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Cheaper Gene Panels Are Useful Alternative to Whole-Genome Sequencing

By Labmedica International staff writers
Posted on 30 Apr 2014
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Image: The MiSeq Next Generation Sequencing System (Photo courtesy of Illumina).
Image: The MiSeq Next Generation Sequencing System (Photo courtesy of Illumina).
About 10% of women with a personal or family history of breast or ovarian cancer have at least one genetic mutation that, if known, would prompt their doctors to recommend changes in their care.

Multiple-gene sequencing is entering practice, but its clinical value is unknown and this has now been evaluated by studying the performance of a customized germline-DNA sequencing panel for cancer-risk assessment in a representative clinical sample.

Scientists at Stanford University School of Medicine (CA, USA) collected blood samples from 198 women who underwent testing for the genes breast cancer 1, early onset (BRCA1) and BRCA2 from 2002 to 2012. Gene panels allowed the scientists to learn the sequences of several genes simultaneously from a single blood sample. The technique usually focuses on fewer than 100 of the approximately 21,000 human genes.

Sequencing was performed at InVitae (San Francisco, CA, USA), a clinical laboratory improvement amendments (CLIA)–approved laboratory. Sequencing libraries were constructed using the SureSelectXT protocol (Agilent; Santa Clara, CA, USA) and were quantified with the KAPA Biosystems Library Quantification Kit (Woburn, MA, USA). These steps were performed in an automated fashion using the Agilent Bravo automated liquid-handling platform. Quantified libraries were sequenced on the MiSeq platform (Illumina; San Diego, CA, USA) using the 2×151 bp configuration to at least 400× average coverage.

Of the 198 women, 57 carried BRCA1/2 mutations, and the team found that 14 of the 141 women without a BRCA1/2 mutation had clinically actionable mutations in one of the 42 genes assessed by the panel. An actionable mutation is a genetic variation correlated strongly enough to an increase in risk that clinicians would recommend a change in routine care, such as increased screening for carriers. Screening with gene panels does not, however, eliminate the problem of variants of uncertain significance. This term is used when a gene sequence deviates from the consensus, but the clinical effect of that change is unknown. Each of the 141 women in the study had about two variants of uncertain significance in the 42 genes studied.

James Ford, MD, a senior author of the study said, “It's a slippery slope at the moment. We need to know how prevalent these cancer-associated mutations are in the general population. We also need to be aware that, at least for a while, it's very likely that every person will harbor one or more variants of uncertain significance. Is that information that a person would want to know? Is it helpful? In 10 years, this is likely to change as we learn more about the clinical significance of these changes.” The study was published on April 14, 2014, in the Journal of Oncology.

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Stanford University School of Medicine 

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