Abstract
Cancer results from genetic and epigenetic aberrations, many of which alter the levels of expressed genes and proteins. In the past, cancer researchers have studied genes mainly one at a time. Increasingly, researchers are using genomic technologies like DNA microarrays and next-generation DNA sequencing to investigate thousands of genes simultaneously, defining genes and pathways relevant to cancer mechanisms, diagnosis, prognostication, and treatment. This chapter details genomics technologies, their use and applications in cancer research, and their potential utility in oncologic practice.
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References
Schena M, Shalon D, Davis RW, Brown PO. Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science. 1995;270:467–70.
Fodor SP, Rava RP, Huang XC, Pease AC, et al. Multiplexed biochemical assays with biological chips. Nature. 1993;364:555–6.
Lockhart DJ, Dong H, Byrne MC, Follettie MT, et al. Expression monitoring by hybridization to high-density oligonucleotide arrays. Nat Biotechnol. 1996;14:1675–80.
Novoradovskaya N, Whitfield ML, Basehore LS, Novoradovsky A, et al. Universal reference RNA as a standard for microarray experiments. BMC Genomics. 2004;5:20.
Eisen MB, Brown PO. DNA arrays for analysis of gene expression. Methods Enzymol. 1999;303:179–205.
Allison DB, Cui X, Page GP, Sabripour M. Microarray data analysis: from disarray to consolidation and consensus. Nat Rev Genet. 2006;7:55–65.
Pavlidis P, Li Q, Noble WS. The effect of replication on gene expression microarray experiments. Bioinformatics. 2003;19:1620–7.
Emmert-Buck MR, Bonner RF, Smith PD, Chuaqui RF, et al. Laser capture microdissection. Science. 1996;274:998–1001.
Perou CM, Sorlie T, Eisen MB, van de Rijn M, et al. Molecular portraits of human breast tumours. Nature. 2000;406:747–52.
Stuart RO, Wachsman W, Berry CC, Wang-Rodriguez J, et al. In silico dissection of cell-type-associated patterns of gene expression in prostate cancer. Proc Natl Acad Sci U S A. 2004;101:615–20.
Van Gelder RN, von Zastrow ME, Yool A, Dement WC, et al. Amplified RNA synthesized from limited quantities of heterogeneous cDNA. Proc Natl Acad Sci U S A. 1990;87:1663–7.
Stears RL, Getts RC, Gullans SR. A novel, sensitive detection system for high-density microarrays using dendrimer technology. Physiol Genomics. 2000;3:93–9.
Ma XJ, Wang Z, Ryan PD, Isakoff SJ, et al. A two-gene expression ratio predicts clinical outcome in breast cancer patients treated with tamoxifen. Cancer Cell. 2004;5:607–16.
April C, Klotzle B, Royce T, Wickham-Garcia E, et al. Whole-genome gene expression profiling of formalin-fixed, paraffin-embedded tissue samples. PLoS One. 2009;4:e8162.
Quackenbush J. Microarray data normalization and transformation. Nat Genet. 2002;32(Suppl):496–501.
Brazma A, Hingamp P, Quackenbush J, Sherlock G, et al. Minimum information about a microarray experiment (MIAME)-toward standards for microarray data. Nat Genet. 2001;29:365–71.
Barrett T, Troup DB, Wilhite SE, Ledoux P, et al. NCBI GEO: mining tens of millions of expression profiles—database and tools update. Nucleic Acids Res. 2007;35:D760–5.
Parkinson H, Kapushesky M, Shojatalab M, Abeygunawardena N, et al. ArrayExpress—a public database of microarray experiments and gene expression profiles. Nucleic Acids Res. 2007;35:D747–50.
Demeter J, Beauheim C, Gollub J, Hernandez-Boussard T, et al. The Stanford Microarray Database: implementation of new analysis tools and open source release of software. Nucleic Acids Res. 2007;35:D766–70.
Xu X, Zhao Y, Simon R. Gene set expression comparison kit for BRB-ArrayTools. Bioinformatics. 2008;24:137–9.
Dresen IM, Husing J, Kruse E, Boes T, Jockel KH. Software packages for quantitative microarray-based gene expression analysis. Curr Pharm Biotechnol. 2003;4:417–37.
Rhodes DR, Kalyana-Sundaram S, Mahavisno V, Varambally R, et al. Oncomine 3.0: genes, pathways, and networks in a collection of 18,000 cancer gene expression profiles. Neoplasia. 2007;9:166–80.
Butte A. The use and analysis of microarray data. Nat Rev Drug Discov. 2002;1:951–60.
Quackenbush J. Computational analysis of microarray data. Nat Rev Genet. 2001;2:418–27.
Tusher VG, Tibshirani R, Chu G. Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci U S A. 2001;98:5116–21.
Golub TR, Slonim DK, Tamayo P, Huard C, et al. Molecular classification of cancer: class discovery and class prediction by gene expression monitoring. Science. 1999;286:531–7.
Tibshirani R, Hastie T, Narasimhan B, Chu G. Diagnosis of multiple cancer types by shrunken centroids of gene expression. Proc Natl Acad Sci U S A. 2002;99:6567–72.
Eisen MB, Spellman PT, Brown PO, Botstein D. Cluster analysis and display of genome-wide expression patterns. Proc Natl Acad Sci U S A. 1998;95:14863–8.
Ashburner M, Ball CA, Blake JA, Botstein D, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000;25:25–9.
Kanehisa M, Goto S, Kawashima S, Nakaya A. The KEGG databases at GenomeNet. Nucleic Acids Res. 2002;30:42–6.
Dahlquist KD, Salomonis N, Vranizan K, Lawlor SC, Conklin BR. GenMAPP, a new tool for viewing and analyzing microarray data on biological pathways. Nat Genet. 2002;31:19–20.
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, et al. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proc Natl Acad Sci U S A. 2005;102:15545–50.
Rhodes DR, Kalyana-Sundaram S, Tomlins SA, Mahavisno V, et al. Molecular concepts analysis links tumors, pathways, mechanisms, and drugs. Neoplasia. 2007;9:443–54.
Ransohoff DF. Rules of evidence for cancer molecular-marker discovery and validation. Nat Rev Cancer. 2004;4:309–14.
Lembersky BC, Thomas LC. Metastases of unknown primary site. Med Clin North Am. 1996;80:153–71.
Abbruzzese JL, Abbruzzese MC, Lenzi R, Hess KR, Raber MN. Analysis of a diagnostic strategy for patients with suspected tumors of unknown origin. J Clin Oncol. 1995;13:2094–103.
Su AI, Welsh JB, Sapinoso LM, Kern SG, et al. Molecular classification of human carcinomas by use of gene expression signatures. Cancer Res. 2001;61:7388–93.
Ramaswamy S, Tamayo P, Rifkin R, Mukherjee S, et al. Multiclass cancer diagnosis using tumor gene expression signatures. Proc Natl Acad Sci U S A. 2001;98:15149–54.
Tothill RW, Kowalczyk A, Rischin D, Bousioutas A, et al. An expression-based site of origin diagnostic method designed for clinical application to cancer of unknown origin. Cancer Res. 2005;65:4031–40.
Monzon FA, Lyons-Weiler M, Buturovic LJ, Rigl CT, et al. Multicenter validation of a 1,550-gene expression profile for identification of tumor tissue of origin. J Clin Oncol. 2009;27:2503–8.
Alizadeh AA, Eisen MB, Davis RE, Ma C, et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature. 2000;403:503–11.
Davis RE, Brown KD, Siebenlist U, Staudt LM. Constitutive nuclear factor kappaB activity is required for survival of activated B cell-like diffuse large B cell lymphoma cells. J Exp Med. 2001;194:1861–74.
Lossos IS, Jones CD, Warnke R, Natkunam Y, et al. Expression of a single gene, BCL-6, strongly predicts survival in patients with diffuse large B-cell lymphoma. Blood. 2001;98:945–51.
Sorlie T, Perou CM, Tibshirani R, Aas T, et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc Natl Acad Sci U S A. 2001;98:10869–74.
Chung CH, Bernard PS, Perou CM. Molecular portraits and the family tree of cancer. Nat Genet. 2002;32(Suppl):533–40.
van 't Veer LJ, Dai H, van de Vijver MJ, He YD, et al. Gene expression profiling predicts clinical outcome of breast cancer. Nature. 2002;415:530–6.
van de Vijver MJ, He YD, van't Veer LJ, Dai H, et al. A gene-expression signature as a predictor of survival in breast cancer. N Engl J Med. 2002;347:1999–2009.
Eden P, Ritz C, Rose C, Ferno M, Peterson C. “Good Old” clinical markers have similar power in breast cancer prognosis as microarray gene expression profilers. Eur J Cancer. 2004;40:1837–41.
Bullinger L, Dohner K, Bair E, Frohling S, et al. Use of gene-expression profiling to identify prognostic subclasses in adult acute myeloid leukemia. N Engl J Med. 2004;350:1605–16.
Radmacher MD, Marcucci G, Ruppert AS, Mrozek K, et al. Independent confirmation of a prognostic gene-expression signature in adult acute myeloid leukemia with a normal karyotype: a Cancer and Leukemia Group B study. Blood. 2006;108:1677–83.
Ramaswamy S, Ross KN, Lander ES, Golub TR. A molecular signature of metastasis in primary solid tumors. Nat Genet. 2003;33:49–54.
Tomlins SA, Rhodes DR, Perner S, Dhanasekaran SM, et al. Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science. 2005;310:644–8.
Armstrong SA, Staunton JE, Silverman LB, Pieters R, et al. MLL translocations specify a distinct gene expression profile that distinguishes a unique leukemia. Nat Genet. 2002;30:41–7.
Armstrong SA, Kung AL, Mabon ME, Silverman LB, et al. Inhibition of FLT3 in MLL. Validation of a therapeutic target identified by gene expression based classification. Cancer Cell. 2003;3:173–83.
Lamb J, Crawford ED, Peck D, Modell JW, et al. The Connectivity Map: using gene-expression signatures to connect small molecules, genes, and disease. Science. 2006;313:1929–35.
Wei G, Twomey D, Lamb J, Schlis K, et al. Gene expression-based chemical genomics identifies rapamycin as a modulator of MCL1 and glucocorticoid resistance. Cancer Cell. 2006;10:331–42.
Kallioniemi A, Kallioniemi OP, Sudar D, Rutovitz D, et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science. 1992;258:818–21.
Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, et al. Matrix-based comparative genomic hybridization: biochips to screen for genomic imbalances. Genes Chromosomes Cancer. 1997;20:399–407.
Pinkel D, Segraves R, Sudar D, Clark S, et al. High resolution analysis of DNA copy number variation using comparative genomic hybridization to microarrays. Nat Genet. 1998;20:207–11.
Pollack JR, Perou CM, Alizadeh AA, Eisen MB, et al. Genome-wide analysis of DNA copy-number changes using cDNA microarrays. Nat Genet. 1999;23:41–6.
Lucito R, Healy J, Alexander J, Reiner A, et al. Representational oligonucleotide microarray analysis: a high-resolution method to detect genome copy number variation. Genome Res. 2003;13:2291–305.
Barrett MT, Scheffer A, Ben-Dor A, Sampas N, et al. Comparative genomic hybridization using oligonucleotide microarrays and total genomic DNA. Proc Natl Acad Sci U S A. 2004;101:17765–70.
Selzer RR, Richmond TA, Pofahl NJ, Green RD, et al. Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer. 2005;44:305–19.
Olshen AB, Venkatraman ES, Lucito R, Wigler M. Circular binary segmentation for the analysis of array-based DNA copy number data. Biostatistics. 2004;5:557–72.
Tibshirani R, Wang P. Spatial smoothing and hot spot detection for CGH data using the fused lasso. Biostatistics. 2008;9:18–29.
Diskin SJ, Eck T, Greshock J, Mosse YP, et al. STAC: a method for testing the significance of DNA copy number aberrations across multiple array-CGH experiments. Genome Res. 2006;16:1149–58.
Beroukhim R, Getz G, Nghiemphu L, Barretina J, et al. Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma. Proc Natl Acad Sci U S A. 2007;104:20007–12.
Feuk L, Carson AR, Scherer SW. Structural variation in the human genome. Nat Rev Genet. 2006;7:85–97.
Kruglyak L, Nickerson DA. Variation is the spice of life. Nat Genet. 2001;27:234–6.
Frazer KA, Ballinger DG, Cox DR, Hinds DA, et al. A second generation human haplotype map of over 3.1 million SNPs. Nature. 2007;449:851–61.
Kennedy GC, Matsuzaki H, Dong S, Liu WM, et al. Large-scale genotyping of complex DNA. Nat Biotechnol. 2003;21:1233–7.
Gunderson KL, Steemers FJ, Ren H, Ng P, et al. Whole-genome genotyping. Methods Enzymol. 2006;410:359–76.
Hirschhorn JN, Daly MJ. Genome-wide association studies for common diseases and complex traits. Nat Rev Genet. 2005;6:95–108.
Stadler ZK, Thom P, Robson ME, Weitzel JN, et al. Genome-wide association studies of cancer. J Clin Oncol. 2010;28:4255–67.
Mei R, Galipeau PC, Prass C, Berno A, et al. Genome-wide detection of allelic imbalance using human SNPs and high-density DNA arrays. Genome Res. 2000;10:1126–37.
Zhao X, Li C, Paez JG, Chin K, et al. An integrated view of copy number and allelic alterations in the cancer genome using single nucleotide polymorphism arrays. Cancer Res. 2004;64:3060–71.
Albertson DG, Ylstra B, Segraves R, Collins C, et al. Quantitative mapping of amplicon structure by array CGH identifies CYP24 as a candidate oncogene. Nat Genet. 2000;25:144–6.
Li J, Yang Y, Peng Y, Austin RJ, et al. Oncogenic properties of PPM1D located within a breast cancer amplification epicenter at 17q23. Nat Genet. 2002;31:133–4.
Garraway LA, Widlund HR, Rubin MA, Getz G, et al. Integrative genomic analyses identify MITF as a lineage survival oncogene amplified in malignant melanoma. Nature. 2005;436:117–22.
Garraway LA, Sellers WR. Lineage dependency and lineage-survival oncogenes in human cancer. Nat Rev Cancer. 2006;6:593–602.
Kendall J, Liu Q, Bakleh A, Krasnitz A, et al. Oncogenic cooperation and coamplification of developmental transcription factor genes in lung cancer. Proc Natl Acad Sci U S A. 2007;104:16663–8.
Weir BA, Woo MS, Getz G, Perner S, et al. Characterizing the cancer genome in lung adenocarcinoma. Nature. 2007;450:893–8.
Kwei KA, Kim YH, Girard L, Kao J, et al. Genomic profiling identifies TITF1 as a lineage-specific oncogene amplified in lung cancer. Oncogene. 2008;27:3635–40.
Kane S, Gottesman M. The role of cathepsin L in malignant transformation. Semin Cancer Biol. 1990;1:127–36.
Carrasco DR, Tonon G, Huang Y, Zhang Y, et al. High-resolution genomic profiles define distinct clinico-pathogenetic subgroups of multiple myeloma patients. Cancer Cell. 2006;9:313–25.
Fridlyand J, Snijders AM, Ylstra B, Li H, et al. Breast tumor copy number aberration phenotypes and genomic instability. BMC Cancer. 2006;6:96.
Hicks J, Krasnitz A, Lakshmi B, Navin NE, et al. Novel patterns of genome rearrangement and their association with survival in breast cancer. Genome Res. 2006;16:1465–79.
Chin K, DeVries S, Fridlyand J, Spellman PT, et al. Genomic and transcriptional aberrations linked to breast cancer pathophysiologies. Cancer Cell. 2006;10:529–41.
Pollack JR, Sorlie T, Perou CM, Rees CA, et al. Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors. Proc Natl Acad Sci U S A. 2002;99:12963–8.
Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, et al. Impact of DNA amplification on gene expression patterns in breast cancer. Cancer Res. 2002;62:6240–5.
Bergamaschi A, Kim YH, Wang P, Sorlie T, et al. Distinct patterns of DNA copy number alteration are associated with different clinicopathological features and gene-expression subtypes of breast cancer. Genes Chromosomes Cancer. 2006;45:1033–40.
Carroll JS, Meyer CA, Song J, Li W, et al. Genome-wide analysis of estrogen receptor binding sites. Nat Genet. 2006;38:1289–97.
Pujana MA, Han JD, Starita LM, Stevens KN, et al. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet. 2007;39:1338–49.
Calvo S, Jain M, Xie X, Sheth SA, et al. Systematic identification of human mitochondrial disease genes through integrative genomics. Nat Genet. 2006;38:576–82.
Weinstein JN. Integromic analysis of the NCI-60 cancer cell lines. Breast Dis. 2004;19:11–22.
Turner NC, Reis-Filho JS. Basal-like breast cancer and the BRCA1 phenotype. Oncogene. 2006;25:5846–53.
Cheok MH, Evans WE. Acute lymphoblastic leukaemia: a model for the pharmacogenomics of cancer therapy. Nat Rev Cancer. 2006;6:117–29.
Herman JG, Baylin SB. Gene silencing in cancer in association with promoter hypermethylation. N Engl J Med. 2003;349:2042–54.
Yan PS, Chen CM, Shi H, Rahmatpanah F, et al. Dissecting complex epigenetic alterations in breast cancer using CpG island microarrays. Cancer Res. 2001;61:8375–80.
Weber M, Davies JJ, Wittig D, Oakeley EJ, et al. Chromosome-wide and promoter-specific analyses identify sites of differential DNA methylation in normal and transformed human cells. Nat Genet. 2005;37:853–62.
Gitan RS, Shi H, Chen CM, Yan PS, Huang TH. Methylation-specific oligonucleotide microarray: a new potential for high-throughput methylation analysis. Genome Res. 2002;12:158–64.
Bernstein BE, Kamal M, Lindblad-Toh K, Bekiranov S, et al. Genomic maps and comparative analysis of histone modifications in human and mouse. Cell. 2005;120:169–81.
Weinmann AS, Yan PS, Oberley MJ, Huang TH, Farnham PJ. Isolating human transcription factor targets by coupling chromatin immunoprecipitation and CpG island microarray analysis. Genes Dev. 2002;16:235–44.
Ziauddin J, Sabatini DM. Microarrays of cells expressing defined cDNAs. Nature. 2001;411:107–10.
Mousses S, Caplen NJ, Cornelison R, Weaver D, et al. RNAi microarray analysis in cultured mammalian cells. Genome Res. 2003;13:2341–7.
Silva JM, Mizuno H, Brady A, Lucito R, Hannon GJ. RNA interference microarrays: high-throughput loss-of-function genetics in mammalian cells. Proc Natl Acad Sci U S A. 2004;101:6548–52.
Haab BB, Dunham MJ, Brown PO. Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions. Genome Biol. 2001;2:RESEARCH0004.
Sreekumar A, Nyati MK, Varambally S, Barrette TR, et al. Profiling of cancer cells using protein microarrays: discovery of novel radiation-regulated proteins. Cancer Res. 2001;61:7585–93.
MacBeath G, Schreiber SL. Printing proteins as microarrays for high-throughput function determination. Science. 2000;289:1760–3.
Scanlan MJ, Welt S, Gordon CM, Chen YT, et al. Cancer-related serological recognition of human colon cancer: identification of potential diagnostic and immunotherapeutic targets. Cancer Res. 2002;62:4041–7.
Kononen J, Bubendorf L, Kallioniemi A, Barlund M, et al. Tissue microarrays for high-throughput molecular profiling of tumor specimens. Nat Med. 1998;4:844–7.
Xu J, Stolk JA, Zhang X, Silva SJ, et al. Identification of differentially expressed genes in human prostate cancer using subtraction and microarray. Cancer Res. 2000;60:1677–82.
Luo J, Zha S, Gage WR, Dunn TA, et al. Alpha-methylacyl-CoA racemase: a new molecular marker for prostate cancer. Cancer Res. 2002;62:2220–6.
Rubin MA, Zhou M, Dhanasekaran SM, Varambally S, et al. Alpha-methylacyl coenzyme A racemase as a tissue biomarker for prostate cancer. JAMA. 2002;287:1662–70.
Glas AM, Floore A, Delahaye LJ, Witteveen AT, et al. Converting a breast cancer microarray signature into a high-throughput diagnostic test. BMC Genomics. 2006;7:278.
Paik S, Shak S, Tang G, Kim C, et al. A multigene assay to predict recurrence of tamoxifen-treated, node-negative breast cancer. N Engl J Med. 2004;351:2817–26.
Chang HY, Sneddon JB, Alizadeh AA, Sood R, et al. Gene expression signature of fibroblast serum response predicts human cancer progression: similarities between tumors and wounds. PLoS Biol. 2004;2:E7.
Glinsky GV, Berezovska O, Glinskii AB. Microarray analysis identifies a death-from-cancer signature predicting therapy failure in patients with multiple types of cancer. J Clin Invest. 2005;115:1503–21.
West RB, Nuyten DS, Subramanian S, Nielsen TO, et al. Determination of stromal signatures in breast carcinoma. PLoS Biol. 2005;3:e187.
Bild AH, Yao G, Chang JT, Wang Q, et al. Oncogenic pathway signatures in human cancers as a guide to targeted therapies. Nature. 2006;439:353–7.
Chi JT, Wang Z, Nuyten DS, Rodriguez EH, et al. Gene expression programs in response to hypoxia: cell type specificity and prognostic significance in human cancers. PLoS Med. 2006;3:e47.
Carter SL, Eklund AC, Kohane IS, Harris LN, Szallasi Z. A signature of chromosomal instability inferred from gene expression profiles predicts clinical outcome in multiple human cancers. Nat Genet. 2006;38:1043–8.
Liu R, Wang X, Chen GY, Dalerba P, et al. The prognostic role of a gene signature from tumorigenic breast-cancer cells. N Engl J Med. 2007;356:217–26.
Petricoin 3rd EF, Hackett JL, Lesko LJ, Puri RK, et al. Medical applications of microarray technologies: a regulatory science perspective. Nat Genet. 2002;32(Suppl):474–9.
Bammler T, Beyer RP, Bhattacharya S, Boorman GA, et al. Standardizing global gene expression analysis between laboratories and across platforms. Nat Methods. 2005;2:351–6.
Irizarry RA, Warren D, Spencer F, Kim IF, et al. Multiple-laboratory comparison of microarray platforms. Nat Methods. 2005;2:345–50.
Fan C, Oh DS, Wessels L, Weigelt B, et al. Concordance among gene-expression-based predictors for breast cancer. N Engl J Med. 2006;355:560–9.
Lander ES, Linton LM, Birren B, Nusbaum C, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921.
Davies H, Bignell GR, Cox C, Stephens P, et al. Mutations of the BRAF gene in human cancer. Nature. 2002;417:949–54.
Samuels Y, Wang Z, Bardelli A, Silliman N, et al. High frequency of mutations of the PIK3CA gene in human cancers. Science. 2004;304:554.
Bachman KE, Argani P, Samuels Y, Silliman N, et al. The PIK3CA gene is mutated with high frequency in human breast cancers. Cancer Biol Ther. 2004;3:772–5.
Campbell IG, Russell SE, Choong DY, Montgomery KG, et al. Mutation of the PIK3CA gene in ovarian and breast cancer. Cancer Res. 2004;64:7678–81.
Sjoblom T, Jones S, Wood LD, Parsons DW, et al. The consensus coding sequences of human breast and colorectal cancers. Science. 2006;314:268–74.
Greenman C, Stephens P, Smith R, Dalgliesh GL, et al. Patterns of somatic mutation in human cancer genomes. Nature. 2007;446:153–8.
Velculescu VE, Zhang L, Vogelstein B, Kinzler KW. Serial analysis of gene expression. Science. 1995;270:484–7.
Matsumura H, Reich S, Ito A, Saitoh H, et al. Gene expression analysis of plant host-pathogen interactions by SuperSAGE. Proc Natl Acad Sci U S A. 2003;100:15718–23.
Shendure JA, Porreca GJ, Church GM. Overview of DNA sequencing strategies. Curr Protoc Mol Biol. 2008. Chapter 7:Unit 7.1.
Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet. 2008;9:387–402.
Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol. 2008;26:1135–45.
Margulies M, Egholm M, Altman WE, Attiya S, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature. 2005;437:376–80.
Shendure J, Porreca GJ, Reppas NB, Lin X, et al. Accurate multiplex polony sequencing of an evolved bacterial genome. Science. 2005;309:1728–32.
Harris TD, Buzby PR, Babcock H, Beer E, et al. Single-molecule DNA sequencing of a viral genome. Science. 2008;320:106–9.
Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing. Hum Mol Genet. 2010;19:R227–40.
Service RF. Gene sequencing. The race for the $1000 genome. Science. 2006;311:1544–6.
Morozova O, Marra MA. Applications of next-generation sequencing technologies in functional genomics. Genomics. 2008;92:255–64.
Wold B, Myers RM. Sequence census methods for functional genomics. Nat Methods. 2008;5:19–21.
Mortazavi A, Williams BA, McCue K, Schaeffer L, Wold B. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nat Methods. 2008;5:621–8.
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63.
Pepke S, Wold B, Mortazavi A. Computation for ChIP-seq and RNA-seq studies. Nat Methods. 2009;6:S22–32.
Maher CA, Kumar-Sinha C, Cao X, Kalyana-Sundaram S, et al. Transcriptome sequencing to detect gene fusions in cancer. Nature. 2009;458:97–101.
Palanisamy N, Ateeq B, Kalyana-Sundaram S, Pflueger D, et al. Rearrangements of the RAF kinase pathway in prostate cancer, gastric cancer and melanoma. Nat Med. 2010;16:793–8.
Beck AH, Weng Z, Witten DM, Zhu S, et al. 3′-End sequencing for expression quantification (3SEQ) from archival tumor samples. PLoS One. 2010;5:e8768.
Barski A, Cuddapah S, Cui K, Roh TY, et al. High-resolution profiling of histone methylations in the human genome. Cell. 2007;129:823–37.
Johnson DS, Mortazavi A, Myers RM, Wold B. Genome-wide mapping of in vivo protein-DNA interactions. Science. 2007;316:1497–502.
Park PJ. ChIP-seq: advantages and challenges of a maturing technology. Nat Rev Genet. 2009;10:669–80.
Brunner AL, Johnson DS, Kim SW, Valouev A, et al. Distinct DNA methylation patterns characterize differentiated human embryonic stem cells and developing human fetal liver. Genome Res. 2009;19:1044–56.
Fouse SD, Nagarajan RP, Costello JF. Genome-scale DNA methylation analysis. Epigenomics. 2010;2:105–17.
Volik S, Zhao S, Chin K, Brebner JH, et al. End-sequence profiling: sequence-based analysis of aberrant genomes. Proc Natl Acad Sci U S A. 2003;100:7696–701.
Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, et al. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet. 2008;40:722–9.
Stephens PJ, McBride DJ, Lin ML, Varela I, et al. Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature. 2009;462:1005–10.
Parsons DW, Jones S, Zhang X, Lin JC, et al. An integrated genomic analysis of human glioblastoma multiforme. Science. 2008;321:1807–12.
Dang L, White DW, Gross S, Bennett BD, et al. Cancer-associated IDH1 mutations produce 2-hydroxyglutarate. Nature. 2009;462:739–44.
Gnirke A, Melnikov A, Maguire J, Rogov P, et al. Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nat Biotechnol. 2009;27:182–9.
Ley TJ, Mardis ER, Ding L, Fulton B, et al. DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature. 2008;456:66–72.
Wiegand KC, Shah SP, Al-Agha OM, Zhao Y, et al. ARID1A mutations in endometriosis-associated ovarian carcinomas. N Engl J Med. 2010;363:1532–43.
Ley TJ, Ding L, Walter MJ, McLellan MD, et al. DNMT3A mutations in acute myeloid leukemia. N Engl J Med. 2010;363:2424–33.
Stratton MR, Campbell PJ, Futreal PA. The cancer genome. Nature. 2009;458:719–24.
Pleasance ED, Stephens PJ, O'Meara S, McBride DJ, et al. A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature. 2009;463:184–90.
Pleasance ED, Cheetham RK, Stephens PJ, McBride DJ, et al. A comprehensive catalogue of somatic mutations from a human cancer genome. Nature. 2010;463:191–6.
Hudson TJ, Anderson W, Artez A, Barker AD, et al. International network of cancer genome projects. Nature. 2010;464:993–8.
Forbes SA, Tang G, Bindal N, Bamford S, et al. COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer. Nucleic Acids Res. 2010;38:D652–7.
MacConaill LE, Campbell CD, Kehoe SM, Bass AJ, et al. Profiling critical cancer gene mutations in clinical tumor samples. PLoS One. 2009;4:e7887.
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Pollack, J.R. (2017). Cancer Genomics. In: Coleman, W., Tsongalis, G. (eds) The Molecular Basis of Human Cancer. Humana Press, New York, NY. https://doi.org/10.1007/978-1-59745-458-2_3
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