-
1
-
-
80052765035
-
Unraveling the genetics of cancer: genome sequencing and beyond
-
10.1146/annurev-genom-082509-141532, 21639794
-
Wong KM, Hudson TJ, McPherson JD. Unraveling the genetics of cancer: genome sequencing and beyond. Annu Rev Genomics Hum Genet 2011, 12:407-430. 10.1146/annurev-genom-082509-141532, 21639794.
-
(2011)
Annu Rev Genomics Hum Genet
, vol.12
, pp. 407-430
-
-
Wong, K.M.1
Hudson, T.J.2
McPherson, J.D.3
-
2
-
-
77956838065
-
Advances in understanding cancer genomes through second-generation sequencing
-
10.1038/nrg2841, 20847746
-
Meyerson M, Gabriel S, Getz G. Advances in understanding cancer genomes through second-generation sequencing. Nat Rev Genet 2010, 11(10):685-696. 10.1038/nrg2841, 20847746.
-
(2010)
Nat Rev Genet
, vol.11
, Issue.10
, pp. 685-696
-
-
Meyerson, M.1
Gabriel, S.2
Getz, G.3
-
3
-
-
79953158399
-
Exploring the genomes of cancer cells: progress and promise
-
10.1126/science.1204040, 21436442
-
Stratton MR. Exploring the genomes of cancer cells: progress and promise. Science 2011, 331(6024):1553-1558. 10.1126/science.1204040, 21436442.
-
(2011)
Science
, vol.331
, Issue.6024
, pp. 1553-1558
-
-
Stratton, M.R.1
-
4
-
-
78650791604
-
Analysis of next-generation genomic data in cancer: accomplishments and challenges
-
10.1093/hmg/ddq391, 2953747, 20843826
-
Ding L, Wendl MC, Koboldt DC, Mardis ER. Analysis of next-generation genomic data in cancer: accomplishments and challenges. Hum Mol Genet 2010, 19(R2):R188-196. 10.1093/hmg/ddq391, 2953747, 20843826.
-
(2010)
Hum Mol Genet
, vol.19
, Issue.R2
-
-
Ding, L.1
Wendl, M.C.2
Koboldt, D.C.3
Mardis, E.R.4
-
5
-
-
84870532434
-
Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes
-
10.1038/ng.2455, 3515204, 23104009, NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program
-
Le Gallo M, O'Hara AJ, Rudd ML, Urick ME, Hansen NF, O'Neil NJ, Price JC, Zhang S, England BM, Godwin AK, Sgroi DC, Hieter P, Mullikin JC, Merino MJ, Bell DW, NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program Exome sequencing of serous endometrial tumors identifies recurrent somatic mutations in chromatin-remodeling and ubiquitin ligase complex genes. Nat Genet 2012, 44(12):1310-1315. 10.1038/ng.2455, 3515204, 23104009, NIH Intramural Sequencing Center (NISC) Comparative Sequencing Program.
-
(2012)
Nat Genet
, vol.44
, Issue.12
, pp. 1310-1315
-
-
Le Gallo, M.1
O'Hara, A.J.2
Rudd, M.L.3
Urick, M.E.4
Hansen, N.F.5
O'Neil, N.J.6
Price, J.C.7
Zhang, S.8
England, B.M.9
Godwin, A.K.10
Sgroi, D.C.11
Hieter, P.12
Mullikin, J.C.13
Merino, M.J.14
Bell, D.W.15
-
6
-
-
84860327480
-
Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes
-
10.1038/ng.2246, 22484628
-
Zang ZJ, Cutcutache I, Poon SL, Zhang SL, McPherson JR, Tao J, Rajasegaran V, Heng HL, Deng N, Gan A, Lim KH, Ong CK, Huang D, Chin SY, Tan IB, Ng CCY, Yu W, Wu Y, Lee M, Wu J, Poh D, Wan WK, Rha SY, So J, Salto-Tellez M, Yeoh KG, Wong WK, Zhu YJ, Futreal PA, Pang B, et al. Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nat Genet 2012, 44(5):570-574. 10.1038/ng.2246, 22484628.
-
(2012)
Nat Genet
, vol.44
, Issue.5
, pp. 570-574
-
-
Zang, Z.J.1
Cutcutache, I.2
Poon, S.L.3
Zhang, S.L.4
McPherson, J.R.5
Tao, J.6
Rajasegaran, V.7
Heng, H.L.8
Deng, N.9
Gan, A.10
Lim, K.H.11
Ong, C.K.12
Huang, D.13
Chin, S.Y.14
Tan, I.B.15
Ng, C.C.Y.16
Yu, W.17
Wu, Y.18
Lee, M.19
Wu, J.20
Poh, D.21
Wan, W.K.22
Rha, S.Y.23
So, J.24
Salto-Tellez, M.25
Yeoh, K.G.26
Wong, W.K.27
Zhu, Y.J.28
Futreal, P.A.29
Pang, B.30
more..
-
7
-
-
79960036578
-
Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia
-
10.1038/nature10113, 3322590, 21642962
-
Puente XS, Pinyol M, Quesada V, Conde L, Ordóñez GR, Villamor N, Escaramis G, Jares P, Beà S, González-Díaz M, Bassaganyas L, Baumann T, Juan M, López-Guerra M, Colomer D, Tubío JMC, López C, Navarro A, Tornador C, Aymerich M, Rozman M, Hernández JM, Puente DA, Freije JMP, Velasco G, Gutiérrez-Fernández A, Costa D, Carrió A, Guijarro S, Enjuanes A, et al. Whole-genome sequencing identifies recurrent mutations in chronic lymphocytic leukaemia. Nature 2011, 475(7354):101-105. 10.1038/nature10113, 3322590, 21642962.
-
(2011)
Nature
, vol.475
, Issue.7354
, pp. 101-105
-
-
Puente, X.S.1
Pinyol, M.2
Quesada, V.3
Conde, L.4
Ordóñez, G.R.5
Villamor, N.6
Escaramis, G.7
Jares, P.8
Beà, S.9
González-Díaz, M.10
Bassaganyas, L.11
Baumann, T.12
Juan, M.13
López-Guerra, M.14
Colomer, D.15
Tubío, J.M.C.16
López, C.17
Navarro, A.18
Tornador, C.19
Aymerich, M.20
Rozman, M.21
Hernández, J.M.22
Puente, D.A.23
Freije, J.M.P.24
Velasco, G.25
Gutiérrez-Fernández, A.26
Costa, D.27
Carrió, A.28
Guijarro, S.29
Enjuanes, A.30
more..
-
8
-
-
79251635938
-
Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma
-
10.1038/nature09639, 3030920, 21248752
-
Varela I, Tarpey P, Raine K, Huang D, Ong CK, Stephens P, Davies H, Jones D, Lin ML, Teague J, Bignell G, Butler A, Cho J, Dalgliesh GL, Galappaththige D, Greenman C, Hardy C, Jia M, Latimer C, Lau KW, Marshall J, McLaren S, Menzies A, Mudie L, Stebbings L, Largaespada DA, Wessels LFA, Richard S, Kahnoski RJ, Anema J, et al. Exome sequencing identifies frequent mutation of the SWI/SNF complex gene PBRM1 in renal carcinoma. Nature 2011, 469(7331):539-542. 10.1038/nature09639, 3030920, 21248752.
-
(2011)
Nature
, vol.469
, Issue.7331
, pp. 539-542
-
-
Varela, I.1
Tarpey, P.2
Raine, K.3
Huang, D.4
Ong, C.K.5
Stephens, P.6
Davies, H.7
Jones, D.8
Lin, M.L.9
Teague, J.10
Bignell, G.11
Butler, A.12
Cho, J.13
Dalgliesh, G.L.14
Galappaththige, D.15
Greenman, C.16
Hardy, C.17
Jia, M.18
Latimer, C.19
Lau, K.W.20
Marshall, J.21
McLaren, S.22
Menzies, A.23
Mudie, L.24
Stebbings, L.25
Largaespada, D.A.26
Wessels, L.F.A.27
Richard, S.28
Kahnoski, R.J.29
Anema, J.30
more..
-
9
-
-
84869091997
-
Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes
-
10.1038/nature11547, 3530898, 23103869
-
Biankin AV, Waddell N, Kassahn KS, Gingras MC, Muthuswamy LB, Johns AL, Miller DK, Wilson PJ, Patch AM, Wu J, Chang DK, Cowley MJ, Gardiner BB, Song S, Harliwong I, Idrisoglu S, Nourse C, Nourbakhsh E, Manning S, Wani S, Gongora M, Pajic M, Scarlett CJ, Gill AJ, Pinho AV, Rooman I, Anderson M, Holmes O, Leonard C, Taylor D, et al. Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes. Nature 2012, 491(7424):399-405. 10.1038/nature11547, 3530898, 23103869.
-
(2012)
Nature
, vol.491
, Issue.7424
, pp. 399-405
-
-
Biankin, A.V.1
Waddell, N.2
Kassahn, K.S.3
Gingras, M.C.4
Muthuswamy, L.B.5
Johns, A.L.6
Miller, D.K.7
Wilson, P.J.8
Patch, A.M.9
Wu, J.10
Chang, D.K.11
Cowley, M.J.12
Gardiner, B.B.13
Song, S.14
Harliwong, I.15
Idrisoglu, S.16
Nourse, C.17
Nourbakhsh, E.18
Manning, S.19
Wani, S.20
Gongora, M.21
Pajic, M.22
Scarlett, C.J.23
Gill, A.J.24
Pinho, A.V.25
Rooman, I.26
Anderson, M.27
Holmes, O.28
Leonard, C.29
Taylor, D.30
more..
-
10
-
-
84862776906
-
Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing
-
10.1038/nature10738, 3267864, 22237025
-
Ding L, Ley TJ, Larson DE, Miller CA, Koboldt DC, Welch JS, Ritchey JK, Young MA, Lamprecht T, McLellan MD, McMichael JF, Wallis JW, Lu C, Shen D, Harris CC, Dooling DJ, Fulton RS, Fulton LL, Chen K, Schmidt H, Kalicki-Veizer J, Magrini VJ, Cook L, McGrath SD, Vickery TL, Wendl MC, Heath S, Watson MA, Link DC, Tomasson MH, et al. Clonal evolution in relapsed acute myeloid leukaemia revealed by whole-genome sequencing. Nature 2012, 481(7382):506-510. 10.1038/nature10738, 3267864, 22237025.
-
(2012)
Nature
, vol.481
, Issue.7382
, pp. 506-510
-
-
Ding, L.1
Ley, T.J.2
Larson, D.E.3
Miller, C.A.4
Koboldt, D.C.5
Welch, J.S.6
Ritchey, J.K.7
Young, M.A.8
Lamprecht, T.9
McLellan, M.D.10
McMichael, J.F.11
Wallis, J.W.12
Lu, C.13
Shen, D.14
Harris, C.C.15
Dooling, D.J.16
Fulton, R.S.17
Fulton, L.L.18
Chen, K.19
Schmidt, H.20
Kalicki-Veizer, J.21
Magrini, V.J.22
Cook, L.23
McGrath, S.D.24
Vickery, T.L.25
Wendl, M.C.26
Heath, S.27
Watson, M.A.28
Link, D.C.29
Tomasson, M.H.30
more..
-
11
-
-
84862526929
-
The clonal and mutational evolution spectrum of primary triple-negative breast cancers
-
Shah SP, Roth A, Goya R, Oloumi A, Ha G, Zhao Y, Turashvili G, Ding J, Tse K, Haffari G, Bashashati A, Prentice LM, Khattra J, Burleigh A, Yap D, Bernard V, McPherson A, Shumansky K, Crisan A, Giuliany R, Heravi-Moussavi A, Rosner J, Lai D, Birol I, Varhol R, Tam A, Dhalla N, Zeng T, Ma K, Chan SK, et al. The clonal and mutational evolution spectrum of primary triple-negative breast cancers. Nature 2012, 486(7403):395-399.
-
(2012)
Nature
, vol.486
, Issue.7403
, pp. 395-399
-
-
Shah, S.P.1
Roth, A.2
Goya, R.3
Oloumi, A.4
Ha, G.5
Zhao, Y.6
Turashvili, G.7
Ding, J.8
Tse, K.9
Haffari, G.10
Bashashati, A.11
Prentice, L.M.12
Khattra, J.13
Burleigh, A.14
Yap, D.15
Bernard, V.16
McPherson, A.17
Shumansky, K.18
Crisan, A.19
Giuliany, R.20
Heravi-Moussavi, A.21
Rosner, J.22
Lai, D.23
Birol, I.24
Varhol, R.25
Tam, A.26
Dhalla, N.27
Zeng, T.28
Ma, K.29
Chan, S.K.30
more..
-
12
-
-
79951494668
-
Initial genome sequencing and analysis of multiple myeloma
-
10.1038/nature09837, 3560292, 21430775
-
Chapman MA, Lawrence MS, Keats JJ, Cibulskis K, Sougnez C, Schinzel AC, Harview CL, Brunet JP, Ahmann GJ, Adli M, Anderson KC, Ardlie KG, Auclair D, Baker A, Bergsagel PL, Bernstein BE, Drier Y, Fonseca R, Gabriel SB, Hofmeister CC, Jagannath S, Jakubowiak AJ, Krishnan A, Levy J, Liefeld T, Lonial S, Mahan S, Mfuko B, Monti S, Perkins LM, et al. Initial genome sequencing and analysis of multiple myeloma. Nature 2011, 471(7339):467-472. 10.1038/nature09837, 3560292, 21430775.
-
(2011)
Nature
, vol.471
, Issue.7339
, pp. 467-472
-
-
Chapman, M.A.1
Lawrence, M.S.2
Keats, J.J.3
Cibulskis, K.4
Sougnez, C.5
Schinzel, A.C.6
Harview, C.L.7
Brunet, J.P.8
Ahmann, G.J.9
Adli, M.10
Anderson, K.C.11
Ardlie, K.G.12
Auclair, D.13
Baker, A.14
Bergsagel, P.L.15
Bernstein, B.E.16
Drier, Y.17
Fonseca, R.18
Gabriel, S.B.19
Hofmeister, C.C.20
Jagannath, S.21
Jakubowiak, A.J.22
Krishnan, A.23
Levy, J.24
Liefeld, T.25
Lonial, S.26
Mahan, S.27
Mfuko, B.28
Monti, S.29
Perkins, L.M.30
more..
-
13
-
-
80052158097
-
The mutational landscape of head and neck squamous cell carcinoma
-
10.1126/science.1208130, 3415217, 21798893
-
Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence M, Sougnez C, McKenna A, Shefler E, Ramos AH, Stojanov P, Carter SL, Voet D, Cortés ML, Auclair D, Berger MF, Saksena G, Guiducci C, Onofrio R, Parkin M, Romkes M, Weissfeld JL, Seethala RR, Wang L, Rangel-Escareño C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, et al. The mutational landscape of head and neck squamous cell carcinoma. Science 2011, 333(6046):1157-1160. 10.1126/science.1208130, 3415217, 21798893.
-
(2011)
Science
, vol.333
, Issue.6046
, pp. 1157-1160
-
-
Stransky, N.1
Egloff, A.M.2
Tward, A.D.3
Kostic, A.D.4
Cibulskis, K.5
Sivachenko, A.6
Kryukov, G.V.7
Lawrence, M.8
Sougnez, C.9
McKenna, A.10
Shefler, E.11
Ramos, A.H.12
Stojanov, P.13
Carter, S.L.14
Voet, D.15
Cortés, M.L.16
Auclair, D.17
Berger, M.F.18
Saksena, G.19
Guiducci, C.20
Onofrio, R.21
Parkin, M.22
Romkes, M.23
Weissfeld, J.L.24
Seethala, R.R.25
Wang, L.26
Rangel-Escareño, C.27
Fernandez-Lopez, J.C.28
Hidalgo-Miranda, A.29
Melendez-Zajgla, J.30
more..
-
14
-
-
77953006634
-
The mutation spectrum revealed by paired genome sequences from a lung cancer patient
-
10.1038/nature09004, 20505728
-
Lee W, Jiang Z, Liu J, Haverty PM, Guan Y, Stinson J, Yue P, Zhang Y, Pant KP, Bhatt D, Ha C, Johnson S, Kennemer MI, Mohan S, Nazarenko I, Watanabe C, Sparks AB, Shames DS, Gentleman R, de Sauvage FJ, Stern H, Pandita A, Ballinger DG, Drmanac R, Modrusan Z, Seshagiri S, Zhang Z. The mutation spectrum revealed by paired genome sequences from a lung cancer patient. Nature 2010, 465(7297):473-477. 10.1038/nature09004, 20505728.
-
(2010)
Nature
, vol.465
, Issue.7297
, pp. 473-477
-
-
Lee, W.1
Jiang, Z.2
Liu, J.3
Haverty, P.M.4
Guan, Y.5
Stinson, J.6
Yue, P.7
Zhang, Y.8
Pant, K.P.9
Bhatt, D.10
Ha, C.11
Johnson, S.12
Kennemer, M.I.13
Mohan, S.14
Nazarenko, I.15
Watanabe, C.16
Sparks, A.B.17
Shames, D.S.18
Gentleman, R.19
de Sauvage, F.J.20
Stern, H.21
Pandita, A.22
Ballinger, D.G.23
Drmanac, R.24
Modrusan, Z.25
Seshagiri, S.26
Zhang, Z.27
more..
-
15
-
-
84871757599
-
From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software
-
10.1093/nar/gks836, 3592472, 22965131
-
Forster M, Forster P, Elsharawy A, Hemmrich G, Kreck B, Wittig M, Thomsen I, Stade B, Barann M, Ellinghaus D, Petersen BS, May S, Melum E, Schilhabel MB, Keller A, Schreiber S, Rosenstiel P, Franke A. From next-generation sequencing alignments to accurate comparison and validation of single-nucleotide variants: the pibase software. Nucleic Acids Res 2013, 41:e16. 10.1093/nar/gks836, 3592472, 22965131.
-
(2013)
Nucleic Acids Res
, vol.41
-
-
Forster, M.1
Forster, P.2
Elsharawy, A.3
Hemmrich, G.4
Kreck, B.5
Wittig, M.6
Thomsen, I.7
Stade, B.8
Barann, M.9
Ellinghaus, D.10
Petersen, B.S.11
May, S.12
Melum, E.13
Schilhabel, M.B.14
Keller, A.15
Schreiber, S.16
Rosenstiel, P.17
Franke, A.18
-
16
-
-
79956314887
-
Genotype and SNP calling from next-generation sequencing data
-
10.1038/nrg2986, 3593722, 21587300
-
Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 2011, 12(6):443-451. 10.1038/nrg2986, 3593722, 21587300.
-
(2011)
Nat Rev Genet
, vol.12
, Issue.6
, pp. 443-451
-
-
Nielsen, R.1
Paul, J.S.2
Albrechtsen, A.3
Song, Y.S.4
-
17
-
-
81355147147
-
Identification and correction of systematic error in high-throughput sequence data
-
10.1186/1471-2105-12-451, 3295828, 22099972
-
Meacham F, Boffelli D, Dhahbi J, Martin DI, Singer M, Pachter L. Identification and correction of systematic error in high-throughput sequence data. BMC Bioinformatics 2011, 12:451. 10.1186/1471-2105-12-451, 3295828, 22099972.
-
(2011)
BMC Bioinformatics
, vol.12
, pp. 451
-
-
Meacham, F.1
Boffelli, D.2
Dhahbi, J.3
Martin, D.I.4
Singer, M.5
Pachter, L.6
-
18
-
-
80052226692
-
Sequence-specific error profile of Illumina sequencers
-
10.1093/nar/gkr344, 3141275, 21576222
-
Nakamura K, Oshima T, Morimoto T, Ikeda S, Yoshikawa H, Shiwa Y, Ishikawa S, Linak MC, Hirai A, Takahashi H, Altaf-Ul-Amin M, Ogasawara N, Kanaya S. Sequence-specific error profile of Illumina sequencers. Nucleic Acids Res 2011, 39(13):e90. 10.1093/nar/gkr344, 3141275, 21576222.
-
(2011)
Nucleic Acids Res
, vol.39
, Issue.13
-
-
Nakamura, K.1
Oshima, T.2
Morimoto, T.3
Ikeda, S.4
Yoshikawa, H.5
Shiwa, Y.6
Ishikawa, S.7
Linak, M.C.8
Hirai, A.9
Takahashi, H.10
Altaf-Ul-Amin, M.11
Ogasawara, N.12
Kanaya, S.13
-
19
-
-
79955483667
-
A framework for variation discovery and genotyping using next-generation DNA sequencing data
-
10.1038/ng.806, 3083463, 21478889
-
Depristo MA, Banks E, Poplin R, Garimella KV, Maguire JR, Hartl C, Philippakis AA, Del Angel G, Rivas MA, Hanna M, McKenna A, Fennell TJ, Kernytsky AM, Sivachenko AY, Cibulskis K, Gabriel SB, Altshuler D, Daly MJ. A framework for variation discovery and genotyping using next-generation DNA sequencing data. Nat Genet 2011, 43(5):491-498. 10.1038/ng.806, 3083463, 21478889.
-
(2011)
Nat Genet
, vol.43
, Issue.5
, pp. 491-498
-
-
Depristo, M.A.1
Banks, E.2
Poplin, R.3
Garimella, K.V.4
Maguire, J.R.5
Hartl, C.6
Philippakis, A.A.7
Del Angel, G.8
Rivas, M.A.9
Hanna, M.10
McKenna, A.11
Fennell, T.J.12
Kernytsky, A.M.13
Sivachenko, A.Y.14
Cibulskis, K.15
Gabriel, S.B.16
Altshuler, D.17
Daly, M.J.18
-
20
-
-
0029795558
-
Random effects models in latent class analysis for evaluating accuracy of diagnostic tests
-
10.2307/2533043, 8805757
-
Qu Y, Tan M, Kutner MH. Random effects models in latent class analysis for evaluating accuracy of diagnostic tests. Biometrics 1996, 52(3):797-810. 10.2307/2533043, 8805757.
-
(1996)
Biometrics
, vol.52
, Issue.3
, pp. 797-810
-
-
Qu, Y.1
Tan, M.2
Kutner, M.H.3
-
21
-
-
53349102224
-
Bayesian latent class models with conditionally dependent diagnostic tests: a case study
-
10.1002/sim.3317, 18551515
-
Menten J, Boelaert M, Lesaffre E. Bayesian latent class models with conditionally dependent diagnostic tests: a case study. Stat Med 2008, 27(22):4469-4488. 10.1002/sim.3317, 18551515.
-
(2008)
Stat Med
, vol.27
, Issue.22
, pp. 4469-4488
-
-
Menten, J.1
Boelaert, M.2
Lesaffre, E.3
-
22
-
-
68549104404
-
The sequence alignment/map format and SAMtools
-
10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup
-
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R, 1000 Genome Project Data Processing Subgroup The sequence alignment/map format and SAMtools. Bioinformatics 2009, 25(16):2078-2079. 10.1093/bioinformatics/btp352, 2723002, 19505943, 1000 Genome Project Data Processing Subgroup.
-
(2009)
Bioinformatics
, vol.25
, Issue.16
, pp. 2078-2079
-
-
Li, H.1
Handsaker, B.2
Wysoker, A.3
Fennell, T.4
Ruan, J.5
Homer, N.6
Marth, G.7
Abecasis, G.8
Durbin, R.9
-
23
-
-
79960405019
-
The variant call format and VCFtools
-
10.1093/bioinformatics/btr330, 3137218, 21653522, 1000 Genomes Project Analysis Group
-
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, Depristo MA, Handsaker RE, Lunter G, Marth GT, Sherry ST, McVean G, Durbin R, 1000 Genomes Project Analysis Group The variant call format and VCFtools. Bioinformatics 2011, 27(15):2156-2158. 10.1093/bioinformatics/btr330, 3137218, 21653522, 1000 Genomes Project Analysis Group.
-
(2011)
Bioinformatics
, vol.27
, Issue.15
, pp. 2156-2158
-
-
Danecek, P.1
Auton, A.2
Abecasis, G.3
Albers, C.A.4
Banks, E.5
Depristo, M.A.6
Handsaker, R.E.7
Lunter, G.8
Marth, G.T.9
Sherry, S.T.10
McVean, G.11
Durbin, R.12
-
24
-
-
80053194792
-
Base-calling for next-generation sequencing platforms
-
10.1093/bib/bbq077, 3178052, 21245079
-
Ledergerber C, Dessimoz C. Base-calling for next-generation sequencing platforms. Brief Bioinform 2011, 12(5):489-497. 10.1093/bib/bbq077, 3178052, 21245079.
-
(2011)
Brief Bioinform
, vol.12
, Issue.5
, pp. 489-497
-
-
Ledergerber, C.1
Dessimoz, C.2
-
25
-
-
0031772593
-
Evaluation of diagnostic tests without gold standards
-
10.1191/096228098671192352, 9871952
-
Hui SL, Zhou XH. Evaluation of diagnostic tests without gold standards. Stat Methods Med Res 1998, 7(4):354-370. 10.1191/096228098671192352, 9871952.
-
(1998)
Stat Methods Med Res
, vol.7
, Issue.4
, pp. 354-370
-
-
Hui, S.L.1
Zhou, X.H.2
-
26
-
-
0037094078
-
Methods for evaluating the performance of diagnostic tests in the absence of a gold standard: a latent class model approach
-
10.1002/sim.1105, 12111879
-
Garrett ES, Eaton WW, Zeger S. Methods for evaluating the performance of diagnostic tests in the absence of a gold standard: a latent class model approach. Stat Med 2002, 21(9):1289-1307. 10.1002/sim.1105, 12111879.
-
(2002)
Stat Med
, vol.21
, Issue.9
, pp. 1289-1307
-
-
Garrett, E.S.1
Eaton, W.W.2
Zeger, S.3
-
27
-
-
34147122602
-
Insights into latent class analysis of diagnostic test performance
-
Pepe MS, Janes H. Insights into latent class analysis of diagnostic test performance. Biostatistics 2007, 8(2):474-484.
-
(2007)
Biostatistics
, vol.8
, Issue.2
, pp. 474-484
-
-
Pepe, M.S.1
Janes, H.2
-
28
-
-
70450227267
-
A probit latent class model with general correlation structures for evaluating accuracy of diagnostic tests
-
10.1111/j.1541-0420.2008.01194.x, 19210729
-
Xu H, Craig BA. A probit latent class model with general correlation structures for evaluating accuracy of diagnostic tests. Biometrics 2009, 65(4):1145-1155. 10.1111/j.1541-0420.2008.01194.x, 19210729.
-
(2009)
Biometrics
, vol.65
, Issue.4
, pp. 1145-1155
-
-
Xu, H.1
Craig, B.A.2
-
29
-
-
84859249611
-
JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data
-
10.1093/bioinformatics/bts053, 3315723, 22285562
-
Roth A, Ding J, Morin R, Crisan A, Ha G, Giuliany R, Bashashati A, Hirst M, Turashvili G, Oloumi A, Marra MA, Aparicio S, Shah SP. JointSNVMix: a probabilistic model for accurate detection of somatic mutations in normal/tumour paired next-generation sequencing data. Bioinformatics 2012, 28(7):907-913. 10.1093/bioinformatics/bts053, 3315723, 22285562.
-
(2012)
Bioinformatics
, vol.28
, Issue.7
, pp. 907-913
-
-
Roth, A.1
Ding, J.2
Morin, R.3
Crisan, A.4
Ha, G.5
Giuliany, R.6
Bashashati, A.7
Hirst, M.8
Turashvili, G.9
Oloumi, A.10
Marra, M.A.11
Aparicio, S.12
Shah, S.P.13
-
30
-
-
84856565531
-
SomaticSniper: identification of somatic point mutations in whole genome sequencing data
-
10.1093/bioinformatics/btr665, 3268238, 22155872
-
Larson DE, Harris CC, Chen K, Koboldt DC, Abbott TE, Dooling DJ, Ley TJ, Mardis ER, Wilson RK, Ding L. SomaticSniper: identification of somatic point mutations in whole genome sequencing data. Bioinformatics 2012, 28(3):311-317. 10.1093/bioinformatics/btr665, 3268238, 22155872.
-
(2012)
Bioinformatics
, vol.28
, Issue.3
, pp. 311-317
-
-
Larson, D.E.1
Harris, C.C.2
Chen, K.3
Koboldt, D.C.4
Abbott, T.E.5
Dooling, D.J.6
Ley, T.J.7
Mardis, E.R.8
Wilson, R.K.9
Ding, L.10
-
31
-
-
84864153492
-
Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs
-
10.1093/bioinformatics/bts271, 22581179
-
Saunders CT, Wong WSW, Swamy S, Becq J, Murray LJ, Cheetham RK. Strelka: accurate somatic small-variant calling from sequenced tumor-normal sample pairs. Bioinformatics 2012, 28(14):1811-1817. 10.1093/bioinformatics/bts271, 22581179.
-
(2012)
Bioinformatics
, vol.28
, Issue.14
, pp. 1811-1817
-
-
Saunders, C.T.1
Wong, W.S.W.2
Swamy, S.3
Becq, J.4
Murray, L.J.5
Cheetham, R.K.6
-
32
-
-
84874025843
-
Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples
-
10.1038/nbt.2514, 23396013
-
Cibulskis K, Lawrence MS, Carter SL, Sivachenko A, Jaffe D, Sougnez C, Gabriel S, Meyerson M, Lander ES, Getz G. Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples. Nat Biotechnol 2013, 31(3):213-219. 10.1038/nbt.2514, 23396013.
-
(2013)
Nat Biotechnol
, vol.31
, Issue.3
, pp. 213-219
-
-
Cibulskis, K.1
Lawrence, M.S.2
Carter, S.L.3
Sivachenko, A.4
Jaffe, D.5
Sougnez, C.6
Gabriel, S.7
Meyerson, M.8
Lander, E.S.9
Getz, G.10
-
33
-
-
84866951075
-
Confidence-based somatic mutation evaluation and prioritization
-
10.1371/journal.pcbi.1002714, 3459886, 23028300
-
Löwer M, Renard BY, de Graaf J, Paret C, Kneip C, Türeci O, Diken M, Britten C, Kreiter S, Koslowski M, Castle JC, Sahin U. Confidence-based somatic mutation evaluation and prioritization. PLoS Comput Biol 2012, 8(9):e1002714. 10.1371/journal.pcbi.1002714, 3459886, 23028300.
-
(2012)
PLoS Comput Biol
, vol.8
, Issue.9
-
-
Löwer, M.1
Renard, B.Y.2
de Graaf, J.3
Paret, C.4
Kneip, C.5
Türeci, O.6
Diken, M.7
Britten, C.8
Kreiter, S.9
Koslowski, M.10
Castle, J.C.11
Sahin, U.12
|