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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Page 40 of 51 March/April 2018 Clinical OMICs 39 Labeling Chemistry Improves Structural Variant Detection Resolution Down to 500 Base Pair Direct Label and Stain (DLS) is a non-destructive labeling chemistry that improves every aspect of Bionano genome mapping. When used in the Bionano workflow, DLS enables unprecedented sensitivity and resolution for structural variant discoveries and the most accurate and contiguous genome assemblies. Because DLS has no destructive steps in the workflow, the systematic molecule breaks of its prior NLRS method are eliminated and involves fewer steps, fewer enzymes and effectively doubles the output of the Sa- phyr system. Genome maps generated using DLS are 50-fold longer, on average. DLS also improves sensitivity for all structural variant calls, yielding detection of heterozygous in- sertions and deletions as small as 500 bp. Applications of Saphyr include SV discovery for translational and clinical research including cancer, undiagnosed genetic disorders, gene discovery, and therapy development. The DLS chemistry makes mapping with Sa- phyr more affordable, allowing high-vol- ume users to map a human genome for as little as $500. Bionano Genomics Exome and Custom Target Enrichment for Next- Generation Sequencing The Human Core Exome Kit provides comprehensive library preparation and target enrichment kit while also offering available Custom Panels that can be tai- lored to individual customer requests. Kit specifications include 33 Mb of highly conserved protein-coding regions based on CCDS, and 120 bp dsDNA probes, 90% of probe sequence within target region to minimize sequencing, and 97% of target- ed regions covered at ≥20x, 150x mean se- quencing depth (4.90Gb). Kit performance is aided by high-fidelity double-stranded DNA probes with probe boosting and ef- ficient amplification, NGS QC of all probes, and uniform enrichment of target regions with no unexpected dropouts and spec- ificity even at high sequencing depths. Due to the kit's high enrichment unifor- mity, researchers can increase the depth of sequencing, or throughput to reduce sequencing costs, while the modular kit struc- ture allows for easy integration into ex- isting protocols. New Products Whole-Exome Sequencing of Tumor DNA and a Matched Sample Tempus xE analyzes the whole exome in a CLIA/CAP validated assay that provides for sequencing the whole-exome tumor DNA and a matched normal sample, along with the whole RNA transcriptome to provide a comprehensive survey of a patient's entire coding genome. The assay detects single nucleotide variants, small insertions and deletions, copy number amplifications, and structural alterations that lead to gene fusions. The test runs on Tempus' research immuno-oncology platform, which uses machine learning to un- cover actionable data for immunotherapy including microsatellite instability (MSI), tumor mutational burden (TMB), neo-antigen load, and human leukocyte antigen (HLA) typing. When paired with whole transcriptome sequencing, the platform provides genetic and expression information for targets such as PD-1, PD-L1, LAG3, TIM3, and CD40. Addition- ally, it provides a solution for adoptive T-cell and cancer vaccine research development. Tempus In-Depth Metabolic Information For Difficult-to-Diagnose Patient Cases The Meta UDx helps clinicians to solve rare disease and difficult-to-diagnose pediatric and adult patient cases. Meta UDx is analytically validated under CLIA as a laboratory-developed test, requiring only a small plasma sample to look for biomarkers or biochemical path- way changes that may indicate metabolic effects associated with diseases or disorders. Using advanced metabolomics technology to simultaneously survey roughly 1,000 metabolites, Meta UDx detects underlying pathway or biomarker abnormalities not measurable by other means. By producing an accurate, comprehensive picture of these changes, Metabolon helps guide clinicians to answers for rare and difficult-to-diagnose diseases. Metabolon Twist Bioscience

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