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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8 Clinical OMICs March/April 2018 News progress to metastatic cancer, match- ing 500 metastatic tumors with 500 primary tumors from the same patients in the same cancer. The most common cancers will be studied, including lung adenocarcinoma, non-squamous cell lung, breast, colon, pancreatic, ovarian, and liver cancers. The company will carry out an inte- grated multiple-omics analysis com- paring metastatic FFPE tumor samples and primary tumor samples from the medical centers using artificial intel- ligence, carrying out whole-genome sequencing to generate SNPs, indels, CNV, RNA-seq, and microRNA data, and DNA methylation—the types of data previously gathered from primary tumors stored by TCGA. Looking for the Difference "What we really want to know is what's the difference between the metastatic and the primary tumors in patients who have recurrence and have bad outcomes?" Gulcher said. "The TCGA collection doesn't tell us the pathways that separate those who do really well with treatment of the pri- mary tumor and those that progress to metastatic disease. Just imagine if you were able to unlock those samples, to allow you to make those comparisons. Our efficient FFPE sequencing pro- vides a way to do these large studies for the first time." He added that efficient forma- lin-fixed sequencing has opened up further studies of large sample collec- tions outside oncology, from central nervous system tissue to liver samples, where the company is proceeding with a comparison of 1,000 non-alcoholic steatohepatitis (NASH) biopsies ver- sus 1,000 fatty liver samples without NASH, to be followed by multi-omics analysis with deep learning. Two different feature reduction meth- ods have been developed at WuXi Nex- tCODE to feasibly apply deep learning methods to large genomics datasets, which are orders of magnitude larger than the features used for facial recog- nition and image-analysis algorithms. One is a modified version of GOSeq designed to cluster genes with similar functions or similar pathways, devel- oped by Thomas Chittenden, Ph.D., D.Phil., founding director of the WuXi NextCODE advanced artificial intel- ligence research laboratory. The other method entails clustering genes based on co-expression or co-correlation. WuXi NextCODE markets three SeqPlus offerings: • SeqPlus Lab, which offers whole-genome sequencing of FFPE samples with a FASTQ file returned. • SeqPlus Secondary, which delivers sequencing of FFPE samples as well as aligned data, with output presented as a BAM file. As with SeqPlus Lab, customers can process as little as a single sample, with pricing based on number of samples—but must conduct their own analysis. • SeqPlus Interpretation, which offers sequencing of 10 or 20 slides, with full analysis. Users get back a report with sample and sequencing QC metrics including DNA quality, coverage, PCR duplicates, numbers of mutations, SNP and indel counts, and sample profile—including mutational signatures and other sample/ cohort specific information. WuXi NextCODE operates from offices in Shanghai; Cambridge, MA; and Reykjavik, Iceland. The company took its present form in 2015 when NextCODE Health was acquired by WuXi PharmaTech for $65 million; NextCODE—a spinout of personal- ized medicine pioneer deCODE Genet- ics, acquired by Amgen in 2012—was merged with WuXi's Genome Center to form WuXi NextCODE. Last year WuXi NextCODE com- pleted a $240 million Series B financing, with proceeds intended to accelerate the extension of its platform infrastruc- ture by attracting new users and data through precision medicine and diag- nostics partnerships. (continued from previous page) "What we really want to know is what's the difference between the metastatic and the primary tumors in patients who have recurrence and have bad outcomes?" —Jeffrey Gulcher WuXi NextCODE CSO Huntstock / Getty Images

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