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NTIS 바로가기BMC genomics, v.19, 2018년, pp.270 -
Yang, Rendong (The Hormel Institute, University of Minnesota, 801 16th AVE NE, Austin, MN 55912 USA) , Van Etten, Jamie L. (Masonic Cancer Center, University of Minnesota, 420 Delaware St SE, Minneapolis, MN 55455 USA) , Dehm, Scott M. (Masonic Cancer Center, University of Minnesota, 420 Delaware St SE, Minneapolis, MN 55455 USA)
BackgroundInsertions and deletions (indels) are a major class of genomic variation associated with human disease. Indels are primarily detected from DNA sequencing (DNA-seq) data but their transcriptional consequences remain unexplored due to challenges in discriminating medium-sized and large indel...
1. Shlien A Raine K Fuligni F Arnold R Nik-Zainal S Dronov S Direct transcriptional consequences of somatic mutation in breast Cancer Cell Rep 2016 16 2032 2046 10.1016/j.celrep.2016.07.028 27498871
2. Radenbaugh AJ Ma S Ewing A Stuart JM Collisson EA Zhu J RADIA: RNA and DNA integrated analysis for somatic mutation detection PLoS One 2014 9 e111516 10.1371/journal.pone.0111516 25405470
3. O’Brien TD Jia P Xia J Saxena U Jin H Vuong H Inconsistency and features of single nucleotide variants detected in whole exome sequencing versus transcriptome sequencing: a case study in lung cancer Methods 2015 83 118 127 10.1016/j.ymeth.2015.04.016 25913717
4. Wilkerson MD Cabanski CR Sun W Hoadley KA Walter V Mose LE Integrated RNA and DNA sequencing improves mutation detection in low purity tumors Nucleic Acids Res 2014 42 e107 10.1093/nar/gku489 24970867
5. McPherson A Wu C Hajirasouliha I Hormozdiari F Hach F Lapuk A Comrad: detection of expressed rearrangements by integrated analysis of RNA-Seq and low coverage genome sequence data Bioinformatics 2011 27 1481 1488 10.1093/bioinformatics/btr184 21478487
6. Piskol R Ramaswami G Li JB Reliable identification of genomic variants from RNA-seq data Am J Hum Genet 2013 93 641 651 10.1016/j.ajhg.2013.08.008 24075185
7. Zhang J White NM Schmidt HK Fulton RS Tomlinson C Warren WC INTEGRATE: gene fusion discovery using whole genome and transcriptome data Genome Res 2016 26 108 118 10.1101/gr.186114.114 26556708
8. Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher J-PA. Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. Brief Bioinform. 2016;18:973–83.
9. Wajnberg G Passetti F Using high-throughput sequencing transcriptome data for INDEL detection: challenges for cancer drug discovery Expert Opin Drug Discov 2016 11 257 268 10.1517/17460441.2016.1143813 26787005
10. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. 2013; Available from: http://arxiv.org/abs/1303.3997 .
11. Li H Handsaker B Wysoker A Fennell T Ruan J Homer N The sequence alignment/map format and SAMtools Bioinformatics 2009 25 2078 2079 10.1093/bioinformatics/btp352 19505943
12. Lai Z Markovets A Ahdesmaki M Chapman B Hofmann O McEwen R VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research Nucleic Acids Res 2016 44 e108 10.1093/nar/gkw227 27060149
13. Yang R Nelson AC Henzler C Thyagarajan B Silverstein KAT ScanIndel: a hybrid framework for indel detection via gapped alignment, split reads and de novo assembly Genome Med 2015 7 127 10.1186/s13073-015-0251-2 26643039
14. Henzler C Li Y Yang R McBride T Ho Y Sprenger C Truncation and constitutive activation of the androgen receptor by diverse genomic rearrangements in prostate cancer Nat Commun 2016 7 13668 10.1038/ncomms13668 27897170
15. Cancer Genome Atlas Research Network The molecular taxonomy of primary prostate Cancer Cell 2015 163 1011 1025 10.1016/j.cell.2015.10.025 26544944
16. Xu H DiCarlo J Satya RV Peng Q Wang Y Comparison of somatic mutation calling methods in amplicon and whole exome sequence data BMC Genomics 2014 15 244 10.1186/1471-2164-15-244 24678773
17. Hinrichs AS Raney BJ Speir ML Rhead B Casper J Karolchik D UCSC data integrator and variant annotation integrator Bioinformatics 2016 32 1430 1432 10.1093/bioinformatics/btv766 26740527
18. Uphoff CC Denkmann S-A Drexler HG Treatment of mycoplasma contamination in cell cultures with Plasmocin J Biomed Biotechnol 2012 2012 267678 10.1155/2012/267678 23091342
19. Dobin A Davis CA Schlesinger F Drenkow J Zaleski C Jha S STAR: ultrafast universal RNA-seq aligner Bioinformatics 2013 29 15 21 10.1093/bioinformatics/bts635 23104886
20. DePristo MA Banks E Poplin R Garimella KV Maguire JR Hartl C A framework for variation discovery and genotyping using next-generation DNA sequencing data Nat Genet 2011 43 491 498 10.1038/ng.806 21478889
21. Ye K Schulz MH Long Q Apweiler R Ning Z Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads Bioinformatics 2009 25 2865 2871 10.1093/bioinformatics/btp394 19561018
22. Narzisi G O’Rawe JA Iossifov I Fang H Lee Y-H Wang Z Accurate de novo and transmitted indel detection in exome-capture data using microassembly Nat Methods 2014 11 1033 1036 10.1038/nmeth.3069 25128977
23. Rimmer A Phan H Mathieson I Iqbal Z Twigg SRF WGS500 Consortium Integrating mapping-, assembly- and haplotype-based approaches for calling variants in clinical sequencing applications Nat Genet 2014 46 912 918 10.1038/ng.3036 25017105
24. Li H FermiKit: assembly-based variant calling for Illumina resequencing data Bioinformatics 2015 31 3694 3696 26220959
25. Rausch T Zichner T Schlattl A Stütz AM Benes V Korbel JO DELLY: structural variant discovery by integrated paired-end and split-read analysis Bioinformatics 2012 28 i333 i339 10.1093/bioinformatics/bts378 22962449
26. Chong Z Ruan J Gao M Zhou W Chen T Fan X novoBreak: local assembly for breakpoint detection in cancer genomes Nat Methods 2017 14 65 67 10.1038/nmeth.4084 27892959
27. Zook JM Chapman B Wang J Mittelman D Hofmann O Hide W Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls Nat Biotechnol 2014 32 246 251 10.1038/nbt.2835 24531798
28. Robinson D Van Allen EM Wu Y-M Schultz N Lonigro RJ Mosquera J-M Integrative clinical genomics of advanced prostate cancer Cell 2015 161 1215 1228 10.1016/j.cell.2015.05.001 26000489
29. Pertea M The human transcriptome: an unfinished story Genes (Basel) 2012 3 344 360 10.3390/genes3030344 22916334
30. Marquez Y Höpfler M Ayatollahi Z Barta A Kalyna M Unmasking alternative splicing inside protein-coding exons defines exitrons and their role in proteome plasticity Genome Res 2015 25 995 1007 10.1101/gr.186585.114 25934563
31. Staiger D Simpson GG Enter exitrons Genome Biol 2015 16 136 10.1186/s13059-015-0704-3 26149172
32. Malik R Khan AP Asangani IA Cieślik M Prensner JR Wang X Targeting the MLL complex in castration-resistant prostate cancer Nat Med 2015 21 344 352 10.1038/nm.3830 25822367
33. Tatard VM Xiang C Biegel JA Dahmane N ZNF238 is expressed in postmitotic brain cells and inhibits brain tumor growth Cancer Res 2010 70 1236 1246 10.1158/0008-5472.CAN-09-2249 20103640
34. Conesa A Madrigal P Tarazona S Gomez-Cabrero D Cervera A McPherson A A survey of best practices for RNA-seq data analysis Genome Biol 2016 17 13 10.1186/s13059-016-0881-8 26813401
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