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For: Krijgsman O, Israeli D, Haan JC, van Essen HF, Smeets SJ, Eijk PP, Steenbergen RDM, Kok K, Tejpar S, Meijer GA, Ylstra B. CGH arrays compared for DNA isolated from formalin-fixed, paraffin-embedded material. Genes Chromosomes Cancer 2011;51:344-52. [PMID: 22162309 DOI: 10.1002/gcc.21920] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2011] [Accepted: 11/07/2011] [Indexed: 12/13/2022]  Open
Number Cited by Other Article(s)
1
Ogbonnaya CN, Alsaedi BSO, Alhussaini AJ, Hislop R, Pratt N, Steele JD, Kernohan N, Nabi G. Radiogenomics Map-Based Molecular and Imaging Phenotypical Characterization in Localised Prostate Cancer Using Pre-Biopsy Biparametric MR Imaging. Int J Mol Sci 2024;25:5379. [PMID: 38791417 PMCID: PMC11121591 DOI: 10.3390/ijms25105379] [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] [Received: 04/13/2024] [Revised: 05/06/2024] [Accepted: 05/13/2024] [Indexed: 05/26/2024]  Open
2
Susman S, Berindan-Neagoe I, Petrushev B, Pirlog R, Florian IS, Mihu CM, Berce C, Craciun L, Grewal R, Tomuleasa C. The role of the pathology department in the preanalytical phase of molecular analyses. Cancer Manag Res 2018;10:745-753. [PMID: 29695931 PMCID: PMC5903845 DOI: 10.2147/cmar.s150851] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]  Open
3
Jung HS, Lefferts JA, Tsongalis GJ. Utilization of the oncoscan microarray assay in cancer diagnostics. ACTA ACUST UNITED AC 2017. [DOI: 10.1186/s41241-016-0007-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
4
Kader T, Goode DL, Wong SQ, Connaughton J, Rowley SM, Devereux L, Byrne D, Fox SB, Mir Arnau G, Tothill RW, Campbell IG, Gorringe KL. Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue. Genome Med 2016;8:121. [PMID: 27846907 PMCID: PMC5111221 DOI: 10.1186/s13073-016-0375-z] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2016] [Accepted: 10/26/2016] [Indexed: 11/10/2022]  Open
5
Obulkasim A, Ylstra B, van Essen HF, Benner C, Stenning S, Langley R, Allum W, Cunningham D, Inam I, Hewitt LC, West NP, Meijer GA, van de Wiel MA, Grabsch HI. Reduced genomic tumor heterogeneity after neoadjuvant chemotherapy is related to favorable outcome in patients with esophageal adenocarcinoma. Oncotarget 2016;7:44084-44095. [PMID: 27286451 PMCID: PMC5190081 DOI: 10.18632/oncotarget.9857] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 04/29/2016] [Indexed: 11/25/2022]  Open
6
Forero-Castro M, Robledo C, Benito R, Abáigar M, África Martín A, Arefi M, Fuster JL, de las Heras N, Rodríguez JN, Quintero J, Riesco S, Hermosín L, de la Fuente I, Recio I, Ribera J, Labrador J, Alonso JM, Olivier C, Sierra M, Megido M, Corchete-Sánchez LA, Ciudad Pizarro J, García JL, Ribera JM, Hernández-Rivas JM. Genome-Wide DNA Copy Number Analysis of Acute Lymphoblastic Leukemia Identifies New Genetic Markers Associated with Clinical Outcome. PLoS One 2016;11:e0148972. [PMID: 26872047 PMCID: PMC4752220 DOI: 10.1371/journal.pone.0148972] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 01/26/2016] [Indexed: 01/13/2023]  Open
7
Biesma HD, Schouten PC, Lacle MM, Sanders J, Brugman W, Kerkhoven R, Mandjes I, van der Groep P, van Diest PJ, Linn SC. Copy number profiling by array comparative genomic hybridization identifies frequently occurring BRCA2-like male breast cancer. Genes Chromosomes Cancer 2015;54:734-44. [DOI: 10.1002/gcc.22284] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 06/25/2015] [Indexed: 11/08/2022]  Open
8
Kalmár A, Péterfia B, Hollósi P, Wichmann B, Bodor A, Patai ÁV, Schöller A, Krenács T, Tulassay Z, Molnár B. Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples. Pathol Oncol Res 2015;21:1149-1156. [PMID: 25991403 DOI: 10.1007/s12253-015-9945-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/06/2014] [Accepted: 05/05/2015] [Indexed: 01/11/2023]
9
Schouten PC, Grigoriadis A, Kuilman T, Mirza H, Watkins JA, Cooke SA, van Dyk E, Severson TM, Rueda OM, Hoogstraat M, Verhagen CVM, Natrajan R, Chin SF, Lips EH, Kruizinga J, Velds A, Nieuwland M, Kerkhoven RM, Krijgsman O, Vens C, Peeper D, Nederlof PM, Caldas C, Tutt AN, Wessels LF, Linn SC. Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms. Mol Oncol 2015;9:1274-86. [PMID: 25825120 PMCID: PMC5528812 DOI: 10.1016/j.molonc.2015.03.002] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2014] [Revised: 03/01/2015] [Accepted: 03/11/2015] [Indexed: 11/30/2022]  Open
10
Focus on 16p13.3 Locus in Colon Cancer. PLoS One 2015. [PMID: 26222184 PMCID: PMC4519182 DOI: 10.1371/journal.pone.0131421] [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: 01/13/2023]  Open
11
Hastings RJ, Bown N, Tibiletti MG, Debiec-Rychter M, Vanni R, Espinet B, van Roy N, Roberts P, van den Berg-de-Ruiter E, Bernheim A, Schoumans J, Chatters S, Zemanova Z, Stevens-Kroef M, Simons A, Heim S, Salido M, Ylstra B, Betts DR. Guidelines for cytogenetic investigations in tumours. Eur J Hum Genet 2015;24:6-13. [PMID: 25804401 DOI: 10.1038/ejhg.2015.35] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Revised: 01/19/2015] [Accepted: 02/03/2015] [Indexed: 12/31/2022]  Open
12
Kuilman T, Velds A, Kemper K, Ranzani M, Bombardelli L, Hoogstraat M, Nevedomskaya E, Xu G, de Ruiter J, Lolkema MP, Ylstra B, Jonkers J, Rottenberg S, Wessels LF, Adams DJ, Peeper DS, Krijgsman O. CopywriteR: DNA copy number detection from off-target sequence data. Genome Biol 2015;16:49. [PMID: 25887352 PMCID: PMC4396974 DOI: 10.1186/s13059-015-0617-1] [Citation(s) in RCA: 160] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2015] [Accepted: 02/20/2015] [Indexed: 12/13/2022]  Open
13
Haan JC, Labots M, Rausch C, Koopman M, Tol J, Mekenkamp LJM, van de Wiel MA, Israeli D, van Essen HF, van Grieken NCT, Voorham QJM, Bosch LJW, Qu X, Kabbarah O, Verheul HMW, Nagtegaal ID, Punt CJA, Ylstra B, Meijer GA. Genomic landscape of metastatic colorectal cancer. Nat Commun 2014;5:5457. [PMID: 25394515 PMCID: PMC4243240 DOI: 10.1038/ncomms6457] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2014] [Accepted: 10/02/2014] [Indexed: 12/21/2022]  Open
14
DNA copy number analysis of fresh and formalin-fixed specimens by shallow whole-genome sequencing with identification and exclusion of problematic regions in the genome assembly. Genome Res 2014;24:2022-32. [PMID: 25236618 PMCID: PMC4248318 DOI: 10.1101/gr.175141.114] [Citation(s) in RCA: 350] [Impact Index Per Article: 31.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
15
Minca EC, Tubbs RR, Portier BP, Wang Z, Lanigan C, Aronow ME, Triozzi PL, Singh A, Cook JR, Saunthararajah Y, Plesec TP, Schoenfield L, Cawich V, Sulpizio S, Schultz RA. Genomic microarray analysis on formalin-fixed paraffin-embedded material for uveal melanoma prognostication. Cancer Genet 2014;207:306-15. [PMID: 25442074 DOI: 10.1016/j.cancergen.2014.08.005] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2014] [Revised: 07/07/2014] [Accepted: 08/21/2014] [Indexed: 11/30/2022]
16
Gebauer N, Gebauer J, Hardel TT, Bernard V, Biersack H, Lehnert H, Rades D, Feller AC, Thorns C. Prevalence of targetable oncogenic mutations and genomic alterations in Epstein–Barr virus-associated diffuse large B-cell lymphoma of the elderly. Leuk Lymphoma 2014;56:1100-6. [DOI: 10.3109/10428194.2014.944522] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
17
Caretti V, Sewing ACP, Lagerweij T, Schellen P, Bugiani M, Jansen MHA, van Vuurden DG, Navis AC, Horsman I, Vandertop WP, Noske DP, Wesseling P, Kaspers GJL, Nazarian J, Vogel H, Hulleman E, Monje M, Wurdinger T. Human pontine glioma cells can induce murine tumors. Acta Neuropathol 2014;127:897-909. [PMID: 24777482 DOI: 10.1007/s00401-014-1272-4] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2012] [Revised: 03/07/2014] [Accepted: 03/20/2014] [Indexed: 01/12/2023]
18
Jonker MJ, de Leeuw WC, Marinković M, Wittink FRA, Rauwerda H, Bruning O, Ensink WA, Fluit AC, Boel CH, Jong MD, Breit TM. Absence/presence calling in microarray-based CGH experiments with non-model organisms. Nucleic Acids Res 2014;42:e94. [PMID: 24771343 PMCID: PMC4066771 DOI: 10.1093/nar/gku343] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]  Open
19
High fidelity copy number analysis of formalin-fixed and paraffin-embedded tissues using Affymetrix Cytoscan HD chip. PLoS One 2014;9:e92820. [PMID: 24699316 PMCID: PMC3974686 DOI: 10.1371/journal.pone.0092820] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2013] [Accepted: 02/26/2014] [Indexed: 11/19/2022]  Open
20
Genomic profiling reveals extensive heterogeneity in somatic DNA copy number aberrations of canine hemangiosarcoma. Chromosome Res 2014;22:305-19. [PMID: 24599718 DOI: 10.1007/s10577-014-9406-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2013] [Revised: 01/22/2014] [Accepted: 01/23/2014] [Indexed: 01/08/2023]
21
Idris SF, Ahmad SS, Scott MA, Vassiliou GS, Hadfield J. The role of high-throughput technologies in clinical cancer genomics. Expert Rev Mol Diagn 2014;13:167-81. [DOI: 10.1586/erm.13.1] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
22
Genomic instability: a stronger prognostic marker than proliferation for early stage luminal breast carcinomas. PLoS One 2013;8:e76496. [PMID: 24143191 PMCID: PMC3797106 DOI: 10.1371/journal.pone.0076496] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2013] [Accepted: 08/27/2013] [Indexed: 01/15/2023]  Open
23
Evaluating the repair of DNA derived from formalin-fixed paraffin-embedded tissues prior to genomic profiling by SNP-CGH analysis. J Transl Med 2013;93:701-10. [PMID: 23568031 DOI: 10.1038/labinvest.2013.54] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
24
Schouten PC, van Dyk E, Braaf LM, Mulder L, Lips EH, de Ronde JJ, Holtman L, Wesseling J, Hauptmann M, Wessels LFA, Linn SC, Nederlof PM. Platform comparisons for identification of breast cancers with a BRCA-like copy number profile. Breast Cancer Res Treat 2013;139:317-27. [PMID: 23670131 DOI: 10.1007/s10549-013-2558-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2013] [Accepted: 04/29/2013] [Indexed: 12/28/2022]
25
Swerdlow SH. Lymphoma classification and the tools of our trade: an introduction to the 2012 USCAP Long Course. Mod Pathol 2013;26 Suppl 1:S1-S14. [PMID: 23281432 DOI: 10.1038/modpathol.2012.177] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
26
Banerjee D. Array comparative genomic hybridization: an overview of protocols, applications, and technology trends. Methods Mol Biol 2013;973:1-13. [PMID: 23412780 DOI: 10.1007/978-1-62703-281-0_1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
27
Campo E. Whole genome profiling and other high throughput technologies in lymphoid neoplasms--current contributions and future hopes. Mod Pathol 2013;26 Suppl 1:S97-S110. [PMID: 23281439 DOI: 10.1038/modpathol.2012.179] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
28
Krijgsman O, Israeli D, van Essen HF, Eijk PP, Berens MLM, Mellink CHM, Nieuwint AW, Weiss MM, Steenbergen RDM, Meijer GA, Ylstra B. Detection limits of DNA copy number alterations in heterogeneous cell populations. Cell Oncol (Dordr) 2012;36:27-36. [PMID: 23117839 DOI: 10.1007/s13402-012-0108-2] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/15/2012] [Indexed: 01/01/2023]  Open
29
Bierkens M, Krijgsman O, Wilting SM, Bosch L, Jaspers A, Meijer GA, Meijer CJLM, Snijders PJF, Ylstra B, Steenbergen RDM. Focal aberrations indicate EYA2 and hsa-miR-375 as oncogene and tumor suppressor in cervical carcinogenesis. Genes Chromosomes Cancer 2012;52:56-68. [PMID: 22987659 DOI: 10.1002/gcc.22006] [Citation(s) in RCA: 73] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Accepted: 08/08/2012] [Indexed: 01/06/2023]  Open
30
Soldini D, Campo E. New insights into the diagnosis of lymphomas. Ann Oncol 2012;23 Suppl 10:x83-8. [DOI: 10.1093/annonc/mds304] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
31
Frankel A. Formalin fixation in the '-omics' era: a primer for the surgeon-scientist. ANZ J Surg 2012;82:395-402. [PMID: 22571596 DOI: 10.1111/j.1445-2197.2012.06092.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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