Sequence-based cancer genomics: progress, lessons and opportunities (original) (raw)
Hanahan, D. & Weinberg, R. A. The hallmarks of cancer. Cell100, 57–70 (2000). CASPubMed Google Scholar
Van Dyke, T. & Jacks, T. Cancer modeling in the modern era: progress and challenges. Cell108, 135–144 (2002). ArticleCASPubMed Google Scholar
Dunn, G. P., Bruce, A. T., Ikeda, H., Old, L. J. & Schreiber, R. D. Cancer immunoediting: from immunosurveillance to tumor escape. Nature Immunol.3, 991–998 (2002). ArticleCAS Google Scholar
Adams, M. D. et al. Sequence identification of 2,375 human brain genes. Nature355, 632–634 (1992).The development and early application of ESTs to study human gene expression. ArticleCASPubMed Google Scholar
Velculescu, V. E., Zhang, L., Vogelstein, B. & Kinzler, K. W. Serial analysis of gene-expression. Science270, 484–487 (1995).The initial description of the serial analysis of gene-expression strategy. ArticleCASPubMed Google Scholar
Strausberg, R. L., Buetow, K. H., Emmert-Buck, M. R. & Klausner, R. D. The cancer genome anatomy project — building an annotated gene index. Trends Genet.16, 103–106 (2000).The launch of the Cancer Genome Anatomy Project. ArticleCASPubMed Google Scholar
Riggins, G. J. et al. SAGEmap: a gene expression resource for the Cancer Genome Anatomy Project. Am. J. Human Genet.67, 357 (2000). Article Google Scholar
Hough, C. D. et al. Large-scale serial analysis of gene expression reveals genes differentially expressed in ovarian cancer. Cancer Res.60, 6281–6287 (2000). CASPubMed Google Scholar
Loging, W. T. et al. Identifying potential tumor markers and antigens by database mining and rapid expression screening. Genome Res.10, 1393–1402 (2000). ArticleCASPubMedPubMed Central Google Scholar
Riggins, G. J. Using serial analysis of gene expression to identify tumor markers and antigens. Dis. Markers17, 41–48 (2001). ArticleCASPubMed Google Scholar
Porter, D. A. et al. A SAGE (serial analysis of gene expression) view of breast tumor progression. Cancer Res.61, 5697–5702 (2001). CASPubMed Google Scholar
St Croix, B. et al. Genes expressed in human tumor endothelium. Science289, 1197–1202 (2000). ArticleCASPubMed Google Scholar
Lal, A. et al. Transcriptional response to hypoxia in human tumors. J. Natl Cancer Inst.93, 1337–1343 (2001). ArticleCASPubMed Google Scholar
Birney, E., Clamp, M. & Hubbard, T. Databases and tools for browsing genomes. Annu. Rev. Genomics Hum. Genet.3, 293–310 (2002). ArticleCASPubMed Google Scholar
Hubbard, T. et al. The Ensembl genome database project. Nucleic Acids Res.30, 38–41 (2002).Ensembl combines many genomic data sources to provide a comprehensive view of the human and other genomes. In the future, cancer genome data could be viewed in a similar way. ArticleCASPubMedPubMed Central Google Scholar
Kirsch, I. R. & Ried, T. Integration of cytogenetic data with genome maps and available probes: present status and future promise. Semin. Hematol.37, 420–428 (2000). ArticleCASPubMed Google Scholar
Kirsch, I. R. et al. A systematic, high-resolution linkage of the cytogenetic and physical maps of the human genome. Nature Genet.24, 339–340 (2000). ArticleCASPubMed Google Scholar
Schaefer, C., Grouse, L., Buetow, K. & Strausberg, R. L. A new cancer genome anatomy project web resource for the community. Cancer J.7, 52–60 (2001). CASPubMed Google Scholar
Neto, E. D. et al. Shotgun sequencing of the human transcriptome with ORF expressed sequence tags. Proc. Natl Acad. Sci. USA97, 3491–3496 (2000).The development and application of ORESTES. Article Google Scholar
Neto, E. D. et al. Mini-libraries constructed from cDNA generated by arbitrarily primed RT-PCR: an alternative to normalized libraries for the generation of ESTs from nanogram quantities of mRNA. Gene186, 135–142 (1997). Article Google Scholar
de Souza, S. J. et al. Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags. Proc. Natl Acad. Sci. USA97, 12690–12693 (2000). ArticleCASPubMedPubMed Central Google Scholar
Camargo, A. A. The contribution of 700,000 ORF sequence tags to the definition of the human transcriptome. Proc. Natl Acad. Sci. USA98, 12103–12108 (2001). ArticlePubMedPubMed Central Google Scholar
The International Human Genome Sequencing Consortium. Initial sequencing and analysis of the human genome. Nature409, 860–921 (2001).
Quackenbush, J. et al. The TIGR Gene Indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res.29, 159–164 (2001). ArticleCASPubMedPubMed Central Google Scholar
Reymond, A. et al. Nineteen additional unpredicted transcripts from human chromosome 21. Genomics79, 824–832 (2002). ArticleCASPubMed Google Scholar
Rondeau, G. et al. Comprehensive analysis of a large genomic sequence at the putative B-cell chronic lymphocytic leukaemia (B-CLL) tumour suppresser gene locus. Mutat. Res.458, 55–70 (2001). CASPubMed Google Scholar
Bullrich, F. et al. Characterization of the 13q14 tumor suppressor locus in CLL: identification of ALT1, an alternative splice variant of the LEU2 gene. Cancer Res.61, 6640–6648 (2001). CASPubMed Google Scholar
Montpetit, A., Boily, G. & Sinnett, D. A detailed transcriptional map of the chromosome 12p12 tumour suppressor locus. Eur. J. Hum. Genet.10, 62–71 (2002). ArticleCASPubMed Google Scholar
Sood, R. et al. Cloning and characterization of 13 novel transcripts and the human RC58 gene from the 1q25 region encompassing the hereditary prostate cancer (HPC1) locus. Genomics73, 211–222 (2001). ArticleCASPubMed Google Scholar
Buetow, K. H. et al. High-throughput development and characterization of a genomewide collection of gene-based single nucleotide polymorphism markers by chip-based matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. Proc. Natl Acad. Sci. USA98, 581–584 (2001). ArticleCASPubMedPubMed Central Google Scholar
Xu, Q., Modrek, B. & Lee, C. Genome-wide detection of tissue-specific alternative splicing in the human transcriptome. Nucleic Acids Res.30, 3754–3766 (2002). ArticleCASPubMedPubMed Central Google Scholar
Xie, H. et al. Computational analysis of alternative splicing using EST tissue information. Genomics80, 326 (2002). ArticleCASPubMed Google Scholar
Correa, R. G., de Carvalho, A. F., Pinheiro, N. A., Simpson, A. J. G. & de Souza, S. J. NABC1 (BCAS1): alternative splicing and downregulation in colorectal tumors. Genomics65, 299–302 (2000). ArticleCASPubMed Google Scholar
Strausberg, R. L., Buetow, K. H., Greenhut, S. F., Grouse, L. H. & Schaefer, C. F. The cancer genome anatomy project: online resources to reveal the molecular signatures of cancer. Cancer Invest.20, 1038–1050 (2002). ArticleCASPubMed Google Scholar
Strausberg, R. L., Greenhut, S. F., Grouse, L. H., Schaefer, C. F. & Buetow, K. H. In silico analysis of cancer through the cancer genome anatomy project. Trends Cell Biol.11, 66–71 (2001). Article Google Scholar
Leerkes, M. R. et al. In silico comparison of the transcriptome derived from purified normal breast cells and breast tumor cell lines reveals candidate upregulated genes in breast tumor cells. Genomics79, 257–265 (2002). ArticleCASPubMed Google Scholar
Schmitt, A. O. et al. Exhaustive mining of EST libraries for genes differentially expressed in normal and tumour tissues. Nucleic Acids Res.27, 4251–4260 (1999). ArticleCASPubMedPubMed Central Google Scholar
Mitas, M. et al. Prostate-specific Ets (PSE) factor: a novel marker for detection of metastatic breast cancer in axillary lymph nodes. Br. J. Cancer86, 899–904 (2002). ArticleCASPubMedPubMed Central Google Scholar
Olsson, P. et al. GDEP, a new gene differentially expressed in normal prostate and prostate cancer. Prostate48, 231–241 (2001). ArticleCASPubMed Google Scholar
Nelson, P. S. et al. Comprehensive analyses of prostate gene expression: convergence of expressed sequence tag databases, transcript profiling and proteomics. Electrophoresis21, 1823–1831 (2000). ArticleCASPubMed Google Scholar
Nelson, P. S. Identifying immunotherapeutic targets for prostate carcinoma through the analysis of gene expression profiles. Ann. NY Acad. Sci.975, 232–245 (2002). ArticleCASPubMed Google Scholar
De Young, M. P., Damania, H., Scheurle, D., Zylberberg, C. & Narayanan, R. Bioinformatics-based discovery of a novel factor with apparent specificity to colon cancer. In Vivo16, 239–248 (2002). CASPubMed Google Scholar
Shillitoe, E. J. et al. Genome-wide analysis of oral cancer — early results from the Cancer Genome Anatomy Project. Oral Oncol.36, 8–16 (2000). ArticleCASPubMed Google Scholar
Patel, V., Leethanakul, C. & Gutkind, J. S. New approaches to the understanding of the molecular basis of oral cancer. Crit. Rev. Oral Biol. Med.12, 55–63 (2001). ArticleCASPubMed Google Scholar
Brinkmann, U. et al. PAGE-1, an X chromosome-linked _GAGE_-like gene that is expressed in normal and neoplastic prostate, testis, and uterus. Proc. Natl Acad. Sci. USA95, 10757–10762 (1998). ArticleCASPubMedPubMed Central Google Scholar
Vinals, C., Gaulis, S. & Coche, T. Using in silico transcriptomics to search for tumor-associated antigens for immunotherapy. Vaccine19, 2607–2614 (2001). ArticleCASPubMed Google Scholar
Scanlan, M. J. et al. Identification of cancer/testis genes by database mining and mRNA expression analysis. Int. J. Cancer98, 485–492 (2002).An excellent example of the use of the EST databases to identify genes that are relevant to cancer. ArticleCASPubMed Google Scholar
Sachidanandam, R. et al. A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature409, 928–933 (2001). ArticleCASPubMed Google Scholar
Davies, H. et al. Mutations of the BRAF gene in human cancer. Nature417, 949–954 (2002).The first report of mutations in the BRAF gene. ArticleCASPubMed Google Scholar
Lowinger, T. B., Riedl, B., Dumas, J. & Smith, R. A. Design and discovery of small molecules targeting Raf-1 kinase. Curr. Pharm. Des.8, 2269–2278 (2002). ArticleCASPubMed Google Scholar
Miller, D. G. On the nature of susceptibility to cancer. The presidential address. Cancer46, 1307–1318 (1980). ArticleCASPubMed Google Scholar
Strausberg, R. L. et al. An international database and integrated analysis tools for the study of cancer gene expression. Pharmacogenomics J.2, 156–164 (2002). ArticleCASPubMed Google Scholar
Sorlie, T. et al. Gene expression patterns of breast carcinomas distinguish tumor subclasses with clinical implications. Proc. Natl Acad. Sci. USA98, 10869–10874 (2001). ArticleCASPubMedPubMed Central Google Scholar
Chung, C. H., Bernard, P. S. & Perou, C. M. Molecular portraits and the family tree of cancer. Nature Genet.32, 533–540 (2002). ArticleCASPubMed Google Scholar
van de Vijver, M. J. et al. A gene-expression signature as a predictor of survival in breast cancer. New Eng. J. Med.347, 1999–2009 (2002). ArticleCASPubMed Google Scholar
Alizadeh, A. A. et al. Distinct types of diffuse large B-cell lymphoma identified by gene expression profiling. Nature403, 503–511 (2000). ArticleCASPubMed Google Scholar
Alizadeh, A. et al. The lymphochip: a specialized cDNA microarray for the genomic-scale analysis of gene expression in normal and malignant lymphocytes. Cold Spring Harb. Symp. Quant. Biol.64, 71–78 (1999). ArticleCASPubMed Google Scholar
Kapranov, P. et al. Large-scale transcriptional activity in chromosomes 21 and 22. Science296, 916–919 (2002). ArticleCASPubMed Google Scholar
Edgar, R., Domrachev, M. & Lash, A. E. Gene expression omnibus: NCBI gene expression and hybridization array data repository. Nucleic Acids Res.30, 207–210 (2002). ArticleCASPubMedPubMed Central Google Scholar
Buetow, K. H. et al. Cancer Molecular Analysis Project: weaving a rich cancer research tapestry. Cancer Cell1, 315–318 (2002). ArticleCASPubMed Google Scholar
Velculescu, V. E., Zhang, L., Vogelstein, B. & Kinzler, K. W. Serial analysis of gene-expression. Science270, 484–487 (1995). ArticleCASPubMed Google Scholar
Druker, B. Signal transduction inhibition: results from phase I clinical trials in chronic myeloid leukemia. Semin. Hematol.38, 9–14 (2001).A classic example of targeted molecular therapeutics. ArticleCASPubMed Google Scholar
Druker, B. J. Imatinib and chronic myeloid leukemia: validating the promise of molecularly targeted therapy. Eur. J. Cancer38, 70–76 (2002). Article Google Scholar
Rozycka, M., Collins, N., Stratton, M. R. & Wooster, R. Rapid detection of DNA sequence variants by conformation-sensitive capillary electrophoresis. Genomics70, 34–40 (2000). ArticleCASPubMed Google Scholar