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Genome wide measurement of DNA copy number changes in neuroblastoma: dissecting amplicons and mapping losses, gains and breakpoints.

Michels E, Vandesompele J, Hoebeeck J, Menten B, De Preter K, Laureys G, Van Roy N, Speleman F.

Cytogenet Genome Res. 2006;115(3-4):273-82.


Breakpoint features of genomic rearrangements in neuroblastoma with unbalanced translocations and chromothripsis.

Boeva V, Jouannet S, Daveau R, Combaret V, Pierre-Eugène C, Cazes A, Louis-Brennetot C, Schleiermacher G, Ferrand S, Pierron G, Lermine A, Rio Frio T, Raynal V, Vassal G, Barillot E, Delattre O, Janoueix-Lerosey I.

PLoS One. 2013 Aug 26;8(8):e72182. doi: 10.1371/journal.pone.0072182. eCollection 2013.


A method for finding consensus breakpoints in the cancer genome from copy number data.

Toloşi L, Theißen J, Halachev K, Hero B, Berthold F, Lengauer T.

Bioinformatics. 2013 Jul 15;29(14):1793-800. doi: 10.1093/bioinformatics/btt300. Epub 2013 May 28.


Directional genomic hybridization for chromosomal inversion discovery and detection.

Ray FA, Zimmerman E, Robinson B, Cornforth MN, Bedford JS, Goodwin EH, Bailey SM.

Chromosome Res. 2013 Apr;21(2):165-74. doi: 10.1007/s10577-013-9345-0. Epub 2013 Apr 10.


Evaluating translocation gene fusions by SNP array data.

Liu H, Zilberstein A, Pannier P, Fleche F, Arendt C, Lengauer C, Hahn CS.

Cancer Inform. 2012;11:15-27. doi: 10.4137/CIN.S8026. Epub 2011 Dec 21.


Identification of a novel recurrent 1q42.2-1qter deletion in high risk MYCN single copy 11q deleted neuroblastomas.

Fieuw A, Kumps C, Schramm A, Pattyn F, Menten B, Antonacci F, Sudmant P, Schulte JH, Van Roy N, Vergult S, Buckley PG, De Paepe A, Noguera R, Versteeg R, Stallings R, Eggert A, Vandesompele J, De Preter K, Speleman F.

Int J Cancer. 2012 Jun 1;130(11):2599-606. doi: 10.1002/ijc.26317. Epub 2011 Aug 29.


Computational method for estimating DNA copy numbers in normal samples, cancer cell lines, and solid tumors using array comparative genomic hybridization.

Abkevich V, Iliev D, Timms KM, Tran T, Skolnick M, Lanchbury JS, Gutin A.

J Biomed Biotechnol. 2010;2010. pii: 386870. doi: 10.1155/2010/386870. Epub 2010 Jul 8.


A statistical change point model approach for the detection of DNA copy number variations in array CGH data.

Chen J, Wang YP.

IEEE/ACM Trans Comput Biol Bioinform. 2009 Oct-Dec;6(4):529-41. doi: 10.1109/TCBB.2008.129.


Tumor genome wide DNA alterations assessed by array CGH in patients with poor and excellent survival following operation for colorectal cancer.

Lagerstedt KK, Staaf J, Jönsson G, Hansson E, Lönnroth C, Kressner U, Lindström L, Nordgren S, Borg A, Lundholm K.

Cancer Inform. 2007 Oct 12;3:341-55.


Combining chromosomal arm status and significantly aberrant genomic locations reveals new cancer subtypes.

Shay T, Lambiv WL, Reiner-Benaim A, Hegi ME, Domany E.

Cancer Inform. 2009;7:91-104. Epub 2009 Mar 12.


Integrated analysis of copy number alteration and RNA expression profiles of cancer using a high-resolution whole-genome oligonucleotide array.

Jung SH, Shin SH, Yim SH, Choi HS, Lee SH, Chung YJ.

Exp Mol Med. 2009 Jul 31;41(7):462-70. doi: 10.3858/emm.2009.41.7.051.


Combined use of expression and CGH arrays pinpoints novel candidate genes in Ewing sarcoma family of tumors.

Savola S, Klami A, Tripathi A, Niini T, Serra M, Picci P, Kaski S, Zambelli D, Scotlandi K, Knuutila S.

BMC Cancer. 2009 Jan 14;9:17. doi: 10.1186/1471-2407-9-17.


Genomic profiling by array comparative genomic hybridization reveals novel DNA copy number changes in breast phyllodes tumours.

Kuijper A, Snijders AM, Berns EM, Kuenen-Boumeester V, van der Wall E, Albertson DG, van Diest PJ.

Cell Oncol. 2009;31(1):31-9.


High-resolution array copy number analyses for detection of deletion, gain, amplification and copy-neutral LOH in primary neuroblastoma tumors: four cases of homozygous deletions of the CDKN2A gene.

Carén H, Erichsen J, Olsson L, Enerbäck C, Sjöberg RM, Abrahamsson J, Kogner P, Martinsson T.

BMC Genomics. 2008 Jul 29;9:353. doi: 10.1186/1471-2164-9-353.


Low-cost dedicated mini-arrays for high-throughput analysis of DNA copy-number alterations in neuroblastoma.

De Preter K, Menten B, De Brouwer S, Kumps C, Michels E, Van Roy N, Vandesompele J, Speleman F.

Cancer Lett. 2008 Sep 28;269(1):111-6. doi: 10.1016/j.canlet.2008.04.031. Epub 2008 Jun 13.


Characterization of amplicons in neuroblastoma: high-resolution mapping using DNA microarrays, relationship with outcome, and identification of overexpressed genes.

Fix A, Lucchesi C, Ribeiro A, Lequin D, Pierron G, Schleiermacher G, Delattre O, Janoueix-Lerosey I.

Genes Chromosomes Cancer. 2008 Oct;47(10):819-34. doi: 10.1002/gcc.20583.


Genome-wide mapping and characterization of hypomethylated sites in human tissues and breast cancer cell lines.

Shann YJ, Cheng C, Chiao CH, Chen DT, Li PH, Hsu MT.

Genome Res. 2008 May;18(5):791-801. doi: 10.1101/gr.070961.107. Epub 2008 Feb 6.


Sparse representation and Bayesian detection of genome copy number alterations from microarray data.

Pique-Regi R, Monso-Varona J, Ortega A, Seeger RC, Triche TJ, Asgharzadeh S.

Bioinformatics. 2008 Feb 1;24(3):309-18. doi: 10.1093/bioinformatics/btm601. Epub 2008 Jan 18.

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