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For: Bengtsson H, Wirapati P, Speed TP. A single-array preprocessing method for estimating full-resolution raw copy numbers from all Affymetrix genotyping arrays including GenomeWideSNP 5 & 6. Bioinformatics 2009;25:2149-56. [PMID: 19535535 PMCID: PMC2734319 DOI: 10.1093/bioinformatics/btp371] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2008] [Revised: 06/01/2009] [Accepted: 06/11/2009] [Indexed: 11/23/2022]  Open
Number Cited by Other Article(s)
1
Chicón‐Bosch M, Sánchez‐Serra S, Rosàs‐Lapeña M, Costa‐Fraga N, Besalú‐Velázquez J, Illa‐Bernadí J, Mateo‐Lozano S, Cidre‐Aranaz F, Grünewald TG, Díaz‐Lagares Á, Lopez‐Alemany R, Tirado ÒM. Multi-omics profiling reveals key factors involved in Ewing sarcoma metastasis. Mol Oncol 2025;19:1002-1028. [PMID: 39757762 PMCID: PMC11977646 DOI: 10.1002/1878-0261.13788] [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: 04/23/2024] [Revised: 08/28/2024] [Accepted: 11/14/2024] [Indexed: 01/07/2025]  Open
2
Sánchez S, Juárez U, Domínguez J, Molina B, Barrientos R, Martínez-Hernández A, Carnevale A, Grether-González P, Mayen DG, Villarroel C, Lieberman E, Yokoyama E, Del Castillo V, Torres L, Frias S. Frequent copy number variants in a cohort of Mexican-Mestizo individuals. Mol Cytogenet 2023;16:2. [PMID: 36631885 PMCID: PMC9835318 DOI: 10.1186/s13039-022-00631-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Accepted: 12/13/2022] [Indexed: 01/13/2023]  Open
3
Encoded hydrogel microparticles with universal mismatch-incorporated DNA probes for highly specific multiplex detection of SNPs. Talanta 2022;245:123480. [DOI: 10.1016/j.talanta.2022.123480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Revised: 04/01/2022] [Accepted: 04/12/2022] [Indexed: 11/22/2022]
4
Fanjul-Fernández M, Brown NJ, Hickey P, Diakumis P, Rafehi H, Bozaoglu K, Green CC, Rattray A, Young S, Alhuzaimi D, Mountford HS, Gillies G, Lukic V, Vick T, Finlay K, Coe BP, Eichler EE, Delatycki MB, Wilson SJ, Bahlo M, Scheffer IE, Lockhart PJ. A family study implicates GBE1 in the etiology of autism spectrum disorder. Hum Mutat 2022;43:16-29. [PMID: 34633740 PMCID: PMC8720068 DOI: 10.1002/humu.24289] [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: 02/13/2021] [Revised: 09/17/2021] [Accepted: 10/07/2021] [Indexed: 11/06/2022]
5
Jiang SH, Mercan S, Papa I, Moldovan M, Walters GD, Koina M, Fadia M, Stanley M, Lea-Henry T, Cook A, Ellyard J, McMorran B, Sundaram M, Thomson R, Canete PF, Hoy W, Hutton H, Srivastava M, McKeon K, de la Rúa Figueroa I, Cervera R, Faria R, D’Alfonso S, Gatto M, Athanasopoulos V, Field M, Mathews J, Cho E, Andrews TD, Kitching AR, Cook MC, Riquelme MA, Bahlo M, Vinuesa CG. Deletions in VANGL1 are a risk factor for antibody-mediated kidney disease. Cell Rep Med 2021;2:100475. [PMID: 35028616 PMCID: PMC8714939 DOI: 10.1016/j.xcrm.2021.100475] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/11/2021] [Accepted: 11/23/2021] [Indexed: 12/11/2022]
6
Bartik Z, Sillén U, Östensson M, Fransson S, Djos A, Sjöberg R, Martinsson T. A genome‑wide scan to locate regions associated with familial vesicoureteral reflux. Exp Ther Med 2021;23:92. [PMID: 34976134 PMCID: PMC8674978 DOI: 10.3892/etm.2021.11015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 07/06/2021] [Indexed: 11/05/2022]  Open
7
Wang L, Lang GT, Xue MZ, Yang L, Chen L, Yao L, Li XG, Wang P, Hu X, Shao ZM. Dissecting the heterogeneity of the alternative polyadenylation profiles in triple-negative breast cancers. Am J Cancer Res 2020;10:10531-10547. [PMID: 32929364 PMCID: PMC7482814 DOI: 10.7150/thno.40944] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Accepted: 08/09/2020] [Indexed: 02/06/2023]  Open
8
Hsin CH, Stoffel MS, Gazzaz M, Schaeffeler E, Schwab M, Fuhr U, Taubert M. Combinations of common SNPs of the transporter gene ABCB1 influence apparent bioavailability, but not renal elimination of oral digoxin. Sci Rep 2020;10:12457. [PMID: 32719417 PMCID: PMC7385621 DOI: 10.1038/s41598-020-69326-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 07/10/2020] [Indexed: 02/07/2023]  Open
9
Yang J, Chen Y, Luo H, Cai H. The Landscape of Somatic Copy Number Alterations in Head and Neck Squamous Cell Carcinoma. Front Oncol 2020;10:321. [PMID: 32226775 PMCID: PMC7080958 DOI: 10.3389/fonc.2020.00321] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2019] [Accepted: 02/24/2020] [Indexed: 02/05/2023]  Open
10
Genome-wide somatic copy number alteration analysis and database construction for cervical cancer. Mol Genet Genomics 2020;295:765-773. [PMID: 31901979 DOI: 10.1007/s00438-019-01636-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/06/2019] [Indexed: 12/24/2022]
11
Li Z, Zhang X, Hou C, Zhou Y, Chen J, Cai H, Ye Y, Liu J, Huang N. Comprehensive identification and characterization of somatic copy number alterations in triple‑negative breast cancer. Int J Oncol 2019;56:522-530. [PMID: 31894314 PMCID: PMC6959384 DOI: 10.3892/ijo.2019.4950] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 08/30/2019] [Indexed: 12/27/2022]  Open
12
Rhie SK, Perez AA, Lay FD, Schreiner S, Shi J, Polin J, Farnham PJ. A high-resolution 3D epigenomic map reveals insights into the creation of the prostate cancer transcriptome. Nat Commun 2019;10:4154. [PMID: 31515496 PMCID: PMC6742760 DOI: 10.1038/s41467-019-12079-8] [Citation(s) in RCA: 87] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/15/2019] [Indexed: 12/27/2022]  Open
13
Trueck C, Hsin CH, Scherf-Clavel O, Schaeffeler E, Lenssen R, Gazzaz M, Gersie M, Taubert M, Quasdorff M, Schwab M, Kinzig M, Sörgel F, Stoffel MS, Fuhr U. A Clinical Drug-Drug Interaction Study Assessing a Novel Drug Transporter Phenotyping Cocktail With Adefovir, Sitagliptin, Metformin, Pitavastatin, and Digoxin. Clin Pharmacol Ther 2019;106:1398-1407. [PMID: 31247117 DOI: 10.1002/cpt.1564] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Accepted: 06/19/2019] [Indexed: 12/30/2022]
14
Dogrusöz M, Ruschel Trasel A, Cao J, Ҫolak S, van Pelt SI, Kroes WGM, Teunisse AFAS, Alsafadi S, van Duinen SG, Luyten GPM, van der Velden PA, Amaro A, Pfeffer U, Jochemsen AG, Jager MJ. Differential Expression of DNA Repair Genes in Prognostically-Favorable versus Unfavorable Uveal Melanoma. Cancers (Basel) 2019;11:cancers11081104. [PMID: 31382494 PMCID: PMC6721581 DOI: 10.3390/cancers11081104] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 07/26/2019] [Accepted: 07/30/2019] [Indexed: 01/20/2023]  Open
15
Schmid MW, Heichinger C, Coman Schmid D, Guthörl D, Gagliardini V, Bruggmann R, Aluri S, Aquino C, Schmid B, Turnbull LA, Grossniklaus U. Contribution of epigenetic variation to adaptation in Arabidopsis. Nat Commun 2018;9:4446. [PMID: 30361538 PMCID: PMC6202389 DOI: 10.1038/s41467-018-06932-5] [Citation(s) in RCA: 83] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2017] [Accepted: 10/05/2018] [Indexed: 12/20/2022]  Open
16
Aiderus A, Black MA, Dunbier AK. Fatty acid oxidation is associated with proliferation and prognosis in breast and other cancers. BMC Cancer 2018;18:805. [PMID: 30092766 PMCID: PMC6085695 DOI: 10.1186/s12885-018-4626-9] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Accepted: 06/21/2018] [Indexed: 02/07/2023]  Open
17
Patel N, Weekes D, Drosopoulos K, Gazinska P, Noel E, Rashid M, Mirza H, Quist J, Brasó-Maristany F, Mathew S, Ferro R, Pereira AM, Prince C, Noor F, Francesch-Domenech E, Marlow R, de Rinaldis E, Grigoriadis A, Linardopoulos S, Marra P, Tutt ANJ. Integrated genomics and functional validation identifies malignant cell specific dependencies in triple negative breast cancer. Nat Commun 2018;9:1044. [PMID: 29535384 PMCID: PMC5849766 DOI: 10.1038/s41467-018-03283-z] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2017] [Accepted: 02/01/2018] [Indexed: 12/31/2022]  Open
18
Hilberg F, Tontsch-Grunt U, Baum A, Le AT, Doebele RC, Lieb S, Gianni D, Voss T, Garin-Chesa P, Haslinger C, Kraut N. Triple Angiokinase Inhibitor Nintedanib Directly Inhibits Tumor Cell Growth and Induces Tumor Shrinkage via Blocking Oncogenic Receptor Tyrosine Kinases. J Pharmacol Exp Ther 2018;364:494-503. [PMID: 29263244 PMCID: PMC6040086 DOI: 10.1124/jpet.117.244129] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Accepted: 12/11/2017] [Indexed: 12/11/2022]  Open
19
ITGB1-dependent upregulation of Caveolin-1 switches TGFβ signalling from tumour-suppressive to oncogenic in prostate cancer. Sci Rep 2018;8:2338. [PMID: 29402961 PMCID: PMC5799174 DOI: 10.1038/s41598-018-20161-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2017] [Accepted: 01/15/2018] [Indexed: 01/10/2023]  Open
20
Efremova M, Rieder D, Klepsch V, Charoentong P, Finotello F, Hackl H, Hermann-Kleiter N, Löwer M, Baier G, Krogsdam A, Trajanoski Z. Targeting immune checkpoints potentiates immunoediting and changes the dynamics of tumor evolution. Nat Commun 2018;9:32. [PMID: 29296022 PMCID: PMC5750210 DOI: 10.1038/s41467-017-02424-0] [Citation(s) in RCA: 185] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 11/28/2017] [Indexed: 02/07/2023]  Open
21
Khan FM, Sadeghi M, Gupta SK, Wolkenhauer O. A Network-Based Integrative Workflow to Unravel Mechanisms Underlying Disease Progression. Methods Mol Biol 2018;1702:247-276. [PMID: 29119509 DOI: 10.1007/978-1-4939-7456-6_12] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
22
Jabs V, Edlund K, König H, Grinberg M, Madjar K, Rahnenführer J, Ekman S, Bergkvist M, Holmberg L, Ickstadt K, Botling J, Hengstler JG, Micke P. Integrative analysis of genome-wide gene copy number changes and gene expression in non-small cell lung cancer. PLoS One 2017;12:e0187246. [PMID: 29112949 PMCID: PMC5675410 DOI: 10.1371/journal.pone.0187246] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Accepted: 10/17/2017] [Indexed: 12/27/2022]  Open
23
Danziger SA, Miller LR, Singh K, Whitney GA, Peskind ER, Li G, Lipshutz RJ, Aitchison JD, Smith JJ. An indicator cell assay for blood-based diagnostics. PLoS One 2017;12:e0178608. [PMID: 28594877 PMCID: PMC5464608 DOI: 10.1371/journal.pone.0178608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 05/16/2017] [Indexed: 11/30/2022]  Open
24
Aure MR, Vitelli V, Jernström S, Kumar S, Krohn M, Due EU, Haukaas TH, Leivonen SK, Vollan HKM, Lüders T, Rødland E, Vaske CJ, Zhao W, Møller EK, Nord S, Giskeødegård GF, Bathen TF, Caldas C, Tramm T, Alsner J, Overgaard J, Geisler J, Bukholm IRK, Naume B, Schlichting E, Sauer T, Mills GB, Kåresen R, Mælandsmo GM, Lingjærde OC, Frigessi A, Kristensen VN, Børresen-Dale AL, Sahlberg KK. Integrative clustering reveals a novel split in the luminal A subtype of breast cancer with impact on outcome. Breast Cancer Res 2017;19:44. [PMID: 28356166 PMCID: PMC5372339 DOI: 10.1186/s13058-017-0812-y] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2016] [Accepted: 02/05/2017] [Indexed: 01/19/2023]  Open
25
van de Ven RA, de Groot JS, Park D, van Domselaar R, de Jong D, Szuhai K, van der Wall E, Rueda OM, Ali HR, Caldas C, van Diest PJ, Hetzer MW, Sahai E, Derksen PW. p120-catenin prevents multinucleation through control of MKLP1-dependent RhoA activity during cytokinesis. Nat Commun 2016;7:13874. [PMID: 28004812 PMCID: PMC5192218 DOI: 10.1038/ncomms13874] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/07/2016] [Indexed: 02/07/2023]  Open
26
van Essen TH, van Pelt SI, Bronkhorst IHG, Versluis M, Némati F, Laurent C, Luyten GPM, van Hall T, van den Elsen PJ, van der Velden PA, Decaudin D, Jager MJ. Upregulation of HLA Expression in Primary Uveal Melanoma by Infiltrating Leukocytes. PLoS One 2016;11:e0164292. [PMID: 27764126 PMCID: PMC5072555 DOI: 10.1371/journal.pone.0164292] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2016] [Accepted: 09/22/2016] [Indexed: 12/22/2022]  Open
27
Kanojia D, Nagata Y, Garg M, Lee DH, Sato A, Yoshida K, Sato Y, Sanada M, Mayakonda A, Bartenhagen C, Klein HU, Doan NB, Said JW, Mohith S, Gunasekar S, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Myklebost O, Yang H, Dugas M, Meza-Zepeda LA, Silberman AW, Forscher C, Tyner JW, Ogawa S, Koeffler HP. Genomic landscape of liposarcoma. Oncotarget 2016;6:42429-44. [PMID: 26643872 PMCID: PMC4767443 DOI: 10.18632/oncotarget.6464] [Citation(s) in RCA: 98] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2015] [Accepted: 11/26/2015] [Indexed: 01/09/2023]  Open
28
Yang J, Liu J, Ouyang L, Chen Y, Liu B, Cai H. CTLPScanner: a web server for chromothripsis-like pattern detection. Nucleic Acids Res 2016;44:W252-8. [PMID: 27185889 PMCID: PMC4987951 DOI: 10.1093/nar/gkw434] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2016] [Accepted: 05/08/2016] [Indexed: 02/05/2023]  Open
29
Three-dimensional disorganization of the cancer genome occurs coincident with long-range genetic and epigenetic alterations. Genome Res 2016;26:719-31. [PMID: 27053337 PMCID: PMC4889976 DOI: 10.1101/gr.201517.115] [Citation(s) in RCA: 221] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 04/04/2016] [Indexed: 12/29/2022]
30
Cutcutache I, Wu AY, Suzuki Y, McPherson JR, Lei Z, Deng N, Zhang S, Wong WK, Soo KC, Chan WH, Ooi LL, Welsch R, Tan P, Rozen SG. Abundant copy-number loss of CYCLOPS and STOP genes in gastric adenocarcinoma. Gastric Cancer 2016;19. [PMID: 26205786 PMCID: PMC4824836 DOI: 10.1007/s10120-015-0514-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
31
Kanojia D, Nagata Y, Garg M, Lee DH, Sato A, Yoshida K, Sato Y, Sanada M, Mayakonda A, Bartenhagen C, Klein HU, Doan NB, Said JW, Mohith S, Gunasekar S, Shiraishi Y, Chiba K, Tanaka H, Miyano S, Myklebost O, Yang H, Dugas M, Meza-Zepeda LA, Silberman AW, Forscher C, Tyner JW, Ogawa S, Koeffler HP. Genomic landscape of liposarcoma. Oncotarget 2015. [PMID: 26643872 DOI: 10.1832/oncotarget.3575] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2023]  Open
32
Ng J, Fass JN, Durbin-Johnson B, Smith DG, Kanthaswamy S. Identifying rhesus macaque gene orthologs using heterospecific human CNV probes. GENOMICS DATA 2015;6:202-7. [PMID: 26697375 PMCID: PMC4664757 DOI: 10.1016/j.gdata.2015.09.016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2015] [Accepted: 09/12/2015] [Indexed: 12/14/2022]
33
Mihailovich M, Bremang M, Spadotto V, Musiani D, Vitale E, Varano G, Zambelli F, Mancuso FM, Cairns DA, Pavesi G, Casola S, Bonaldi T. miR-17-92 fine-tunes MYC expression and function to ensure optimal B cell lymphoma growth. Nat Commun 2015;6:8725. [PMID: 26555894 PMCID: PMC4667639 DOI: 10.1038/ncomms9725] [Citation(s) in RCA: 83] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Accepted: 09/22/2015] [Indexed: 01/07/2023]  Open
34
Petrovics G, Li H, Stümpel T, Tan SH, Young D, Katta S, Li Q, Ying K, Klocke B, Ravindranath L, Kohaar I, Chen Y, Ribli D, Grote K, Zou H, Cheng J, Dalgard CL, Zhang S, Csabai I, Kagan J, Takeda D, Loda M, Srivastava S, Scherf M, Seifert M, Gaiser T, McLeod DG, Szallasi Z, Ebner R, Werner T, Sesterhenn IA, Freedman M, Dobi A, Srivastava S. A novel genomic alteration of LSAMP associates with aggressive prostate cancer in African American men. EBioMedicine 2015;2:1957-64. [PMID: 26844274 PMCID: PMC4703707 DOI: 10.1016/j.ebiom.2015.10.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Revised: 10/22/2015] [Accepted: 10/29/2015] [Indexed: 02/03/2023]  Open
35
Torabi K, Miró R, Fernández-Jiménez N, Quintanilla I, Ramos L, Prat E, del Rey J, Pujol N, Killian JK, Meltzer PS, Fernández PL, Ried T, Lozano JJ, Camps J, Ponsa I. Patterns of somatic uniparental disomy identify novel tumor suppressor genes in colorectal cancer. Carcinogenesis 2015;36:1103-10. [PMID: 26243311 PMCID: PMC4598814 DOI: 10.1093/carcin/bgv115] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2015] [Revised: 07/06/2015] [Accepted: 07/29/2015] [Indexed: 01/17/2023]  Open
36
Alentorn A, Dehais C, Ducray F, Carpentier C, Mokhtari K, Figarella-Branger D, Chinot O, Cohen-Moyal E, Ramirez C, Loiseau H, Elouahdani-Hamdi S, Beauchesne P, Langlois O, Desenclos C, Guillamo JS, Dam-Hieu P, Ghiringhelli F, Colin P, Godard J, Parker F, Dhermain F, Carpentier AF, Frenel JS, Menei P, Bauchet L, Faillot T, Fesneau M, Fontaine D, Motuo-Fotso MJ, Vauleon E, Gaultier C, Le Guerinel C, Gueye EM, Noel G, Desse N, Durando X, Barrascout E, Wager M, Ricard D, Carpiuc I, Delattre JY, Idbaih A. Allelic loss of 9p21.3 is a prognostic factor in 1p/19q codeleted anaplastic gliomas. Neurology 2015;85:1325-31. [PMID: 26385879 DOI: 10.1212/wnl.0000000000002014] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2014] [Accepted: 06/17/2015] [Indexed: 12/18/2022]  Open
37
Chen C, Zhang Y, Loomis MM, Upton MP, Lohavanichbutr P, Houck JR, Doody DR, Mendez E, Futran N, Schwartz SM, Wang P. Genome-Wide Loss of Heterozygosity and DNA Copy Number Aberration in HPV-Negative Oral Squamous Cell Carcinoma and Their Associations with Disease-Specific Survival. PLoS One 2015;10:e0135074. [PMID: 26247464 PMCID: PMC4527746 DOI: 10.1371/journal.pone.0135074] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2014] [Accepted: 07/17/2015] [Indexed: 01/15/2023]  Open
38
Nutsua ME, Fischer A, Nebel A, Hofmann S, Schreiber S, Krawczak M, Nothnagel M. Family-Based Benchmarking of Copy Number Variation Detection Software. PLoS One 2015. [PMID: 26197066 PMCID: PMC4510559 DOI: 10.1371/journal.pone.0133465] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]  Open
39
Mohammed H, Russell IA, Stark R, Rueda OM, Hickey TE, Tarulli GA, Serandour AAA, Birrell SN, Bruna A, Saadi A, Menon S, Hadfield J, Pugh M, Raj GV, Brown GD, D’Santos C, Robinson JLL, Silva G, Launchbury R, Perou CM, Stingl J, Caldas C, Tilley WD, Carroll JS. Progesterone receptor modulates ERα action in breast cancer. Nature 2015;523:313-7. [PMID: 26153859 PMCID: PMC4650274 DOI: 10.1038/nature14583] [Citation(s) in RCA: 482] [Impact Index Per Article: 48.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 05/22/2015] [Indexed: 01/27/2023]
40
Liu Y, Li A, Feng H, Wang M. TAFFYS: An Integrated Tool for Comprehensive Analysis of Genomic Aberrations in Tumor Samples. PLoS One 2015;10:e0129835. [PMID: 26111017 PMCID: PMC4482394 DOI: 10.1371/journal.pone.0129835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2014] [Accepted: 05/13/2015] [Indexed: 01/13/2023]  Open
41
Marquard AM, Eklund AC, Joshi T, Krzystanek M, Favero F, Wang ZC, Richardson AL, Silver DP, Szallasi Z, Birkbak NJ. Pan-cancer analysis of genomic scar signatures associated with homologous recombination deficiency suggests novel indications for existing cancer drugs. Biomark Res 2015;3:9. [PMID: 26015868 PMCID: PMC4443545 DOI: 10.1186/s40364-015-0033-4] [Citation(s) in RCA: 210] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2015] [Accepted: 03/25/2015] [Indexed: 02/08/2023]  Open
42
McGranahan N, Favero F, de Bruin EC, Birkbak NJ, Szallasi Z, Swanton C. Clonal status of actionable driver events and the timing of mutational processes in cancer evolution. Sci Transl Med 2015;7:283ra54. [PMID: 25877892 PMCID: PMC4636056 DOI: 10.1126/scitranslmed.aaa1408] [Citation(s) in RCA: 534] [Impact Index Per Article: 53.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
43
Kim H, Zheng S, Amini SS, Virk SM, Mikkelsen T, Brat DJ, Grimsby J, Sougnez C, Muller F, Hu J, Sloan AE, Cohen ML, Van Meir EG, Scarpace L, Laird PW, Weinstein JN, Lander ES, Gabriel S, Getz G, Meyerson M, Chin L, Barnholtz-Sloan JS, Verhaak RGW. Whole-genome and multisector exome sequencing of primary and post-treatment glioblastoma reveals patterns of tumor evolution. Genome Res 2015;25:316-27. [PMID: 25650244 PMCID: PMC4352879 DOI: 10.1101/gr.180612.114] [Citation(s) in RCA: 304] [Impact Index Per Article: 30.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
44
Khaled WT, Choon Lee S, Stingl J, Chen X, Raza Ali H, Rueda OM, Hadi F, Wang J, Yu Y, Chin SF, Stratton M, Futreal A, Jenkins NA, Aparicio S, Copeland NG, Watson CJ, Caldas C, Liu P. BCL11A is a triple-negative breast cancer gene with critical functions in stem and progenitor cells. Nat Commun 2015;6:5987. [PMID: 25574598 PMCID: PMC4338552 DOI: 10.1038/ncomms6987] [Citation(s) in RCA: 116] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Accepted: 11/28/2014] [Indexed: 01/03/2023]  Open
45
Single cell-derived clonal analysis of human glioblastoma links functional and genomic heterogeneity. Proc Natl Acad Sci U S A 2015;112:851-6. [PMID: 25561528 DOI: 10.1073/pnas.1320611111] [Citation(s) in RCA: 289] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
46
Vollan HKM, Rueda OM, Chin SF, Curtis C, Turashvili G, Shah S, Lingjærde OC, Yuan Y, Ng CK, Dunning MJ, Dicks E, Provenzano E, Sammut S, McKinney S, Ellis IO, Pinder S, Purushotham A, Murphy LC, Kristensen VN, Brenton JD, Pharoah PDP, Børresen-Dale AL, Aparicio S, Caldas C. A tumor DNA complex aberration index is an independent predictor of survival in breast and ovarian cancer. Mol Oncol 2015;9:115-27. [PMID: 25169931 PMCID: PMC4286124 DOI: 10.1016/j.molonc.2014.07.019] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2014] [Revised: 07/23/2014] [Accepted: 07/25/2014] [Indexed: 01/27/2023]  Open
47
Favero F, Joshi T, Marquard AM, Birkbak NJ, Krzystanek M, Li Q, Szallasi Z, Eklund AC. Sequenza: allele-specific copy number and mutation profiles from tumor sequencing data. Ann Oncol 2015;26:64-70. [PMID: 25319062 PMCID: PMC4269342 DOI: 10.1093/annonc/mdu479] [Citation(s) in RCA: 542] [Impact Index Per Article: 54.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Revised: 10/08/2014] [Accepted: 10/09/2014] [Indexed: 12/23/2022]  Open
48
Grimonprez Q, Celisse A, Blanck S, Cheok M, Figeac M, Marot G. MPAgenomics: an R package for multi-patient analysis of genomic markers. BMC Bioinformatics 2014;15:394. [PMID: 25495450 PMCID: PMC4269855 DOI: 10.1186/s12859-014-0394-y] [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] [Received: 07/23/2014] [Accepted: 11/19/2014] [Indexed: 01/10/2023]  Open
49
Rall K, Eisenbeis S, Barresi G, Rückner D, Walter M, Poths S, Wallwiener D, Riess O, Bonin M, Brucker S. Mayer-Rokitansky-Küster-Hauser syndrome discordance in monozygotic twins: matrix metalloproteinase 14, low-density lipoprotein receptor-related protein 10, extracellular matrix, and neoangiogenesis genes identified as candidate genes in a tissue-specific mosaicism. Fertil Steril 2014;103:494-502.e3. [PMID: 25492683 DOI: 10.1016/j.fertnstert.2014.10.053] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2014] [Revised: 10/31/2014] [Accepted: 10/31/2014] [Indexed: 11/30/2022]
50
Cai H, Gupta S, Rath P, Ai N, Baudis M. arrayMap 2014: an updated cancer genome resource. Nucleic Acids Res 2014;43:D825-30. [PMID: 25428357 PMCID: PMC4383937 DOI: 10.1093/nar/gku1123] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
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