Detection of Loss of Heterozygosity by Matrix-Assisted Laser Desorption/Ionization Time-of-Flight Mass Spectrometry-Based Analysis of Single-Nucleotide Polymorphisms

A variety of genetic alterations are associated with the initial steps of carcinogenesis in sporadic tumors. Inactivation of tumor suppressor genes frequently occurs in a sequential process of genomic deletion of one allele and missense or nonsense mutation of the other allele in somatic cells (1). Cytogenetically undetectable deletions can be identified at the molecular level as loss of heterozygosity (LOH). Comparative genotyping of polymorphic markers such as microsatellites or single-nucleotide polymorphisms (SNPs) in healthy and tumor tissue can detect the loss of one allele by demonstrating the conversion of a heterozygous marker to a hemizygous genotype. LOH analysis of solid tumors does not necessarily show 100% deletion of one allele, as blood and immune cells without LOH may contaminate the tumor. Therefore, LOH analysis often shows a reduction, rather than a complete disappearance, of one allele. Genotyping of polymorphic markers has been performed predominantly by gel-based methods, using microsatellites or short tandem repeats. Because of the repetitive nature of these polymorphic structures, PCR amplification often leads to so-called “shadow bands” resulting from DNA polymerase slippage. Shadow bands may overlap with major polymorphic bands and are frequently sources of genotyping ambiguities, particularly in the case of apparent incomplete deletion of one allele (2). Breast cancer is the most common malignancy of women, with up to 95% of cases sporadic (3). Cytogenetic investigations and microsatellite LOH analysis have revealed deletions in the terminal part of Xp in breast carcinoma (4)(5). On the basis of analysis of 13 SNPs within the genomic region of the potential tumor suppressor gene PPP2R3B , located in the terminal band Xp22.3 (6)(7), we established a matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) approach to analyze LOH in nonmicrodissected tissue. Comparative sequencing of PCR-amplified fragments in tumor and healthy tissue revealed reduced …