping is an indicator of poor prognosis in acute myeloid leukemia. J. Clin. Oncol.31, 3898–3905 (2013). ArticlePubMed Google Scholar
Merlo, L.M.F. et al. A comprehensive survey of clonal diversity measures in Barrett’s esophagus as biomarkers of progression to esophageal adenocarcinoma. Cancer Prev. Res. (Phila.)3, 1388–1397 (2010). Article Google Scholar
Maley, C.C. et al. Genetic clonal diversity predicts progression to esophageal adenocarcinoma. Nat. Genet.38, 468–473 (2006). ArticleCASPubMed Google Scholar
Cibulskis, K. et al. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat. Biotechnol.31, 213–219 (2013). ArticleCASPubMedPubMed Central Google Scholar
Roth, A. et al. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal-tumor–paired next-generation sequencing data. Bioinformatics28, 907–913 (2012). ArticleCASPubMedPubMed Central Google Scholar
Sathirapongsasuti, J.F. et al. Exome sequencing–based copy-number variation and loss of heterozygosity detection: ExomeCNV. Bioinformatics27, 2648–2654 (2011). ArticleCASPubMedPubMed Central Google Scholar
Andor, N., Harness, J.V., Müller, S., Mewes, H.W. & Petritsch, C. EXPANDS: expanding ploidy and allele frequency on nested subpopulations. Bioinformatics30, 50–60 (2014). ArticleCASPubMed Google Scholar
Goode, A., Gilbert, B., Harkes, J., Jukic, D. & Satyanarayanan, M. OpenSlide: a vendor-neutral software foundation for digital pathology. J. Pathol. Inform.4, 27 (2013). ArticlePubMedPubMed Central Google Scholar
Kircher, M. et al. A general framework for estimating the relative pathogenicity of human genetic variants. Nat. Genet.46, 310–315 (2014). ArticleCASPubMedPubMed Central Google Scholar
Huang, D.W., Sherman, B.T. & Lempicki, R.A. Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources. Nat. Protoc.4, 44–57 (2009). ArticleCAS Google Scholar
Huang, D.W., Sherman, B.T. & Lempicki, R.A. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res.37, 1–13 (2009). ArticleCAS Google Scholar