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Issue link: https://clinicalomics.epubxp.com/i/853204
42 Clinical OMICs July/August 2017 www.clinicalomics.com Precision Medicine New Association Aims to Advance GATK for Precision Medicine in China Intel, Inspur, Beijing Genomics Institute (BGI), and Alibaba Cloud—the cloud computing arm of Alibaba Group—have launched a group focused on advancing the adoption and use of the Genome Analysis Toolkit (GATK), among Chinese users for precision medicine. The GATK Chinese Association for Preci- sion Medicine will seek to broaden usage of GATK—developed at the Broad Insti- tute—which offers a variety of tools with a primary emphasis on variant discovery and genotyping. In May, the Broad and Intel announced a breakthrough architecture, the Broad-In- tel Genomics Stack (BIGstack), that would be made available to run GATK4. The part- ners said BIGstack can run GATK4 up to five times faster than previous versions of the Toolkit through the use of In- tel's CPUs, Omni-Path Fabric, and solid-state drives. Intel's genome database is embedded in Inspur's Genomics Appliance, which is designed to perform data analysis for the en- tire genome, and allow addition- al resequencing input with second-gener- ation analyzers. BGI has said it will adopt the most current GATK tools, including the Broad and Intel optimizations, in a move toward global alignment of stan- dards in the rapidly growing genomics community. them move away, and once they are connected to Geisinger they tend to stay. Further, Geisinger serves approx- imately 4 million patients, about 1 to 1.5 million of whom are consid- ered "active," because they are seen regularly. Geisinger also recently acquired AtlantiCare in New Jer- sey. That acquisition will not only add more patients to the database but also increases diversity. "Our patients in Pennsylvania are about 96% of northern European decent," explains Dr. Williams. "Atlanti- Care's patients are much more diverse." Recruitment in New Jersey has been brisk, within just the first 8 months more than 8,000 patients signed up for MyCode. The issue of diversity will be a growing concern for biobanks such as Geising- er 's. The largest genetic studies in many diseases have so far largely comprised people of northern E u ro p e a n d e s c e n t . " M o s t b i g s t u d - ies in diabetes have been done in Cauca- sians," said Dr. Rotter. LABioMed has specif- ically worked to make sure their biobank is diverse. "We have already found novel variants in diabetes that are specific to people of Chinese descent," he said. Geisinger hasn't shared how much the system has invested in the project. Faucette said the sample collection costs about $100 per person. Re-entering has helped raise funding for the biobank and the recruitment process. "Clinical inter- pretation is all funded with research dollars," he said. One of the keys to the success of this project, said Dr. Williams, is that "we have spent a lot of time engaging and listening to the patient voice, so that we can deliver back to them what they consider valuable." Faucett adds that "I think one reason we've gotten so many is that it's open to all our patients," he said. "There are many projects focused on one condition or another, but ours lets everyone participate." Dr. Reid and Gruen, who both work for companies supplying the underbelly of such efforts, see some key trends ahead for biobanks such as MyCode. "We are seeing more localities and governments diving in," said Dr. Reid. Gruen, mean- while, said "the market is exploding. But it is all well and good to buy a large sequencer and use it, the hump is managing and analyzing the data." "Large scale genetics is on the cusp of transforming medicine," he added. (continued from previous page) Aysunbk / Getty Images "The majority of people want to know about their results, and almost half are also interested in helping us do research."—Marc S. Williams, Director, Geisinger's Genomic Medicine Institute