title: Segmentation-based detection of allelic imbalance and loss-of-heterozygosity in cancer cells using whole genome SNP arrays.
abstract: We present a strategy for detection of loss-of-heterozygosity and allelic imbalance in cancer cells from whole genome single nucleotide polymorphism genotyping data. Using a dilution series of a tumor cell line mixed with its paired normal cell line and data generated on Affymetrix and Illumina platforms, including paired tumor-normal samples and tumors characterized by fluorescent in situ hybridization, we demonstrate a high sensitivity and specificity of the strategy for detecting both minute and gross allelic imbalances in heterogeneous tumor samples.
authors.affiliation: Department of Oncology, Clinical Sciences, Lund University, Lund, Sweden. johan.staaf@med.lu.se
authors.forename: Johan
authors.initials: J
authors.lastname: Staaf
authors.forename: David
authors.initials: D
authors.lastname: Lindgren
authors.forename: Johan
authors.initials: J
authors.lastname: Vallon-Christersson
authors.forename: Anders
authors.initials: A
authors.lastname: Isaksson
authors.forename: Hanna
authors.initials: H
authors.lastname: Göransson
authors.forename: Gunnar
authors.initials: G
authors.lastname: Juliusson
authors.forename: Richard
authors.initials: R
authors.lastname: Rosenquist
authors.forename: Mattias
authors.initials: M
authors.lastname: Höglund
authors.forename: Ake
authors.initials: A
authors.lastname: Borg
authors.forename: Markus
authors.initials: M
authors.lastname: Ringnér
mesh_terms: D022981:Allelic Imbalance; D001943:Breast Neoplasms / Q000235:genetics*; D045744:Cell Line, Tumor; D018628:Gene Dosage; D005821:Genetic Techniques; D006801:Humans; D019656:Loss of Heterozygosity; D020411:Oligonucleotide Array Sequence Analysis; D020641:Polymorphism, Single Nucleotide; D012680:Sensitivity and Specificity
references.citation: Nucleic Acids Res. 2007;35(6):2013-25
references.pmid: 17341461
references.citation: Genome Res. 2006 Sep;16(9):1136-48
references.pmid: 16899659
references.citation: Int J Cancer. 1998 Dec 9;78(6):766-74
references.pmid: 9833771
references.citation: BMC Biotechnol. 2003 Oct 28;3:20
references.pmid: 14583097
references.citation: Nat Genet. 2003 Aug;34(4):369-76
references.pmid: 12923544
references.citation: Am J Hum Genet. 2007 Jul;81(1):114-26
references.pmid: 17564968
references.citation: Nat Genet. 2005 Jun;37 Suppl:S11-7
references.pmid: 15920524
references.citation: PLoS One. 2007 Oct 31;2(10):e1093
references.pmid: 17971856
references.citation: Genes Chromosomes Cancer. 2008 Aug;47(8):697-711
references.pmid: 18484635
references.citation: BMC Genomics. 2007 Oct 22;8:382
references.pmid: 17953745
references.citation: PLoS Comput Biol. 2006 May;2(5):e41
references.pmid: 16699594
references.citation: Nat Genet. 2005 May;37(5):549-54
references.pmid: 15838508
references.citation: PLoS Comput Biol. 2005 Nov;1(6):e65
references.pmid: 16322765
references.citation: Am J Hum Genet. 2008 Apr;82(4):903-15
references.pmid: 18355774
references.citation: Mol Vis. 2002 Nov 06;8:416-21
references.pmid: 12432341
references.citation: Bioinformatics. 2004 May 22;20(8):1233-40
references.pmid: 14871870
references.citation: Nat Methods. 2004 Nov;1(2):109-11
references.pmid: 15782172
references.citation: Cancer Res. 2005 Jul 15;65(14):6071-9
references.pmid: 16024607
references.citation: Bioinformatics. 2005 Oct 1;21(19):3763-70
references.pmid: 16081473
references.citation: Genome Res. 2007 Nov;17(11):1665-74
references.pmid: 17921354
references.citation: Nat Genet. 1998 Oct;20(2):207-11
references.pmid: 9771718
references.citation: Cell. 2000 Jan 7;100(1):57-70
references.pmid: 10647931
references.citation: BMC Bioinformatics. 2008 Apr 21;9:204
references.pmid: 18426588
references.citation: Bioinformatics. 2006 Jan 1;22(1):7-12
references.pmid: 16267090
references.citation: Bioinformatics. 2007 Mar 15;23(6):657-63
references.pmid: 17234643
references.citation: BMC Bioinformatics. 2007 Nov 09;8:434
references.pmid: 17996079