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For: 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. ACTA ACUST UNITED AC 2012;28:907-13. [PMID: 22285562 PMCID: PMC3315723 DOI: 10.1093/bioinformatics/bts053] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Number Cited by Other Article(s)
1
Atzeni R, Massidda M, Pieroni E, Rallo V, Pisu M, Angius A. A Novel Affordable and Reliable Framework for Accurate Detection and Comprehensive Analysis of Somatic Mutations in Cancer. Int J Mol Sci 2024;25:8044. [PMID: 39125613 PMCID: PMC11311285 DOI: 10.3390/ijms25158044] [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: 06/10/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/12/2024]  Open
2
Krull JE, Wenzl K, Hopper MA, Manske MK, Sarangi V, Maurer MJ, Larson MC, Mondello P, Yang Z, Novak JP, Serres M, Whitaker KR, Villasboas Bisneto JC, Habermann TM, Witzig TE, Link BK, Rimsza LM, King RL, Ansell SM, Cerhan JR, Novak AJ. Follicular lymphoma B cells exhibit heterogeneous transcriptional states with associated somatic alterations and tumor microenvironments. Cell Rep Med 2024;5:101443. [PMID: 38428430 PMCID: PMC10983045 DOI: 10.1016/j.xcrm.2024.101443] [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: 09/16/2022] [Revised: 08/14/2023] [Accepted: 02/05/2024] [Indexed: 03/03/2024]
3
Shiraishi Y, Koya J, Chiba K, Okada A, Arai Y, Saito Y, Shibata T, Kataoka K. Precise characterization of somatic complex structural variations from tumor/control paired long-read sequencing data with nanomonsv. Nucleic Acids Res 2023;51:e74. [PMID: 37336583 PMCID: PMC10415145 DOI: 10.1093/nar/gkad526] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 05/23/2023] [Accepted: 06/07/2023] [Indexed: 06/21/2023]  Open
4
Boßelmann CM, Leu C, Lal D. Technological and computational approaches to detect somatic mosaicism in epilepsy. Neurobiol Dis 2023:106208. [PMID: 37343892 DOI: 10.1016/j.nbd.2023.106208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 06/23/2023]  Open
5
Li S, Hu R, Small C, Kang TY, Liu CC, Zhou XJ, Li W. cfSNV: a software tool for the sensitive detection of somatic mutations from cell-free DNA. Nat Protoc 2023;18:1563-1583. [PMID: 36849599 PMCID: PMC10411976 DOI: 10.1038/s41596-023-00807-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Accepted: 11/24/2022] [Indexed: 03/01/2023]
6
Vaisband M, Schubert M, Gassner FJ, Geisberger R, Greil R, Zaborsky N, Hasenauer J. Validation of genetic variants from NGS data using deep convolutional neural networks. BMC Bioinformatics 2023;24:158. [PMID: 37081386 PMCID: PMC10116675 DOI: 10.1186/s12859-023-05255-7] [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: 05/25/2022] [Accepted: 03/27/2023] [Indexed: 04/22/2023]  Open
7
Huang AY, Lee EA. Identification of Somatic Mutations From Bulk and Single-Cell Sequencing Data. FRONTIERS IN AGING 2022;2:800380. [PMID: 35822012 PMCID: PMC9261417 DOI: 10.3389/fragi.2021.800380] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/23/2021] [Accepted: 12/08/2021] [Indexed: 12/26/2022]
8
Identification and Validation of Ikaros (IKZF1) as a Cancer Driver Gene for Marek’s Disease Virus-Induced Lymphomas. Microorganisms 2022;10:microorganisms10020401. [PMID: 35208856 PMCID: PMC8877892 DOI: 10.3390/microorganisms10020401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 01/24/2022] [Accepted: 01/25/2022] [Indexed: 12/29/2022]  Open
9
Ji S, Montierth MD, Wang W. MuSE: A Novel Approach to Mutation Calling with Sample-Specific Error Modeling. Methods Mol Biol 2022;2493:21-27. [PMID: 35751806 DOI: 10.1007/978-1-0716-2293-3_2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
10
Chang TC, Xu K, Cheng Z, Wu G. Somatic and Germline Variant Calling from Next-Generation Sequencing Data. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2022;1361:37-54. [DOI: 10.1007/978-3-030-91836-1_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
11
A Retrospective Statistical Validation Approach for Panel of Normal-Based Single-Nucleotide Variant Detection in Tumor Sequencing. J Mol Diagn 2022;24:41-47. [PMID: 34974877 DOI: 10.1016/j.jmoldx.2021.09.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 08/28/2021] [Accepted: 09/28/2021] [Indexed: 11/22/2022]  Open
12
Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis. Nat Commun 2021;12:4172. [PMID: 34234141 PMCID: PMC8263778 DOI: 10.1038/s41467-021-24457-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/18/2021] [Indexed: 02/06/2023]  Open
13
Spatial Distribution of Private Gene Mutations in Clear Cell Renal Cell Carcinoma. Cancers (Basel) 2021;13:cancers13092163. [PMID: 33946379 PMCID: PMC8124666 DOI: 10.3390/cancers13092163] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/02/2021] [Accepted: 04/27/2021] [Indexed: 12/15/2022]  Open
14
Ramirez-Valles EG, Rodríguez-Pulido A, Barraza-Salas M, Martínez-Velis I, Meneses-Morales I, Ayala-García VM, Alba-Fierro CA. A Quest for New Cancer Diagnosis, Prognosis and Prediction Biomarkers and Their Use in Biosensors Development. Technol Cancer Res Treat 2020;19:1533033820957033. [PMID: 33107395 PMCID: PMC7607814 DOI: 10.1177/1533033820957033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]  Open
15
Wang M, Luo W, Jones K, Bian X, Williams R, Higson H, Wu D, Hicks B, Yeager M, Zhu B. SomaticCombiner: improving the performance of somatic variant calling based on evaluation tests and a consensus approach. Sci Rep 2020;10:12898. [PMID: 32732891 PMCID: PMC7393490 DOI: 10.1038/s41598-020-69772-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2020] [Accepted: 07/16/2020] [Indexed: 02/06/2023]  Open
16
Hunter SM, Dall GV, Doyle MA, Lupat R, Li J, Allan P, Rowley SM, Bowtell D, Campbell IG, Gorringe KL. Molecular comparison of pure ovarian fibroma with serous benign ovarian tumours. BMC Res Notes 2020;13:349. [PMID: 32698852 PMCID: PMC7376903 DOI: 10.1186/s13104-020-05194-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/17/2020] [Indexed: 01/10/2023]  Open
17
Moriyama T, Imoto S, Hayashi S, Shiraishi Y, Miyano S, Yamaguchi R. A Bayesian model integration for mutation calling through data partitioning. Bioinformatics 2020;35:4247-4254. [PMID: 30924874 PMCID: PMC6821361 DOI: 10.1093/bioinformatics/btz233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Revised: 09/06/2018] [Accepted: 03/28/2019] [Indexed: 11/25/2022]  Open
18
Cao C, Mak L, Jin G, Gordon P, Ye K, Long Q. PRESM: personalized reference editor for somatic mutation discovery in cancer genomics. Bioinformatics 2020;35:1445-1452. [PMID: 30247633 DOI: 10.1093/bioinformatics/bty812] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 08/27/2018] [Accepted: 09/19/2018] [Indexed: 12/16/2022]  Open
19
SomaticSeq: An Ensemble and Machine Learning Method to Detect Somatic Mutations. Methods Mol Biol 2020. [PMID: 32124311 DOI: 10.1007/978-1-0716-0327-7_4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2025]
20
Mannakee BK, Gutenkunst RN. BATCAVE: calling somatic mutations with a tumor- and site-specific prior. NAR Genom Bioinform 2020;2:lqaa004. [PMID: 32051931 PMCID: PMC7003682 DOI: 10.1093/nargab/lqaa004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 01/13/2020] [Accepted: 01/23/2020] [Indexed: 02/06/2023]  Open
21
Geng Y, Zhao Z, Liu J. [Reconstruction of tumor clonal haplotypes based on an improved spanning algorithm]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2019;39:1287-1292. [PMID: 31852653 DOI: 10.12122/j.issn.1673-4254.2019.11.04] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
22
Liu F, Zhang Y, Zhang L, Li Z, Fang Q, Gao R, Zhang Z. Systematic comparative analysis of single-nucleotide variant detection methods from single-cell RNA sequencing data. Genome Biol 2019;20:242. [PMID: 31744515 PMCID: PMC6862814 DOI: 10.1186/s13059-019-1863-4] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Accepted: 10/23/2019] [Indexed: 12/30/2022]  Open
23
Bewicke-Copley F, Arjun Kumar E, Palladino G, Korfi K, Wang J. Applications and analysis of targeted genomic sequencing in cancer studies. Comput Struct Biotechnol J 2019;17:1348-1359. [PMID: 31762958 PMCID: PMC6861594 DOI: 10.1016/j.csbj.2019.10.004] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2019] [Revised: 10/18/2019] [Accepted: 10/22/2019] [Indexed: 12/31/2022]  Open
24
Bartha Á, Győrffy B. Comprehensive Outline of Whole Exome Sequencing Data Analysis Tools Available in Clinical Oncology. Cancers (Basel) 2019;11:E1725. [PMID: 31690036 PMCID: PMC6895801 DOI: 10.3390/cancers11111725] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 10/31/2019] [Accepted: 11/01/2019] [Indexed: 12/17/2022]  Open
25
Cho Y, Lee S, Hong JH, Kim BJ, Hong WY, Jung J, Lee HB, Sung J, Kim HN, Kim HL, Jung J. Development of the variant calling algorithm, ADIScan, and its use to estimate discordant sequences between monozygotic twins. Nucleic Acids Res 2019;46:e92. [PMID: 29873758 PMCID: PMC6125643 DOI: 10.1093/nar/gky445] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 05/15/2018] [Indexed: 12/30/2022]  Open
26
Singer J, Irmisch A, Ruscheweyh HJ, Singer F, Toussaint NC, Levesque MP, Stekhoven DJ, Beerenwinkel N. Bioinformatics for precision oncology. Brief Bioinform 2019;20:778-788. [PMID: 29272324 PMCID: PMC6585151 DOI: 10.1093/bib/bbx143] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Revised: 09/29/2017] [Indexed: 12/13/2022]  Open
27
Calling Variants in the Clinic: Informed Variant Calling Decisions Based on Biological, Clinical, and Laboratory Variables. Comput Struct Biotechnol J 2019;17:561-569. [PMID: 31049166 PMCID: PMC6482431 DOI: 10.1016/j.csbj.2019.04.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/12/2019] [Accepted: 04/03/2019] [Indexed: 01/10/2023]  Open
28
Dorri F, Jewell S, Bouchard-Côté A, Shah SP. Somatic mutation detection and classification through probabilistic integration of clonal population information. Commun Biol 2019;2:44. [PMID: 30729182 PMCID: PMC6355807 DOI: 10.1038/s42003-019-0291-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Accepted: 12/20/2018] [Indexed: 01/06/2023]  Open
29
Sun S, Murray SS. Bioinformatics Basics for High-Throughput Hybridization-Based Targeted DNA Sequencing from FFPE-Derived Tumor Specimens: From Reads to Variants. Methods Mol Biol 2019;1908:37-48. [PMID: 30649719 DOI: 10.1007/978-1-4939-9004-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
30
Ulintz PJ, Wu W, Gates CM. Bioinformatics Analysis of Whole Exome Sequencing Data. Methods Mol Biol 2019;1881:277-318. [PMID: 30350213 DOI: 10.1007/978-1-4939-8876-1_21] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
31
Wang C, Liang C. MSIpred: a python package for tumor microsatellite instability classification from tumor mutation annotation data using a support vector machine. Sci Rep 2018;8:17546. [PMID: 30510242 PMCID: PMC6277498 DOI: 10.1038/s41598-018-35682-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Accepted: 10/28/2018] [Indexed: 12/19/2022]  Open
32
Chamberlain CE, German MS, Yang K, Wang J, VanBrocklin H, Regan M, Shokat KM, Ducker GS, Kim GE, Hann B, Donner DB, Warren RS, Venook AP, Bergsland EK, Lee D, Wang Y, Nakakura EK. A Patient-derived Xenograft Model of Pancreatic Neuroendocrine Tumors Identifies Sapanisertib as a Possible New Treatment for Everolimus-resistant Tumors. Mol Cancer Ther 2018;17:2702-2709. [PMID: 30254185 DOI: 10.1158/1535-7163.mct-17-1204] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 07/18/2018] [Accepted: 09/20/2018] [Indexed: 12/11/2022]
33
Sun Z, Bhagwate A, Prodduturi N, Yang P, Kocher JPA. Indel detection from RNA-seq data: tool evaluation and strategies for accurate detection of actionable mutations. Brief Bioinform 2018;18:973-983. [PMID: 27473065 PMCID: PMC5862335 DOI: 10.1093/bib/bbw069] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2016] [Indexed: 11/29/2022]  Open
34
Ren Y, Zhao J, Li R, Xie Y, Jiang S, Zhou H, Liu H, You Y, Chen F, Wang W, Gao Y, Meng Y, Lu Y. Noninvasive prenatal test for FGFR3-related skeletal dysplasia based on next-generation sequencing and plasma cell-free DNA: Test performance analysis and feasibility exploration. Prenat Diagn 2018;38:821-828. [PMID: 30048571 DOI: 10.1002/pd.5334] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 07/13/2018] [Accepted: 07/14/2018] [Indexed: 12/22/2022]
35
A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing. Genome Med 2018;10:44. [PMID: 29880027 PMCID: PMC5992758 DOI: 10.1186/s13073-018-0547-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2017] [Accepted: 05/07/2018] [Indexed: 12/16/2022]  Open
36
Wang Y, Guo L, Feng L, Zhang W, Xiao T, Di X, Chen G, Zhang K. Single nucleotide variant profiles of viable single circulating tumour cells reveal CTC behaviours in breast cancer. Oncol Rep 2018;39:2147-2159. [PMID: 29565466 PMCID: PMC5928770 DOI: 10.3892/or.2018.6325] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2017] [Accepted: 03/16/2018] [Indexed: 12/21/2022]  Open
37
Muller E, Goardon N, Brault B, Rousselin A, Paimparay G, Legros A, Fouillet R, Bruet O, Tranchant A, Domin F, San C, Quesnelle C, Frebourg T, Ricou A, Krieger S, Vaur D, Castera L. OutLyzer: software for extracting low-allele-frequency tumor mutations from sequencing background noise in clinical practice. Oncotarget 2018;7:79485-79493. [PMID: 27825131 PMCID: PMC5346729 DOI: 10.18632/oncotarget.13103] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2016] [Accepted: 10/11/2016] [Indexed: 01/01/2023]  Open
38
Sun JX, He Y, Sanford E, Montesion M, Frampton GM, Vignot S, Soria JC, Ross JS, Miller VA, Stephens PJ, Lipson D, Yelensky R. A computational approach to distinguish somatic vs. germline origin of genomic alterations from deep sequencing of cancer specimens without a matched normal. PLoS Comput Biol 2018;14:e1005965. [PMID: 29415044 PMCID: PMC5832436 DOI: 10.1371/journal.pcbi.1005965] [Citation(s) in RCA: 197] [Impact Index Per Article: 28.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2015] [Revised: 03/01/2018] [Accepted: 01/05/2018] [Indexed: 12/31/2022]  Open
39
Xu C. A review of somatic single nucleotide variant calling algorithms for next-generation sequencing data. Comput Struct Biotechnol J 2018;16:15-24. [PMID: 29552334 PMCID: PMC5852328 DOI: 10.1016/j.csbj.2018.01.003] [Citation(s) in RCA: 153] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/20/2018] [Accepted: 01/28/2018] [Indexed: 02/06/2023]  Open
40
Manheimer KB, Richter F, Edelmann LJ, D'Souza SL, Shi L, Shen Y, Homsy J, Boskovski MT, Tai AC, Gorham J, Yasso C, Goldmuntz E, Brueckner M, Lifton RP, Chung WK, Seidman CE, Seidman JG, Gelb BD. Robust identification of mosaic variants in congenital heart disease. Hum Genet 2018;137:183-193. [PMID: 29417219 PMCID: PMC5997246 DOI: 10.1007/s00439-018-1871-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Accepted: 01/30/2018] [Indexed: 12/15/2022]
41
Santos C, Almeida NF, Alves ML, Horres R, Krezdorn N, Leitão ST, Aznar-Fernández T, Rotter B, Winter P, Rubiales D, Vaz Patto MC. First genetic linkage map of Lathyrus cicera based on RNA sequencing-derived markers: Key tool for genetic mapping of disease resistance. HORTICULTURE RESEARCH 2018;5:45. [PMID: 30181885 PMCID: PMC6119197 DOI: 10.1038/s41438-018-0047-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Revised: 03/05/2018] [Accepted: 04/30/2018] [Indexed: 05/10/2023]
42
Dimitrakopoulos L, Prassas I, Diamandis EP, Charames GS. Onco-proteogenomics: Multi-omics level data integration for accurate phenotype prediction. Crit Rev Clin Lab Sci 2017;54:414-432. [DOI: 10.1080/10408363.2017.1384446] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
43
Bohnert R, Vivas S, Jansen G. Comprehensive benchmarking of SNV callers for highly admixed tumor data. PLoS One 2017;12:e0186175. [PMID: 29020110 PMCID: PMC5636151 DOI: 10.1371/journal.pone.0186175] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2017] [Accepted: 09/26/2017] [Indexed: 12/30/2022]  Open
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Roman T, Xie L, Schwartz R. Automated deconvolution of structured mixtures from heterogeneous tumor genomic data. PLoS Comput Biol 2017;13:e1005815. [PMID: 29059177 PMCID: PMC5695636 DOI: 10.1371/journal.pcbi.1005815] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2017] [Revised: 11/02/2017] [Accepted: 10/10/2017] [Indexed: 11/23/2022]  Open
45
Kohmoto T, Masuda K, Naruto T, Tange S, Shoda K, Hamada J, Saito M, Ichikawa D, Tajima A, Otsuji E, Imoto I. Construction of a combinatorial pipeline using two somatic variant  calling  methods  for whole exome sequence data of gastric cancer. THE JOURNAL OF MEDICAL INVESTIGATION 2017;64:233-240. [PMID: 28954988 DOI: 10.2152/jmi.64.233] [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: 11/14/2022]
46
Huang AY, Zhang Z, Ye AY, Dou Y, Yan L, Yang X, Zhang Y, Wei L. MosaicHunter: accurate detection of postzygotic single-nucleotide mosaicism through next-generation sequencing of unpaired, trio, and paired samples. Nucleic Acids Res 2017;45:e76. [PMID: 28132024 PMCID: PMC5449543 DOI: 10.1093/nar/gkx024] [Citation(s) in RCA: 51] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2016] [Revised: 12/24/2016] [Accepted: 01/26/2017] [Indexed: 02/07/2023]  Open
47
Flynn A, Dwight T, Benn D, Deb S, Colebatch AJ, Fox S, Harris J, Duncan EL, Robinson B, Hogg A, Ellul J, To H, Duong C, Miller JA, Yates C, James P, Trainer A, Gill AJ, Clifton-Bligh R, Hicks RJ, Tothill RW. Cousins not twins: intratumoural and intertumoural heterogeneity in syndromic neuroendocrine tumours. J Pathol 2017;242:273-283. [PMID: 28369925 DOI: 10.1002/path.4900] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2017] [Revised: 03/01/2017] [Accepted: 03/23/2017] [Indexed: 12/23/2022]
48
Kuipers J, Jahn K, Beerenwinkel N. Advances in understanding tumour evolution through single-cell sequencing. Biochim Biophys Acta Rev Cancer 2017;1867:127-138. [PMID: 28193548 PMCID: PMC5813714 DOI: 10.1016/j.bbcan.2017.02.001] [Citation(s) in RCA: 79] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2016] [Revised: 02/02/2017] [Accepted: 02/04/2017] [Indexed: 12/14/2022]
49
Moriyama T, Shiraishi Y, Chiba K, Yamaguchi R, Imoto S, Miyano S. OVarCall: Bayesian Mutation Calling Method Utilizing Overlapping Paired-End Reads. IEEE Trans Nanobioscience 2017;16:116-122. [PMID: 28278479 DOI: 10.1109/tnb.2017.2670601] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
50
Salehi S, Steif A, Roth A, Aparicio S, Bouchard-Côté A, Shah SP. ddClone: joint statistical inference of clonal populations from single cell and bulk tumour sequencing data. Genome Biol 2017;18:44. [PMID: 28249593 PMCID: PMC5333399 DOI: 10.1186/s13059-017-1169-3] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/10/2017] [Indexed: 12/16/2022]  Open
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