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For: Campbell PJ, Stephens PJ, Pleasance ED, O'Meara S, Li H, Santarius T, Stebbings LA, Leroy C, Edkins S, Hardy C, Teague JW, Menzies A, Goodhead I, Turner DJ, Clee CM, Quail MA, Cox A, Brown C, Durbin R, Hurles ME, Edwards PAW, Bignell GR, Stratton MR, Futreal PA. Identification of somatically acquired rearrangements in cancer using genome-wide massively parallel paired-end sequencing. Nat Genet 2008;40:722-9. [PMID: 18438408 PMCID: PMC2705838 DOI: 10.1038/ng.128] [Citation(s) in RCA: 609] [Impact Index Per Article: 35.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2008] [Accepted: 02/27/2008] [Indexed: 12/29/2022]
Number Cited by Other Article(s)
151
Next-Generation Sequencing Approaches in Cancer: Where Have They Brought Us and Where Will They Take Us? Cancers (Basel) 2015;7:1925-58. [PMID: 26404381 PMCID: PMC4586802 DOI: 10.3390/cancers7030869] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2015] [Accepted: 09/15/2015] [Indexed: 12/20/2022]  Open
152
Buisine N, Ruan X, Bilesimo P, Grimaldi A, Alfama G, Ariyaratne P, Mulawadi F, Chen J, Sung WK, Liu ET, Demeneix BA, Ruan Y, Sachs LM. Xenopus tropicalis Genome Re-Scaffolding and Re-Annotation Reach the Resolution Required for In Vivo ChIA-PET Analysis. PLoS One 2015;10:e0137526. [PMID: 26348928 PMCID: PMC4562602 DOI: 10.1371/journal.pone.0137526] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2015] [Accepted: 08/19/2015] [Indexed: 12/11/2022]  Open
153
CNV-CH: A Convex Hull Based Segmentation Approach to Detect Copy Number Variations (CNV) Using Next-Generation Sequencing Data. PLoS One 2015;10:e0135895. [PMID: 26291322 PMCID: PMC4546278 DOI: 10.1371/journal.pone.0135895] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2014] [Accepted: 07/28/2015] [Indexed: 11/19/2022]  Open
154
Duan J, Wan M, Deng HW, Wang YP. A Sparse Model Based Detection of Copy Number Variations From Exome Sequencing Data. IEEE Trans Biomed Eng 2015;63:496-505. [PMID: 26258935 DOI: 10.1109/tbme.2015.2464674] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
155
Gao G, Smith DI. Mate-Pair Sequencing as a Powerful Clinical Tool for the Characterization of Cancers with a DNA Viral Etiology. Viruses 2015;7:4507-28. [PMID: 26262638 PMCID: PMC4576192 DOI: 10.3390/v7082831] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/16/2015] [Accepted: 07/29/2015] [Indexed: 01/18/2023]  Open
156
Fong KM, Daniels M, Goh F, Yang IA, Bowman RV. The current and future roles of genomics. Lung Cancer 2015. [DOI: 10.1183/2312508x.10009614] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
157
Zhang G, Wang J, Yang J, Li W, Deng Y, Li J, Huang J, Hu S, Zhang B. Comparison and evaluation of two exome capture kits and sequencing platforms for variant calling. BMC Genomics 2015;16:581. [PMID: 26242175 PMCID: PMC4524363 DOI: 10.1186/s12864-015-1796-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 07/23/2015] [Indexed: 12/30/2022]  Open
158
Matsui A, Ihara T, Suda H, Mikami H, Semba K. Gene amplification: mechanisms and involvement in cancer. Biomol Concepts 2015;4:567-82. [PMID: 25436757 DOI: 10.1515/bmc-2013-0026] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2013] [Accepted: 09/02/2013] [Indexed: 11/15/2022]  Open
159
Mittal VK, McDonald JF. Integrated sequence and expression analysis of ovarian cancer structural variants underscores the importance of gene fusion regulation. BMC Med Genomics 2015;8:40. [PMID: 26177635 PMCID: PMC4504069 DOI: 10.1186/s12920-015-0118-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2014] [Accepted: 07/09/2015] [Indexed: 12/25/2022]  Open
160
Microplitis demolitor Bracovirus Proviral Loci and Clustered Replication Genes Exhibit Distinct DNA Amplification Patterns during Replication. J Virol 2015;89:9511-23. [PMID: 26157119 DOI: 10.1128/jvi.01388-15] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2015] [Accepted: 07/01/2015] [Indexed: 01/25/2023]  Open
161
Tattini L, D'Aurizio R, Magi A. Detection of Genomic Structural Variants from Next-Generation Sequencing Data. Front Bioeng Biotechnol 2015;3:92. [PMID: 26161383 PMCID: PMC4479793 DOI: 10.3389/fbioe.2015.00092] [Citation(s) in RCA: 169] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 06/10/2015] [Indexed: 01/16/2023]  Open
162
Li W, Mills AA. Architects of the genome: CHD dysfunction in cancer, developmental disorders and neurological syndromes. Epigenomics 2015;6:381-95. [PMID: 25333848 DOI: 10.2217/epi.14.31] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
163
Mertens F, Johansson B, Fioretos T, Mitelman F. The emerging complexity of gene fusions in cancer. Nat Rev Cancer 2015;15:371-81. [PMID: 25998716 DOI: 10.1038/nrc3947] [Citation(s) in RCA: 492] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
164
Ju YS, Tubio JMC, Mifsud W, Fu B, Davies HR, Ramakrishna M, Li Y, Yates L, Gundem G, Tarpey PS, Behjati S, Papaemmanuil E, Martin S, Fullam A, Gerstung M, Nangalia J, Green AR, Caldas C, Borg Å, Tutt A, Lee MTM, van't Veer LJ, Tan BKT, Aparicio S, Span PN, Martens JWM, Knappskog S, Vincent-Salomon A, Børresen-Dale AL, Eyfjörd JE, Myklebost O, Flanagan AM, Foster C, Neal DE, Cooper C, Eeles R, Bova SG, Lakhani SR, Desmedt C, Thomas G, Richardson AL, Purdie CA, Thompson AM, McDermott U, Yang F, Nik-Zainal S, Campbell PJ, Stratton MR. Frequent somatic transfer of mitochondrial DNA into the nuclear genome of human cancer cells. Genome Res 2015;25:814-24. [PMID: 25963125 PMCID: PMC4448678 DOI: 10.1101/gr.190470.115] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 04/14/2015] [Indexed: 12/11/2022]
165
Tubio JMC. Somatic structural variation and cancer. Brief Funct Genomics 2015;14:339-51. [PMID: 25903743 DOI: 10.1093/bfgp/elv016] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]  Open
166
Dixon-McIver A. Emerging technologies in paediatric leukaemia. Transl Pediatr 2015;4:116-24. [PMID: 26835367 PMCID: PMC4729090 DOI: 10.3978/j.issn.2224-4336.2015.03.02] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
167
Cooper CS, Eeles R, Wedge DC, Van Loo P, Gundem G, Alexandrov LB, Kremeyer B, Butler A, Lynch AG, Camacho N, Massie CE, Kay J, Luxton HJ, Edwards S, Kote-Jarai ZS, Dennis N, Merson S, Leongamornlert D, Zamora J, Corbishley C, Thomas S, Nik-Zainal S, O'Meara S, Matthews L, Clark J, Hurst R, Mithen R, Bristow RG, Boutros PC, Fraser M, Cooke S, Raine K, Jones D, Menzies A, Stebbings L, Hinton J, Teague J, McLaren S, Mudie L, Hardy C, Anderson E, Joseph O, Goody V, Robinson B, Maddison M, Gamble S, Greenman C, Berney D, Hazell S, Livni N, Fisher C, Ogden C, Kumar P, Thompson A, Woodhouse C, Nicol D, Mayer E, Dudderidge T, Shah NC, Gnanapragasam V, Voet T, Campbell P, Futreal A, Easton D, Warren AY, Foster CS, Stratton MR, Whitaker HC, McDermott U, Brewer DS, Neal DE. Analysis of the genetic phylogeny of multifocal prostate cancer identifies multiple independent clonal expansions in neoplastic and morphologically normal prostate tissue. Nat Genet 2015;47:367-372. [PMID: 25730763 PMCID: PMC4380509 DOI: 10.1038/ng.3221] [Citation(s) in RCA: 337] [Impact Index Per Article: 33.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 01/21/2015] [Indexed: 01/12/2023]
168
Nakagawa H, Wardell CP, Furuta M, Taniguchi H, Fujimoto A. Cancer whole-genome sequencing: present and future. Oncogene 2015;34:5943-50. [PMID: 25823020 DOI: 10.1038/onc.2015.90] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2015] [Revised: 02/27/2015] [Accepted: 02/27/2015] [Indexed: 12/26/2022]
169
Wang M, Beck CR, English AC, Meng Q, Buhay C, Han Y, Doddapaneni HV, Yu F, Boerwinkle E, Lupski JR, Muzny DM, Gibbs RA. PacBio-LITS: a large-insert targeted sequencing method for characterization of human disease-associated chromosomal structural variations. BMC Genomics 2015;16:214. [PMID: 25887218 PMCID: PMC4376517 DOI: 10.1186/s12864-015-1370-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Accepted: 02/20/2015] [Indexed: 11/24/2022]  Open
170
Priyadarshana WJRM, Sofronov G. Multiple Break-Points Detection in Array CGH Data via the Cross-Entropy Method. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2015;12:487-498. [PMID: 26357234 DOI: 10.1109/tcbb.2014.2361639] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
171
ICRmax: an optimized approach to detect tumor-specific interchromosomal rearrangements for clinical application. Genomics 2015;105:265-72. [PMID: 25666663 DOI: 10.1016/j.ygeno.2015.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Revised: 01/23/2015] [Accepted: 01/26/2015] [Indexed: 01/26/2023]
172
Brynildsrud O, Snipen LG, Bohlin J. CNOGpro: detection and quantification of CNVs in prokaryotic whole-genome sequencing data. Bioinformatics 2015;31:1708-15. [DOI: 10.1093/bioinformatics/btv070] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 01/28/2015] [Indexed: 01/22/2023]  Open
173
Yasuda T, Miyano S. Inferring the global structure of chromosomes from structural variations. BMC Genomics 2015;16 Suppl 2:S13. [PMID: 25707904 PMCID: PMC4331713 DOI: 10.1186/1471-2164-16-s2-s13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]  Open
174
de Pagter MS, Kloosterman WP. The Diverse Effects of Complex Chromosome Rearrangements and Chromothripsis in Cancer Development. Recent Results Cancer Res 2015;200:165-193. [PMID: 26376877 DOI: 10.1007/978-3-319-20291-4_8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
175
Saber A, van der Wekken A, Hiltermann TJ, Kok K, van den Berg A, Groen HJ. Genomic aberrations guiding treatment of non-small cell lung cancer patients. ACTA ACUST UNITED AC 2015. [DOI: 10.1016/j.ctrc.2015.03.005] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
176
Oleksiewicz U, Tomczak K, Woropaj J, Markowska M, Stępniak P, Shah PK. Computational characterisation of cancer molecular profiles derived using next generation sequencing. Contemp Oncol (Pozn) 2015;19:A78-91. [PMID: 25691827 PMCID: PMC4322529 DOI: 10.5114/wo.2014.47137] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
177
A comprehensive transcriptional portrait of human cancer cell lines. Nat Biotechnol 2014;33:306-12. [PMID: 25485619 DOI: 10.1038/nbt.3080] [Citation(s) in RCA: 476] [Impact Index Per Article: 43.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2014] [Accepted: 10/15/2014] [Indexed: 12/17/2022]
178
Hofmeister W, Nilsson D, Topa A, Anderlid BM, Darki F, Matsson H, Tapia Páez I, Klingberg T, Samuelsson L, Wirta V, Vezzi F, Kere J, Nordenskjöld M, Syk Lundberg E, Lindstrand A. CTNND2-a candidate gene for reading problems and mild intellectual disability. J Med Genet 2014;52:111-22. [PMID: 25473103 DOI: 10.1136/jmedgenet-2014-102757] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
179
Vogt N, Gibaud A, Lemoine F, de la Grange P, Debatisse M, Malfoy B. Amplicon rearrangements during the extrachromosomal and intrachromosomal amplification process in a glioma. Nucleic Acids Res 2014;42:13194-205. [PMID: 25378339 PMCID: PMC4245956 DOI: 10.1093/nar/gku1101] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2014] [Revised: 10/22/2014] [Accepted: 10/23/2014] [Indexed: 01/18/2023]  Open
180
Toward product attribute control: developments from genome sequencing. Curr Opin Biotechnol 2014;30:40-4. [DOI: 10.1016/j.copbio.2014.05.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 05/02/2014] [Indexed: 01/16/2023]
181
Gonçalves da Silva A, Barendse W, Kijas JW, Barris WC, McWilliam S, Bunch RJ, McCullough R, Harrison B, Hoelzel AR, England PR. SNP discovery in nonmodel organisms: strand bias and base-substitution errors reduce conversion rates. Mol Ecol Resour 2014;15:723-36. [PMID: 25388640 DOI: 10.1111/1755-0998.12343] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2014] [Revised: 10/31/2014] [Accepted: 11/03/2014] [Indexed: 11/28/2022]
182
Frenkel-Morgenstern M, Gorohovski A, Vucenovic D, Maestre L, Valencia A. ChiTaRS 2.1--an improved database of the chimeric transcripts and RNA-seq data with novel sense-antisense chimeric RNA transcripts. Nucleic Acids Res 2014;43:D68-75. [PMID: 25414346 PMCID: PMC4383979 DOI: 10.1093/nar/gku1199] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
183
Pikor L, Thu K, Vucic E, Lam W. The detection and implication of genome instability in cancer. Cancer Metastasis Rev 2014;32:341-52. [PMID: 23633034 PMCID: PMC3843371 DOI: 10.1007/s10555-013-9429-5] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
184
Gillet-Markowska A, Richard H, Fischer G, Lafontaine I. Ulysses: accurate detection of low-frequency structural variations in large insert-size sequencing libraries. ACTA ACUST UNITED AC 2014;31:801-8. [PMID: 25380961 DOI: 10.1093/bioinformatics/btu730] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
185
Detection of MYD88 L265P Mutation by Real-Time Allele-Specific Oligonucleotide Polymerase Chain Reaction. Appl Immunohistochem Mol Morphol 2014;22:768-73. [DOI: 10.1097/pai.0000000000000020] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
186
Somatic mutations, genome mosaicism, cancer and aging. Curr Opin Genet Dev 2014;26:141-9. [PMID: 25282114 DOI: 10.1016/j.gde.2014.04.002] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2014] [Revised: 04/04/2014] [Accepted: 04/11/2014] [Indexed: 01/11/2023]
187
Wright CM, Yang IA, Bowman RV, Fong KM. The potential of genome-wide analyses to improve non-small-cell lung cancer care. Lung Cancer Manag 2014. [DOI: 10.2217/lmt.14.31] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]  Open
188
Chinen Y, Sakamoto N, Nagoshi H, Taki T, Maegawa S, Tatekawa S, Tsukamoto T, Mizutani S, Shimura Y, Yamamoto-Sugitani M, Kobayashi T, Matsumoto Y, Horiike S, Kuroda J, Taniwaki M. 8q24 amplified segments involve novel fusion genes between NSMCE2 and long noncoding RNAs in acute myelogenous leukemia. J Hematol Oncol 2014;7:68. [PMID: 25245984 PMCID: PMC4176872 DOI: 10.1186/s13045-014-0068-2] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 09/11/2014] [Indexed: 11/22/2022]  Open
189
Wu J, Lee WP, Ward A, Walker JA, Konkel MK, Batzer MA, Marth GT. Tangram: a comprehensive toolbox for mobile element insertion detection. BMC Genomics 2014;15:795. [PMID: 25228379 PMCID: PMC4180832 DOI: 10.1186/1471-2164-15-795] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2014] [Accepted: 09/03/2014] [Indexed: 11/10/2022]  Open
190
Drabovich AP, Martínez-Morillo E, Diamandis EP. Toward an integrated pipeline for protein biomarker development. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014;1854:677-86. [PMID: 25218201 DOI: 10.1016/j.bbapap.2014.09.006] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 08/08/2014] [Accepted: 09/04/2014] [Indexed: 01/06/2023]
191
Liu B, Morrison CD, Johnson CS, Trump DL, Qin M, Conroy JC, Wang J, Liu S. Computational methods for detecting copy number variations in cancer genome using next generation sequencing: principles and challenges. Oncotarget 2014;4:1868-81. [PMID: 24240121 PMCID: PMC3875755 DOI: 10.18632/oncotarget.1537] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
192
Kadalayil L, Rafiq S, Rose-Zerilli MJJ, Pengelly RJ, Parker H, Oscier D, Strefford JC, Tapper WJ, Gibson J, Ennis S, Collins A. Exome sequence read depth methods for identifying copy number changes. Brief Bioinform 2014;16:380-92. [PMID: 25169955 DOI: 10.1093/bib/bbu027] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2014] [Accepted: 07/10/2014] [Indexed: 01/04/2023]  Open
193
Duan J, Zhang JG, Wan M, Deng HW, Wang YP. Population clustering based on copy number variations detected from next generation sequencing data. J Bioinform Comput Biol 2014;12:1450021. [PMID: 25152046 DOI: 10.1142/s0219720014500218] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
194
Milavec M, Dobnik D, Yang L, Zhang D, Gruden K, Zel J. GMO quantification: valuable experience and insights for the future. Anal Bioanal Chem 2014;406:6485-97. [PMID: 25182968 DOI: 10.1007/s00216-014-8077-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Revised: 07/23/2014] [Accepted: 07/28/2014] [Indexed: 11/30/2022]
195
Lighten J, van Oosterhout C, Bentzen P. Critical review of NGS analyses for de novo genotyping multigene families. Mol Ecol 2014;23:3957-72. [DOI: 10.1111/mec.12843] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2014] [Revised: 06/08/2014] [Accepted: 06/17/2014] [Indexed: 01/16/2023]
196
L'Abbate A, Macchia G, D'Addabbo P, Lonoce A, Tolomeo D, Trombetta D, Kok K, Bartenhagen C, Whelan CW, Palumbo O, Severgnini M, Cifola I, Dugas M, Carella M, De Bellis G, Rocchi M, Carbone L, Storlazzi CT. Genomic organization and evolution of double minutes/homogeneously staining regions with MYC amplification in human cancer. Nucleic Acids Res 2014;42:9131-45. [PMID: 25034695 PMCID: PMC4132716 DOI: 10.1093/nar/gku590] [Citation(s) in RCA: 86] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]  Open
197
Expanding the computational toolbox for mining cancer genomes. Nat Rev Genet 2014;15:556-70. [PMID: 25001846 DOI: 10.1038/nrg3767] [Citation(s) in RCA: 132] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
198
Quek K, Nones K, Patch AM, Fink JL, Newell F, Cloonan N, Miller D, Fadlullah MZH, Kassahn K, Christ AN, Bruxner TJC, Manning S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Wani S, Steptoe A, Anderson M, Holmes O, Leonard C, Taylor D, Wood S, Xu Q, Wilson P, Biankin AV, Pearson JV, Waddell N, Grimmond SM. A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing. Biotechniques 2014;57:31-8. [PMID: 25005691 DOI: 10.2144/000114189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Accepted: 06/12/2014] [Indexed: 11/23/2022]  Open
199
Daniels MG, Bowman RV, Yang IA, Govindan R, Fong KM. An emerging place for lung cancer genomics in 2013. J Thorac Dis 2014;5 Suppl 5:S491-7. [PMID: 24163742 DOI: 10.3978/j.issn.2072-1439.2013.10.06] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2013] [Accepted: 10/12/2013] [Indexed: 12/11/2022]
200
Saxena RK, Edwards D, Varshney RK. Structural variations in plant genomes. Brief Funct Genomics 2014;13:296-307. [PMID: 24907366 PMCID: PMC4110416 DOI: 10.1093/bfgp/elu016] [Citation(s) in RCA: 123] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]  Open
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