Mass 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.
As 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.
van Puijenbroek
Marjo
M
Leiden University Medical Center, Department of Pathology, Building L1Q, P.O. Box 9600, 2300 RC Leiden, The Netherlands.
Dierssen
Jan Willem F
JW
Stanssens
Patrick
P
van Eijk
Ronald
R
Cleton-Jansen
Anne Marie
AM
van Wezel
Tom
T
Morreau
Hans
H
D000368:Aged; D000369:Aged, 80 and over; D000483:Alleles; D016022:Case-Control Studies; D015179:Colorectal Neoplasms / Q000235:genetics*; D003362:Cost-Benefit Analysis; D005091:Exons / Q000235:genetics; D005434:Flow Cytometry; D005820:Genetic Testing / Q000379:methods*; D006801:Humans; D019656:Loss of Heterozygosity / Q000235:genetics*; D013058:Mass Spectrometry; D008875:Middle Aged; D016612:Paraffin Embedding; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D017027:Protein Tyrosine Phosphatases / Q000235:genetics*; D054631:Receptor-Like Protein Tyrosine Phosphatases, Class 3; D015203:Reproducibility of Results; D017422:Sequence Analysis, DNA
C486288:PTPRJ protein, human; D017027:Protein Tyrosine Phosphatases; D054631:Receptor-Like Protein Tyrosine Phosphatases, Class 3