Although existing methods of sequencing are effective, the researchers noted a couple of limitations. Both BRCA1
are fairly large genes when it comes to sequencing, and there is a lack of mutation hot spots that are easily identified. They suggested that complementary techniques are required to identify large genomic rearrangements of these genes.
The researchers used the BRCA MASTR kit, a molecular diagnostic assay that identifies mutations in the coding regions of the BRCA1
genes, followed by the small-scale GS Junior, a high-throughput sequencer that is available as a laboratory bench top system. Through a variety of validation analyses, the researchers determined that the algorithm had 100% sensitivity and specificity in the samples that were analyzed. Additionally, the algorithm is designed to eliminate false positives.
“This approach allows [us] to identify all point mutations and small deletions and insertions analyzed, even in regions of high technical difficulty, such as homopolymeric regions,” said Conxi Lázaro, PhD, a researcher at the Catalan Institute of Oncology at the Bellvitge Biomedical Research Institute who headed the study, in a statement.
Matloff said that while the algorithm requires further validation, the results of the study were encouraging.
“I don't know if this would be better than the existing methods, but I hope it will be,” Matloff said.
Currently, Myriad Genetics holds the patents on the BRCA1
genes in the United States and also manufactures the only test currently available to identify the presence of mutations in those genes. These patents were the focus of an intense legal battle. In August, a federal appellate court ruled that Myriad could maintain the patent, stating that the isolated BRCA1
genes are not found that way in nature and could therefore be patented. This may have an impact on the eventual commercial availability of these tests, Matloff said.
Salmon AY, Salmon-Divon M, Zahavi T, et al. Determination of molecular markers for BRCA1 and BRCA2 heterozygosity using gene expression profiling [published online ahead of print January 22, 2013]. Cancer Prev Res. doi:10.1158/1940-6207.CAPR-12-0105.
Feliubaladó L, Lopez-Doriga A, Castellagué E, et al. Next-generation sequencing meets genetic diagnostics: development of a comprehensive workflow for the analysis of BRCA1 and BRCA2 genes [published online ahead of print December 19, 2012]. Eur J Hum Genet. doi:0.1038/ejhg.2012.270.