Method to Detect CNV via Mated Short Reads
Medvedev, Fiume et al., Genome Research
Researchers at the University of Toronto describe a method to detect copy-number variation via mated short reads, wherein "matepairs mapping discordantly to the reference serve to indicate the presence of variation." CNVer — the team's algorithm — combines this information and allows researchers to "mitigate the sequencing biases that cause uneven local coverage and accurately predict CNVs." The team used CNVer on a recently described genome of a Yoruban individual and detected 4,879 CNVs. "CNVer can reconstruct the absolute copy counts of segments of the donor genome and evaluate the feasibility of using CNVer with low coverage datasets," the authors add.
AACC: Assessing the Cost-Effectiveness of PGx Testing
In several talks given here at the American Association for Clinical Chemistry's annual meeting in Anaheim, Calif., investigators have highlighted the importance of conducting prospective clinical trials to determine the cost-effectiveness of pharmacogenomic approaches for personalized medicine. Speaking to an audience of pathologists, clinical chemists, medical technologists, and others, Columbia University Medical Center's Alex Rai said that issues related to regulation, education, standardization, and reimbursement remain challenges for the adoption of genetic testing for disease stratification and therapeutic drug management. In order for the latter to be achieved, Rai noted, "payers will need to appreciate the importance of biomarkers and pharmacogenetic testing in reducing health care costs."
In a another session, Luke Chen, CEO of the Xizhi, Taiwan-based Pharmigene, spoke of what he called the "most clear case" for genetic testing to date. Chen described a 5,000 patient study that investigated the cost-effectiveness of HLA-B*1502 genotyping for individuals prescribed carbemazepine who are at risk for developing Stevens-Johnson syndrome, a condition which often leads to toxic epidermal necrosis — and potential handicap or death — as a result of taking the drug. The HLA-B*1502 allele most frequently occurs in Han Chinese and Southeast Asian populations and puts individuals at a 1,000-fold increased risk of developing SJS-TEN, he said. In Taiwan, Chen added, approximately 50,000 patients are prescribed carbemazepine annually. Of those 50,000, approximately 115 individuals will develop SJS-TEN — and, statistically speaking, 106 patients will experience "severe symptoms" associated with the disease, three will experience "complications" resulting in a handicap, and six will die. His team, in collaboration with the Taiwan Drug Relief Foundation, calculated that testing every individual prescribed CBZ for the variant would save the equivalent of $2.97 million.