Clinical OMICS

MAR-APR 2018

Healthcare magazine for research scientists, labs, pathologists, hospitals, cancer centers, physicians and biopharma companies providing news articles, expert interviews and videos about molecular diagnostics in precision medicine

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6 Clinical OMICs March/April 2018 www.clinicalomics.com News M ost of the world's tumor samples stored by medical centers for pathological diagnosis are preserved as formalin-fixed, paraffin-embedded (FFPE) tissue specimens, often paired with clinical and outcome data. The formalin cross-links proteins, creating a web that complicates efforts to extract DNA efficiently, typically resulting in small DNA fragments of poor quality that are difficult to sequence. While some medical cen- ters opt for preserving samples as fresh frozen tissue, frozen samples are harder to obtain and store and yield smaller numbers of samples, making them a costlier alternative to FFPE. In what the company says is a solu- tion to these limitation of FFPE, WuXi NextCODE introduced late last year its answer to the problem—a novel FFPE method that has proven capable of extracting DNA fragments of higher molecular weight. Dubbed SeqPlus, the technology is designed to enable whole-genome sequencing of FFPE samples by pro- ducing sequence alignments that cover 98% of the genome, at a depth of 20x—coming close to the results obtained with fresh frozen samples at comparable levels of sequencing, with similar numbers of heterozygous and homozygous calls. SeqPlus offers a whole-genome alternative to panel-based sequencing for FFPE samples, which perform at a median depth of coverage of >500x for sensitive and specific detection of alterations at low frequency, compared with the typical 30x when sequencing a whole genome. "Instead of going to 1,000 or 2,000- fold coverage for a whole genome, we're able to achieve very good cov- erage of the whole genome with just 60x or 70x coverage, very reasonable coverage for a tumor sample," WuXi NextCODE CSO Jeffrey Gulcher, M.D., Ph.D., said. 'More Gently Pulling the DNA Out' Gulcher said SeqPlus is able to extract larger DNA samples through a method the company won't disclose, except to say it avoids traditional methods that break up the proteins, through long- term incubation in proteinase K. "The method basically is a way of more gently pulling the DNA out to get results, much larger fragments, and we have about a 99% success rate at whole-genome sequencing," Gulcher said. "The result is, you can get more efficient sequencing, which results in getting better coverage at a much smaller price. Normally you'd have to do 500x to 1,000x to get good coverage on FFPE and even that would generally fail to provide broad coverage over the entire genome. Here you can do it at 40x to 90x." The company has launched SeqPlus pilot studies with the NIH's National Cancer Institute (NCI), biopharma companies, and academic medical centers in the U.S. and Europe, aimed at testing SeqPlus on their samples. One undisclosed biopharma, accord- ing to WuXi NextCODE, achieved a three-fold increase in efficiency com- pared to conventional methods, even with whole-exome sequencing. "With whole-exome sequencing, what most people do is they increase the sequencing coverage by 500 to 1,000 to get good coverage," Gulcher said. "Of course, it ends up being much more costly than when you nor- mally do whole exome sequencing at about 100x coverage. Furthermore, it A Weightier Alternative WuXi NextCODE's FFPE Method Aims to Deliver Larger DNA Fragments at Lower Cost By Alex Philippidis WuXi NextCODE team viewing genome at its research facility in Shanghai, China.

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