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Items: 11

1.

Quantification of normal cell fraction and copy number neutral LOH in clinical lung cancer samples using SNP array data.

Göransson H, Edlund K, Rydåker M, Rasmussen M, Winquist J, Ekman S, Bergqvist M, Thomas A, Lambe M, Rosenquist R, Holmberg L, Micke P, Botling J, Isaksson A.

PLoS One. 2009 Jun 26;4(6):e6057. doi: 10.1371/journal.pone.0006057.

2.

Copy number analysis indicates monoclonal origin of lethal metastatic prostate cancer.

Liu W, Laitinen S, Khan S, Vihinen M, Kowalski J, Yu G, Chen L, Ewing CM, Eisenberger MA, Carducci MA, Nelson WG, Yegnasubramanian S, Luo J, Wang Y, Xu J, Isaacs WB, Visakorpi T, Bova GS.

Nat Med. 2009 May;15(5):559-65. doi: 10.1038/nm.1944. Epub 2009 Apr 12. Erratum in: Nat Med. 2009 Jul;15(7):819.

3.

SNP arrays in heterogeneous tissue: highly accurate collection of both germline and somatic genetic information from unpaired single tumor samples.

Assié G, LaFramboise T, Platzer P, Bertherat J, Stratakis CA, Eng C.

Am J Hum Genet. 2008 Apr;82(4):903-15. doi: 10.1016/j.ajhg.2008.01.012. Epub 2008 Mar 20.

4.

Estimation and assessment of raw copy numbers at the single locus level.

Bengtsson H, Irizarry R, Carvalho B, Speed TP.

Bioinformatics. 2008 Mar 15;24(6):759-67. doi: 10.1093/bioinformatics/btn016. Epub 2008 Jan 19.

PMID:
18204055
5.

The properties of high-dimensional data spaces: implications for exploring gene and protein expression data.

Clarke R, Ressom HW, Wang A, Xuan J, Liu MC, Gehan EA, Wang Y.

Nat Rev Cancer. 2008 Jan;8(1):37-49. Review.

6.

Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma.

Beroukhim R, Getz G, Nghiemphu L, Barretina J, Hsueh T, Linhart D, Vivanco I, Lee JC, Huang JH, Alexander S, Du J, Kau T, Thomas RK, Shah K, Soto H, Perner S, Prensner J, Debiasi RM, Demichelis F, Hatton C, Rubin MA, Garraway LA, Nelson SF, Liau L, Mischel PS, Cloughesy TF, Meyerson M, Golub TA, Lander ES, Mellinghoff IK, Sellers WR.

Proc Natl Acad Sci U S A. 2007 Dec 11;104(50):20007-12. Epub 2007 Dec 6.

7.

A Hidden Markov Model to estimate population mixture and allelic copy-numbers in cancers using Affymetrix SNP arrays.

Lamy P, Andersen CL, Dyrskjot L, Torring N, Wiuf C.

BMC Bioinformatics. 2007 Nov 9;8:434.

8.

SiDCoN: a tool to aid scoring of DNA copy number changes in SNP chip data.

Nancarrow DJ, Handoko HY, Stark MS, Whiteman DC, Hayward NK.

PLoS One. 2007 Oct 31;2(10):e1093.

9.

Highly sensitive method for genomewide detection of allelic composition in nonpaired, primary tumor specimens by use of affymetrix single-nucleotide-polymorphism genotyping microarrays.

Yamamoto G, Nannya Y, Kato M, Sanada M, Levine RL, Kawamata N, Hangaishi A, Kurokawa M, Chiba S, Gilliland DG, Koeffler HP, Ogawa S.

Am J Hum Genet. 2007 Jul;81(1):114-26. Epub 2007 Jun 5.

10.

High-resolution genomic profiling of chromosomal aberrations using Infinium whole-genome genotyping.

Peiffer DA, Le JM, Steemers FJ, Chang W, Jenniges T, Garcia F, Haden K, Li J, Shaw CA, Belmont J, Cheung SW, Shen RM, Barker DL, Gunderson KL.

Genome Res. 2006 Sep;16(9):1136-48. Epub 2006 Aug 9.

11.

Microarray analysis reveals a major direct role of DNA copy number alteration in the transcriptional program of human breast tumors.

Pollack JR, Sørlie T, Perou CM, Rees CA, Jeffrey SS, Lonning PE, Tibshirani R, Botstein D, Børresen-Dale AL, Brown PO.

Proc Natl Acad Sci U S A. 2002 Oct 1;99(20):12963-8. Epub 2002 Sep 24.

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