Sức mạnh của công nghệ giải trình tự thế hệ mới (NGS) trong việc xác định tổ chức genome ở bệnh ung thư: từ đột biến đến biến thể cấu trúc và thay đổi biểu sinh

Krawitz, P. M., Schweiger, M. R., Rodelsperger, C., Marcelis, C., Kolsch, U., et al. (2010). Identity-by-descent filtering of exome sequence data identifies PIGV mutations in hyperphosphatasia mental retardation syndrome. Nature Genetics, 42, 827–829. Ng, S. B., Turner, E. H., Robertson, P. D., Flygare, S. D., Bigham, A. W., et al. (2009). Targeted capture and massively parallel sequencing of 12 human exomes. Nature, 461, 272–276. Bagnyukova, T., Serebriiskii, I. G., Zhou, Y., Hopper-Borge, E. A., Golemis, E. A., et al. (2010). Chemotherapy and signaling: how can targeted therapies supercharge cytotoxic agents? Cancer Biol Ther, 10(9), 839–853. Branton, D., Deamer, D. W., Marziali, A., Bayley, H., Benner, S. A., et al. (2008). The potential and challenges of nanopore sequencing. Nature Biotechnology, 26, 1146–1153. Pleasance, E. D., Stephens, P. J., O’Meara, S., McBride, D. J., Meynert, A., et al. (2010). A small-cell lung cancer genome with complex signatures of tobacco exposure. Nature, 463, 184–190. Pleasance, E. D., Cheetham, R. K., Stephens, P. J., McBride, D. J., Humphray, S. J., et al. (2010). A comprehensive catalogue of somatic mutations from a human cancer genome. Nature, 463, 191–196. Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., et al. (2008). DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome. Nature, 456, 66–72. Shah, S. P., Morin, R. D., Khattra, J., Prentice, L., Pugh, T., et al. (2009). Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution. Nature, 461, 809–813. Gilbert, M. T., Haselkorn, T., Bunce, M., Sanchez, J. J., Lucas, S. B., et al. (2007). The isolation of nucleic acids from fixed, paraffin-embedded tissues-which methods are useful when? PLoS ONE, 2, e537. Schweiger, M. R., Kerick, M., Timmermann, B., Albrecht, M. W., Borodina, T., et al. (2009). Genome-wide massively parallel sequencing of formaldehyde fixed-paraffin embedded (FFPE) tumor tissues for copy-number- and mutation-analysis. PLoS ONE, 4, e5548. Bian, Y. S., Yan, P., Osterheld, M. C., Fontolliet, C., & Benhattar, J. (2001). Promoter methylation analysis on microdissected paraffin-embedded tissues using bisulfite treatment and PCR-SSCP. Biotechniques, 30, 66–72. Chiu, R. W., Chan, K. C., Gao, Y., Lau, V. Y., Zheng, W., et al. (2008). Noninvasive prenatal diagnosis of fetal chromosomal aneuploidy by massively parallel genomic sequencing of DNA in maternal plasma. Proceedings of the National Academy of Sciences of the United States of America, 105, 20458–20463. Kerjean, A., Vieillefond, A., Thiounn, N., Sibony, M., Jeanpierre, M., et al. (2001). Bisulfite genomic sequencing of microdissected cells. Nucleic Acids Research, 29, E106–106. Fan, H. C., Blumenfeld, Y. J., Chitkara, U., Hudgins, L., & Quake, S. R. (2008). Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood. Proceedings of the National Academy of Sciences of the United States of America, 105, 16266–16271. van der Vaart, M., Semenov, D. V., Kuligina, E. V., Richter, V. A., & Pretorius, P. J. (2009). Characterisation of circulating DNA by parallel tagged sequencing on the 454 platform. Clinica Chimica Acta, 409, 21–27. Beck, J., Urnovitz, H. B., Mitchell, W. M., & Schutz, E. (2010). Next generation sequencing of serum circulating nucleic acids from patients with invasive ductal breast cancer reveals differences to healthy and nonmalignant controls. Molecular Cancer Research, 8, 335–342. McBride, D. J., Orpana, A. K., Sotiriou, C., Joensuu, H., Stephens, P. J., et al. (2010). Use of cancer-specific genomic rearrangements to quantify disease burden in plasma from patients with solid tumors. Genes, Chromosomes & Cancer, 49, 1062–1069. Maxam, A. M., & Gilbert, W. (1977). A new method for sequencing DNA. Proceedings of the National Academy of Sciences of the United States of America, 74, 560–564. Sanger, F., Nicklen, S., & Coulson, A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proceedings of the National Academy of Sciences of the United States of America, 74, 5463–5467. The International Human Genome Sequencing Consortium (2004). Finishing the euchromatic sequence of the human genome. Nature, 431, 931–945. Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., et al. (2001). Initial sequencing and analysis of the human genome. Nature, 409, 860–921. Mardis, E. R. (2008). Next-generation DNA sequencing methods. Annual Review of Genomics and Human Genetics, 9, 387–402. Shendure, J., & Ji, H. (2008). Next-generation DNA sequencing. Nature Biotechnology, 26, 1135–1145. Metzker, M. L. (2010). Sequencing technologies—the next generation. Nature Reviews. Genetics, 11, 31–46. Ding, L., Wendl, M. C., Koboldt, D. C., & Mardis, E. R. (2010). Analysis of next-generation genomic data in cancer: accomplishments and challenges. Human Molecular Genetics, 19, R188–R196. Meyerson, M., Gabriel, S., & Getz, G. (2010). Advances in understanding cancer genomes through second-generation sequencing. Nature Reviews. Genetics, 11, 685–696. Rothberg, J. M., & Leamon, J. H. (2008). The development and impact of 454 sequencing. Nature Biotechnology, 26, 1117–1124. Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., et al. (2005). Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376–380. Ronaghi, M. (2001). Pyrosequencing sheds light on DNA sequencing. Genome Research, 11, 3–11. Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., et al. (2008). Accurate whole human genome sequencing using reversible terminator chemistry. Nature, 456, 53–59. Shendure, J., Porreca, G. J., Reppas, N. B., Lin, X., McCutcheon, J. P., et al. (2005). Accurate multiplex polony sequencing of an evolved bacterial genome. Science, 309, 1728–1732. Blow, N. (2008). DNA sequencing: generation next-next. Nat Methods, 5(6), 267–274. Clarke, J., Wu, H. C., Jayasinghe, L., Patel, A., Reid, S., et al. (2009). Continuous base identification for single-molecule nanopore DNA sequencing. Nature Nanotechnology, 4, 265–270. Greenleaf, W. J., & Block, S. M. (2006). Single-molecule, motion-based DNA sequencing using RNA polymerase. Science, 313, 801. Sugiyama, S. (2006). Application of scanning probe microscopy to genetic analysis. Japanese journal of applied physics, 45, 4. Pourmand, N., Karhanek, M., Persson, H. H., Webb, C. D., Lee, T. H., et al. (2006). Direct electrical detection of DNA synthesis. Proceedings of the National Academy of Sciences of the United States of America, 103, 6466–6470. Albert, T. J., Molla, M. N., Muzny, D. M., Nazareth, L., Wheeler, D., et al. (2007). Direct selection of human genomic loci by microarray hybridization. Nat Methods, 4, 903–905. Choi, M., Scholl, U. I., Ji, W., Liu, T., Tikhonova, I. R., et al. (2009). Genetic diagnosis by whole exome capture and massively parallel DNA sequencing. Proceedings of the National Academy of Sciences of the United States of America, 106, 19096–19101. Gnirke, A., Melnikov, A., Maguire, J., Rogov, P., LeProust, E. M., et al. (2009). Solution hybrid selection with ultra-long oligonucleotides for massively parallel targeted sequencing. Nature Biotechnology, 27, 182–189. Hodges, E., Xuan, Z., Balija, V., Kramer, M., Molla, M. N., et al. (2007). Genome-wide in situ exon capture for selective resequencing. Nature Genetics, 39, 1522–1527. Porreca, G. J., Zhang, K., Li, J. B., Xie, B., Austin, D., et al. (2007). Multiplex amplification of large sets of human exons. Nat Methods, 4, 931–936. The Cancer Genome Atlas Research Network (2008). Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature, 455, 1061–1068. Bardelli, A., Parsons, D. W., Silliman, N., Ptak, J., Szabo, S., et al. (2003). Mutational analysis of the tyrosine kinome in colorectal cancers. Science, 300, 949. Greenman, C., Stephens, P., Smith, R., Dalgliesh, G. L., Hunter, C., et al. (2007). Patterns of somatic mutation in human cancer genomes. Nature, 446, 153–158. Jones, S., Zhang, X., Parsons, D. W., Lin, J. C., Leary, R. J., et al. (2008). Core signaling pathways in human pancreatic cancers revealed by global genomic analyses. Science, 321, 1801–1806. Parsons, D. W., Jones, S., Zhang, X., Lin, J. C., Leary, R. J., et al. (2008). An integrated genomic analysis of human glioblastoma multiforme. Science, 321, 1807–1812. Sjoblom, T., Jones, S., Wood, L. D., Parsons, D. W., Lin, J., et al. (2006). The consensus coding sequences of human breast and colorectal cancers. Science, 314, 268–274. Wood, L. D., Parsons, D. W., Jones, S., Lin, J., Sjoblom, T., et al. (2007). The genomic landscapes of human breast and colorectal cancers. Science, 318, 1108–1113. Mardis, E. R., Ding, L., Dooling, D. J., Larson, D. E., McLellan, M. D., et al. (2009). Recurring mutations found by sequencing an acute myeloid leukemia genome. The New England Journal of Medicine, 361, 1058–1066. Fredman, D., White, S. J., Potter, S., Eichler, E. E., Den Dunnen, J. T., et al. (2004). Complex SNP-related sequence variation in segmental genome duplications. Nature Genetics, 36, 861–866. Druker, B. J. (2008). Translation of the Philadelphia chromosome into therapy for CML. Blood, 112, 4808–4817. Park, J. W., Neve, R. M., Szollosi, J., & Benz, C. C. (2008). Unraveling the biologic and clinical complexities of HER2. Clinical Breast Cancer, 8, 392–401. Campbell, P. J., Stephens, P. J., Pleasance, E. D., O’Meara, S., Li, H., et al. (2008). Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nature Genetics, 40, 722–729. Stephens, P. J., McBride, D. J., Lin, M. L., Varela, I., Pleasance, E. D., et al. (2009). Complex landscapes of somatic rearrangement in human breast cancer genomes. Nature, 462, 1005–1010. Beck, S., & Rakyan, V. K. (2008). The methylome: approaches for global DNA methylation profiling. Trends in Genetics, 24, 231–237. Feinberg, A. P. (2007). Phenotypic plasticity and the epigenetics of human disease. Nature, 447, 433–440. Banerjee, H. N., & Verma, M. (2009). Epigenetic mechanisms in cancer. Biomarkers Medicine, 3, 14. Lister, R., & Ecker, J. R. (2009). Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Research, 19, 959–966. Ball, M. P., Li, J. B., Gao, Y., Lee, J. H., LeProust, E. M., et al. (2009). Targeted and genome-scale strategies reveal gene-body methylation signatures in human cells. Nature Biotechnology, 27, 361–368. Rakyan, V. K., Down, T. A., Thorne, N. P., Flicek, P., Kulesha, E., et al. (2008). An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Genome Research, 18, 1518–1529. Morozova, O., Hirst, M., & Marra, M. A. (2009). Applications of new sequencing technologies for transcriptome analysis. Annual Review of Genomics and Human Genetics, 10, 135–151. Sultan, M., Schulz, M. H., Richard, H., Magen, A., Klingenhoff, A., et al. (2008). A global view of gene activity and alternative splicing by deep sequencing of the human transcriptome. Science, 321, 956–960. Friedel, C. C., & Dolken, L. (2009). Metabolic tagging and purification of nascent RNA: implications for transcriptomics. Molecular Biosystems, 5, 1271–1278. Klein, C. A. (2009). Parallel progression of primary tumours and metastases. Nature Reviews. Cancer, 9, 302–312. Campbell, P. J., Yachida, S., Mudie, L. J., Stephens, P. J., Pleasance, E. D., et al. (2010). The patterns and dynamics of genomic instability in metastatic pancreatic cancer. Nature, 467, 1109–1113. Ding, L., Ellis, M. J., Li, S., Larson, D. E., Chen, K., et al. (2010). Genome remodelling in a basal-like breast cancer metastasis and xenograft. Nature, 464, 999–1005.