Multiplex ligation-dependent probe amplification (MLPA) should be incorporated into standard BRCA1/BRCA2 mutation testing because full gene sequencing alone may miss large genomic rearrangements (LGRs) that account for more than 6 percent of mutations in individuals at high risk for hereditary breast/ovarian cancer, new data from Hong Kong have shown.

Sanger sequencing and next-generation sequencing (NGS), commonly used in BRCA mutation testing, can identify small point mutations but not LGRs. “This leads to an underestimation of the rate of mutation and, therefore, a risk of giving patients a false-negative genetic report,” wrote researchers from The University of Hong Kong (HKU), Hong Kong Sanatorium and Hospital, and Stanford University School of Medicine. [Cancer Genet 2015;208:448-454]

In 1,236 high-risk patients with breast and/or ovarian cancer recruited through the Hong Kong Hereditary Breast Cancer Family Registry between 2007 and 2014, MLPA identified 8 LGRs that were not detected by Sanger sequencing or NGS. These LGRs accounted for 6.67 percent of the 120 deleterious BRCA mutations identified in the study population (8.77 percent [5 of 57] of BRCA1 mutations and 4.76 percent [3 of 63] of BRCA2 mutations).

Patients in the study underwent MLPA together with full gene sequencing for BRCA1 and BRCA2 by Sanger sequencing or NGS. The NGS platform used had a sensitivity at least equal to that of gold-standard Sanger sequencing.

“Validation of sequencing is important for laboratories to ensure good quality mutation testing,” lead investigator Dr. Ava Kwong of the HKU and the Hong Kong Hereditary Breast Cancer Family Registry  told MIMS Oncology. “The relatively high frequency of LGRs identified in BRCA mutation carriers in our study indicates the need for combining MLPA and full gene sequencing to provide more comprehensive information in routine BRCA1 and BRCA2 mutation screening.”