Clinical OMICS

JAN-FEB 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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www.clinicalomics.com January/February 2018 Clinical OMICs 41 New Insights on Structural Variants About three quarters of all the human genome DNA bases that make people different from each other, and can potentially cause inherited dis- eases, are not in single-base variants, but instead are contained in larger chunks of DNA that vary from individual to individual. These so-called structural variants (SVs) currently are largely inaccessible with short-read next-generation sequencing and are thus clinically not available to inform about a patient's genetic makeup and potential underlying disease cause. In a medical first, a team of clinical researchers led by Jason Merker and Euan Ashley (Stanford University) used long-read sequencing to determine the cause of a patient's inherited disease. The patient had previously been subjected to NGS but the underlying cause of the disease had remained elusive. The long-read sequencing data uncov- ered a structural variant (a large, multi-kilobase heterozygous deletion) affecting a gene impli- cated in a certain inherited heart disease, and thus revealing the cause of the patient's disease. We can anticipate that many more such exam- ples will follow, thereby paving a promising and exciting path to diagnose the diseases of many patients that currently remain undiagnosed. Improved Pharmacogenetic Profiling Prescribing the appropriate dose of medicine is a crucial aspect for treating patients. Individuals can vary markedly in their propensity to metab- olize drugs, and a large fraction of the genetic component of breaking down drugs lies in the family of cytochrome P450 oxidases, therefore the genetic analysis of a patient's pharmacogenetics profile is of great importance. However, some of these genes are very complex which has ham- pered their analysis. New methods developed by researchers at the Icahn School of Medicine at Mount Sinai and at Leiden University Medi- cal Center now utilize long-read PacBio sequenc- ing to fully characterize genes like CYP2D6 for more contiguous and accurate profiling, combin- ing long-range PCR with direct full-length gene sequencing and diplotype variant calling. It is anticipated that such improved CYP2D6 metab- olizer phenotype prediction will benefit many research and clinical testing applications in the future, as well as for cohort stratification as part of drug development pipelines. JONAS KORLACH Chief Scientific Officer Pacific Biosciences ERIC SCHADT Chief Executive Officer Sema4 Artificial Intelligence Positioned to Revolutionize Clinical Care AI is entering a golden era, with intelligent machines such as AlphaGo Zero not only capable of beating all human players the Go board game, but beating its predecessor AlphaGo by learning to play Go without any human knowledge, thus freeing it to uncover novel strategies not thought of before by any human player. Such advances, however, are not constrained to games. A study this year demonstrated that the accuracy of pre- dicting cardiovascular risk could be significantly improved by applying machine learning algo- rithms, with this smart AI approach identifying at-risk patients that had been missed by clinicians. AI could also bring healthcare into our homes—a melanoma analysis system, trained using nearly 130,000 images of skin lesions, detected skin can- cer as accurately as dermatologists, which could pave the way for smartphone-based diagnosis. Mobile devices and wearable technology, col- lecting large amounts of data that can be used in conjunction with other high-dimensional clini- cal, molecular, and environmental data to further optimize personalized clinical outcomes. Major Advances in Cancer Immunotherapy Curing, or the effective, life-long management of cancer while ensuring a high-quality of life, is among the most pressing problems of our day. Grand solutions have seemingly been on the horizon for decades, but have nevertheless mostly remained elusive. But this past year, with combined advances in immunotherapy and genome editing, striking examples have emerged that signal an inflection point in this we may be entering a new era regarding the ability to wipe (continued on next page) Berya113 / Getty Images

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