New strategy uses PCR to improve detection of mutations in hereditary colorectal cancer

Using next generation genetic techniques and PCR could help doctors identify people with Lynch syndrome caused by a mutation in the PMS2 gene. The results are published in the Journal of Molecular Diagnostics.

Chromosome 7

Lynch syndrome (also known as hereditary non-polyposis colorectal cancer or HNPCC), is usually caused by heterozygous germline mutations in the DNA mismatch repair genes MLH1 and MSH2, which can be identified using current methods for DNA sequencing and deletion analysis. This allows people to be screened to identify early stage cancers, as well as allowing access to genetic counselling for them and their close relatives, as recommended by the Evaluation of Genomic Applications in Practice and Prevention (EGAPP) Working Group in 2009. However, a mutation in another mismatch repair gene, PMS2 (PMS 1 homolog 2, mismatch repair system component), also plays a role in the syndrome, and this cannot be detected as easily.

“PMS2 mutations have been grossly underestimated due to technical difficulties in handling complex genomic structure. A comprehensive approach to unequivocally identify PMS2 mutations remained to be developed,” explains lead investigator Lee-Jun C Wong, PhD, of Baylor Miraca Genetic Laboratory and Department of Molecular and Human Genetics, Baylor College of Medicine. These issues include the presence of a large number of highly homologous sequences in other genomic regions and the frequent sequence exchange between active and pseudogenes, together with the high frequency of negative staining of PMS2 by immunohistochemistry, he explains.

A team of researchers from the Baylor Miraca Genetics Laboratories and the Department of Molecular and Human Genetics at Baylor College of Medicine have worked together to develop an improved diagnostic technique using targeted capture next-generation sequencing (NGS), multiplex ligation-dependent probe amplification, and long-range PCR followed by NGS. This has allowed them to detect point mutations and copy number changes of the PMS2 gene simultaneously.

“The results from three methods serve as cross validation for enhanced accuracy and reduced turn-around time,” says co-investigator Victor Wei Zhang, MD, PhD, of the Department of Molecular and Human Genetics, Baylor College of Medicine.

The researchers were able to find deletions in the coding region of the gene, duplications in two chromosomes, and a nonsense mutation. This included a novel supplication in a patient who had café au lait spots and was diagnosed with uterine cancer at age 27 and colon cancer at age 43.

“This combined strategy provides us with a new tool for reliable molecular analysis of any genes containing multiple copies of highly homologous sequences and should improve the positive finding rate for patients with Lynch syndrome if the PMS2 gene is suspected to be defective,” says Wong.

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