Validation and Implementation of Targeted Capture and Sequencing for the Detection of Actionable Mutation, Copy Number Variation, and Gene Rearrangement in Clinical Cancer Specimens
Tài liệu tham khảo
Slamon, 2001, Use of chemotherapy plus a monoclonal antibody against HER2 for metastatic breast cancer that overexpresses HER2, N Engl J Med, 344, 783, 10.1056/NEJM200103153441101
Lynch, 2004, Activating mutations in the epidermal growth factor receptor underlying responsiveness of non-small-cell lung cancer to gefitinib, N Engl J Med, 350, 2129, 10.1056/NEJMoa040938
Paez, 2004, EGFR mutations in lung cancer: correlation with clinical response to gefitinib therapy, Science, 304, 1497, 10.1126/science.1099314
Pao, 2004, EGF receptor gene mutations are common in lung cancers from “never smokers” and are associated with sensitivity of tumors to gefitinib and erlotinib, Proc Natl Acad Sci U S A, 101, 13306, 10.1073/pnas.0405220101
Chapman, 2011, Improved survival with vemurafenib in melanoma with BRAF V600E mutation, N Engl J Med, 364, 2507, 10.1056/NEJMoa1103782
Kwak, 2010, Anaplastic lymphoma kinase inhibition in non-small-cell lung cancer, N Engl J Med, 363, 1693, 10.1056/NEJMoa1006448
Wei, 2011, Exome sequencing identifies GRIN2A as frequently mutated in melanoma, Nat Genet, 43, 442, 10.1038/ng.810
Stark, 2012, Frequent somatic mutations in MAP3K5 and MAP3K9 in metastatic melanoma identified by exome sequencing, Nat Genet, 44, 165, 10.1038/ng.1041
Nikolaev, 2012, Exome sequencing identifies recurrent somatic MAP2K1 and MAP2K2 mutations in melanoma, Nat Genet, 44, 133, 10.1038/ng.1026
Leary, 2010, Development of personalized tumor biomarkers using massively parallel sequencing, Sci Transl Med, 2, 20ra14, 10.1126/scitranslmed.3000702
Roychowdhury, 2011, Personalized oncology through integrative high-throughput sequencing: a pilot study, Sci Transl Med, 3, 111ra121, 10.1126/scitranslmed.3003161
Wu, 2012, Somatic histone H3 alterations in pediatric diffuse intrinsic pontine gliomas and non-brainstem glioblastomas, Nat Genet, 44, 251, 10.1038/ng.1102
MacConaill, 2009, Profiling critical cancer gene mutations in clinical tumor samples, PLoS One, 4, e7887, 10.1371/journal.pone.0007887
Su, 2011, A platform for rapid detection of multiple oncogenic mutations with relevance to targeted therapy in non-small-cell lung cancer, J Mol Diagn, 13, 74, 10.1016/j.jmoldx.2010.11.010
Harismendy, 2011, Detection of low prevalence somatic mutations in solid tumors with ultra-deep targeted sequencing, Genome Biol, 12, R124, 10.1186/gb-2011-12-12-r124
Wagle, 2012, High-throughput detection of actionable genomic alterations in clinical tumor samples by targeted, massively parallel sequencing, Cancer Discov, 2, 82, 10.1158/2159-8290.CD-11-0184
Beltran, 2013, Targeted next-generation sequencing of advanced prostate cancer identifies potential therapeutic targets and disease heterogeneity, Eur Urol, 63, 920, 10.1016/j.eururo.2012.08.053
Pritchard, 2012, ColoSeq provides comprehensive lynch and polyposis syndrome mutational analysis using massively parallel sequencing, J Mol Diagn, 14, 357, 10.1016/j.jmoldx.2012.03.002
Li, 2010, Fast and accurate long-read alignment with Burrows-Wheeler transform, Bioinformatics, 26, 589, 10.1093/bioinformatics/btp698
Li, 2009, 1000 Genome Project Data Processing Subgroup: The Sequence Alignment/Map format and SAMtools, Bioinformatics, 25, 2078, 10.1093/bioinformatics/btp352
DePristo, 2011, A framework for variation discovery and genotyping using next-generation DNA sequencing data, Nat Genet, 43, 491, 10.1038/ng.806
Koboldt, 2012, VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing, Genome Res, 22, 568, 10.1101/gr.129684.111
Robinson, 2011, Integrative genomics viewer, Nature Biotechnol, 29, 24, 10.1038/nbt.1754
Ye, 2009, Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads, Bioinformatics, 25, 2865, 10.1093/bioinformatics/btp394
Wang, 2011, CREST maps somatic structural variation in cancer genomes with base-pair resolution, Nat Methods, 8, 652, 10.1038/nmeth.1628
Li, 2012, CONTRA: copy number analysis for targeted resequencing, Bioinformatics, 28, 1307, 10.1093/bioinformatics/bts146
Wickham, 2009
Wang, 2010, ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data, Nucleic Acids Res, 38, e164, 10.1093/nar/gkq603
Abecasis, 2012, An integrated map of genetic variation from 1,092 human genomes, Nature, 491, 56, 10.1038/nature11632
Koboldt, 2009, VarScan: variant detection in massively parallel sequencing of individual and pooled samples, Bioinformatics, 25, 2283, 10.1093/bioinformatics/btp373
Spencer, 2013, Detection of FLT3 internal tandem duplication in targeted. short-read-length, next-generation sequencing data, J Mol Diagn, 15, 81, 10.1016/j.jmoldx.2012.08.001
Schmitt, 2012, Detection of ultra-rare mutations by next-generation sequencing, Proc Natl Acad Sci U S A, 109, 14508, 10.1073/pnas.1208715109
Ng, 2012, A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer, Nat Med, 18, 521, 10.1038/nm.2713
Shendure, 2011, Next-generation human genetics, Genome Biol, 12, 408, 10.1186/gb-2011-12-9-408
2012, Comprehensive molecular portraits of human breast tumours, Nature, 490, 61, 10.1038/nature11412
Schnittger, 2013, ASXL1 exon 12 mutations are frequent in AML with intermediate risk karyotype and are independently associated with an adverse outcome, Leukemia, 27, 82, 10.1038/leu.2012.262
Wheeler, 2002, Zeta-sarcoglycan, a novel component of the sarcoglycan complex, is reduced in muscular dystrophy, Hum Mol Genet, 11, 2147, 10.1093/hmg/11.18.2147
Quayle, 2012, Somatic mutations of PIK3R1 promote gliomagenesis, PLoS One, 7, e49466, 10.1371/journal.pone.0049466
Cheung, 2011, High frequency of PIK3R1 and PIK3R2 mutations in endometrial cancer elucidates a novel mechanism for regulation of PTEN protein stability, Cancer Discov, 1, 170, 10.1158/2159-8290.CD-11-0039
Shen, 2011, Gene mutation patterns and their prognostic impact in a cohort of 1185 patients with acute myeloid leukemia, Blood, 118, 5593, 10.1182/blood-2011-03-343988
Somervaille, 2010, Grist for the MLL: how do MLL oncogenic fusion proteins generate leukemia stem cells?, Int J Hematol, 91, 735, 10.1007/s12185-010-0579-8
Szpirer, 1994, The genes encoding the glutamate receptor subunits KA1 and KA2 (GRIK4 and GRIK5) are located on separate chromosomes in human, mouse, and rat, Proc Natl Acad Sci U S A, 91, 11849, 10.1073/pnas.91.25.11849
Choi, 2011, Expression of the metabotropic glutamate receptor 5 (mGluR5) induces melanoma in transgenic mice, Proc Natl Acad Sci U S A, 108, 15219, 10.1073/pnas.1107304108
Song, 2012, Blocking glutamate-mediated signalling inhibits human melanoma growth and migration, Exp Dermatol, 21, 926, 10.1111/exd.12048
Martino, 2013, Metabotropic glutamate receptor 1 (Grm1) is an oncogene in epithelial cells, Oncogene, 32, 4366, 10.1038/onc.2012.471
Neiman, 2012, Library preparation and multiplex capture for massive parallel sequencing applications made efficient and easy, PLoS One, 7, e48616, 10.1371/journal.pone.0048616
Rohland, 2012, Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture, Genome Res, 22, 939, 10.1101/gr.128124.111