Analytical challenges in the genetic diagnosis of Lynch syndrome – difficult detection of germ-line mutations in sequences surrounding homopolymers

A genetic diagnosis is essential in families with a suspicion of Lynch syndrome, as it allows the use of proper and specific surveillance programs for high-risk individuals who carry a pathogenic mutation. The prediction and prevention schemes reduce the impact of cancer in high-risk families in a cost-effective manner. Genetic tests for LS are well standardized and broadly used, although there remain some specific difficulties that need to be addressed to reach an optimal diagnosis. In this report, we addressed the problem raised by the detection of mutations at intronic-splicing consensus sites located near mononucleotide repeats. A standard procedure was applied for LS diagnosis in all cases. PCR and Sanger sequencing results of the whole coding sequences and intron–exon boundaries of the MSH2 gene were analyzed. Moreover, we designed quality-control procedures to verify the attainment of the intended quality of results regarding sequences located in complex contexts. We found eight families with point mutations at intron 5 of the MSH2 gene located near the BAT26 mononucleotide marker, which could be missed in a regular diagnostic process. Four families had the c.942+2T>A mutation, and the remaining four families had the c.942+3A>T mutation. In conclusion, the detection of pathogenic Corresponding author: José Luis Soto Molecular Genetics Laboratory Elche University Hospital Camino Almazara no 11 03203 Elche. Spain Phone: (+34) 966 616185 E-mail: [email protected]