Linked Life Data

16258161

Source:http://linkedlifedata.com/resource/pubmed/id/16258161

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pubmed-article:16258161pubmed:abstractTextAs the number of identified single-nucleotide polymorphisms (SNPs) increases, high-throughput methods are required to characterize the informative loci in large patient series. We investigated the feasibility of MassEXTEND LOH analysis using Sequenom's MassArray RT software, a mass spectrometry method, as an alternative to determine loss of heterozygosity (LOH). For this purpose, we studied the c.827A>C SNP (1176A>C p.Gln276Pro) in protein tyrosine phosphatase receptor type-J (PTPRJ), which is frequently deleted in human cancers. In sporadic colorectal cancer (CRC), c.827A>C showed allele-specific LOH of the c.827A allele, which is important because LOH of PTPRJ may be an early event during sporadic CRC. To elucidate the impact of this low-penetrance gene on familial CRC, we studied c.827A>C in 222 familial CRC cases and 156 controls. In 6.2% of the A/C genotyped CRC samples, LOH of c.827A was observed with MassEXTEND LOH analysis and confirmed by conventional sequencing. Furthermore, a case with LOH of c.827A showed no LOH in 22 synchronously detected adenomas, including one with malignant transformation. The importance of the PTPRJ- c.827A>C SNP appears to be limited in familial CRC. We conclude that MassEXTEND LOH analysis (using Sequenom's MassARRAY RT software) is a sensitive, high-throughput, and cost-effective method to screen SNP loci for LOH in formalin-fixed paraffin-embedded tissue.lld:pubmed
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pubmed-article:16258161pubmed:authorpubmed-author:van WezelTomTlld:pubmed
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pubmed-article:16258161pubmed:dateRevised2009-11-19lld:pubmed
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pubmed-article:16258161pubmed:articleTitleMass spectrometry-based loss of heterozygosity analysis of single-nucleotide polymorphism loci in paraffin embedded tumors using the MassEXTEND assay: single-nucleotide polymorphism loss of heterozygosity analysis of the protein tyrosine phosphatase receptor type J in familial colorectal cancer.lld:pubmed
pubmed-article:16258161pubmed:affiliationLeiden University Medical Center, Department of Pathology, Building L1Q, P.O. Box 9600, 2300 RC Leiden, The Netherlands.lld:pubmed
pubmed-article:16258161pubmed:publicationTypeJournal Articlelld:pubmed
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