Clinical OMICS

MAR-APR 2017

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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32 Clinical OMICs March/April 2017 Data & Informatics 10x Genomics Launches Single-Cell RNA-Seq Software Suite Single -cell genomics tools provider 10x Genomix has launched a new suite of software tools to help researchers analyze and visualize single-cell RNA sequencing (RNA-Seq) data generated by the company 's Chromium Single Cell 3' Solution. The suite contains the Loupe Cell Browser and an expanded offering via the company's CellRanger, all intended to provide detailed sin- gle-cell gene expression and profiling information. "Advances in single-cell RNA quan- tification techniques have enabled the comprehensive study of gene expression dynamics within single cells but scalable software solutions have been a barrier to expanding their application," said Alexan- der Wong, vice president of software and Salk Institute's New Tool Helps Researchers Find Hidden Disease- Causing Regions within DNA The Salk Institute has announced a new algorithm that can help pinpoint key disease-causing regions within a genome with more accuracy . The new system, called "regulatory-element prediction based on tissue-specific local epigenomic signatures"—or REPTILE, for short—combines histone modification and meth- ylation data to predict regions of the genome that contain sections of DNA called enhancers, which have proven to be important to disease research . Only 2% of DNA is made up of genes; the rest was considered to be "junk," according to Salk researchers . REPTILE is helping to prove that this so-called junk is not really junk at all, but instead plays a valuable role in disease research . Sec- tions of this "junk DNA" contain enhancers that show where and when the gene information is read out. Mutations in enhancers are now tied to disease, but find- ing these enhancers has been difficult in the past. "These regions don't code for proteins, but they still contain genetic variants that cause disease," said Joseph Ecker, Ph.D., senior author of the study, Howard Hughes Medical Institute investigator and director of Salk's Genomic Analysis Laboratory. "We just haven't had very effective tools to locate these areas in a variety of tissues and cell types—until now." According to Salk, REPTILE allows for "vastly more targeted searches for dis- ease-causing genetic variants in the human genome," including those that pro- mote cancer or cause metabolic disorders . "The novelty of this method is that it uses DNA methylation to really narrow down the candidate regulatory sequences suggested by histone modification data," said lead study investigator Yupeng He, a graduate student at the Salk Institute . "We were then able to test REPTILE's predictions in the lab and validate them with experimental data, which gave us a high degree of confidence in the algorithm's ability to find enhancers." "The nice thing about this tool is you can train it on one type of data and use it on another type of data," Eckers said. Training the tool on stem cells first will allow REPTILE to search for enhancers on more difficult cells.—Diana Manos Jezperklauzen / Getty Images infrastructure for 10x Genomics. "With this in mind, we designed our new soft- ware as part of a comprehensive solution to make scalable single-cell gene expres- sion analysis possible for every lab, from sample to discovery." According to information provided by the company, the Chromium Single Cell 3' system can run massively parallel sin- gle-cell RNA-Seq analysis of as many as a million cells. This scale allows research- ers to potentially conduct tissue and cell atlas studies. n

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