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The recent high profile decision of the film star Angelina Jolie to have preventive surgery due to her family history and genetic profile for breast cancer has placed the subject of genetic screening for gene mutations that increase breast cancer risk firmly in the spotlight. Ms Jolie announced that she is a carrier of a mutation in the BRCA1 gene, the same mutation carried by her mother who tragically died from breast cancer. Mutations in BRCA1 and BRCA2 are known to increase risk both of breast cancer and ovarian cancer, with a unique group of patients having hereditary breast and ovarian cancer (HBOC) syndrome. These patients are diagnosed younger and have an increased lifetime risk for developing both breast, ovarian and other cancers.

Standard methodology for screening for BRCA1 and BRCA2 relies on conventional Sanger dideoxy sequencing, on which the Human Genome Project was based. This is an expensive and time-consuming process. Research has therefore been on-going to attempt to develop second-generation cancer genome-sequencing to a standard that is clinically validated. Second generation sequencing gives an output which is orders of magnitude higher than that achieved with Sanger sequencing and with much lower cost per base. A study has just been published in The Journal of Molecular Diagnostics from the Cancer Genetics Laboratory of the BC Cancer Agency in Vancouver along with the Department of Pathology and Laboratory Medicine of the University of British Columbia, also in Vancouver (Bosdet et al 2013). These laboratories have tested a second generation sequencing method on both the coding exons and on the intron-exon boundaries of BRCA1 and BRCA2 in 91 hereditary breast cancer patient samples. The results are encouraging. The groups achieved high-quality sequence coverage across all targeted regions, and detection was sensitive and specific, with complete agreement with results from standard dideoxy sequencing methodology, and no false-positive or false-negative results. The authors are confident that their method, which is based on sequencing of automated small-amplicon PCR followed by sample pooling, represents a breakthrough in identifying a method for sensitive, automatable, high-throughput sequence variant detection.

Given that other gene regions are also implicated in breast cancer risk, this represents a technique with potentially wider applicability beyond BRCA1 and BRCA2. For example in HBOC syndrome, a plethora of other cancer susceptibility gene clusters are implicated, including the Fanconi anemia (FA) cluster (FANCD2, FANCA and FANCC), mismatch repair (MMR) cluster (MLH1, MSH2, PMS1, PMS2 and MSH6), DNA repair cluster (ATM, ATR and CHK1/2), and tumour suppressor cluster (TP53, SKT11 and PTEN). There is also the potential to extend this type of methodology to allow personalisation of medical treatment. For example, second generation sequencing technology was recently used to obtain the complete genomic DNA sequence of a 55 years old, self-declared healthy, anonymous male of Malay descent whose family medical history was known. Several unique variants were identified, including in 4 drug transport genes, 2 drug metabolizing enzyme genes and 33 target genes harbouring deleterious SNVs involved in pharmacological pathways. So this breakthrough in identifying a second generation sequencing methodology which is clinically validated has implications even beyond the immediate applicability to BRCA1 and BRCA2 screening in breast cancer. Further development of third generation sequencing using nanopore systems is underway offering even further hope for increased efficiency and accuracy and reduced cost of genetic screening for the future.

Sources

BOSDET, I.E. et al., 2013. A Clinically Validated Diagnostic Second-Generation Sequencing Assay for Detection of Hereditary BRCA1 and BRCA2 Mutations. The Journal Of Molecular Diagnostics: JMD, DOI: 10.1016/j.jmoldx.2013.07.004

GUT, I.G., 2013. New sequencing technologies. Clinical & Translational Oncology: Official Publication Of The Federation Of Spanish Oncology Societies And Of The National Cancer Institute Of Mexico

KOBAYASHI, H. et al., 2013. Hereditary breast and ovarian cancer susceptibility genes (Review). Oncology reports

MERIC-BERNSTAM, F. et al., 2013. Genotype in BRCA-associated breast cancers. The breast journal, 19(1), pp. 87-91

MWENIFUMBO, J.C. and MARRA, M.A., 2013. Cancer genome-sequencing study design. Nature Reviews.Genetics, 14(5), pp. 321-332

SALLEH, M.Z. et al., 2013. Systematic pharmacogenomics analysis of a malay whole genome: proof of concept for personalized medicine. Plos One, 8(8), pp. e71554-e71554

Elsevier Health Sciences (2013, October 7). New diagnostic test for detecting BRCA1 and BRCA2 mutations. ScienceDaily. Retrieved October 10