Small-pool PCR analysis of microsatellite instability in HNPCC

The contributions and limitations of the traditional method for evaluating microsatellite instability by standard polymerase chain reaction (PCR) in identifying mismatch repair (MMR) gene mutations in the Lynch syndrome form of hereditary nonpolyposis colon cancer (HNPCC) are discussed. A new form of HNPCC (familial colon cancer type X or FCCX), in which deleterious mutations in major MMR genes and microsatellite instability have not been identified, was viewed as possibly having attenuating mutations in MMR genes as its genetic basis. A highly sensitive and quantitative method of microsatellite instability analysis, small-pool PCR, is needed to explore this possibility, and small-pool PCR procedures to address that task must be validated. An algorithm for the use of small-pool PCR to identify patients with FCCX having such attenuating mutations is put forward as a means of detecting single nucleotide polymorphisms (SNPs) for the future diagnosis of cancer in those at risk.