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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www.clinicalomics.com March/April 2017 Clinical OMICs 11 N ext-generation sequencing (NGS) is one of the most exciting new technologies to enter the OMICS world in recent years . It has trans- formed the study and application of molecular biology and genomics in the research lab and clinic . While NGS has helped researchers uncover a wide range of predictive biomarker data, we believe it's important to consider how new discoveries and targets can subsequently be confirmed on estab- lished technologies . Today, we are see- ing that Sanger sequencing (Sanger), qPCR, and microarrays are ideal plat- forms on which to rapidly confirm NGS results or to perform ongoing screening for these new markers . Sanger, qPCR, and microarrays are also well adapted for use in health- care-related solutions because they are established technologies that are very familiar to the lab community . For example, once disease-causing organ- isms are identified with NGS, qPCR is ideal for detecting and quantifying microorganisms in diagnostic labs since it is quick, cost-effective, and automation-friendly . Likewise, frag- ment analysis using a Sanger platform enables labs to test multiple markers in the same reaction . Both can provide a rapid yes-or-no answer for a num- ber of targeted assays at low costs per sample . Another example of these technolo- gies working together is in antibiotic resistance, where markers discovered by NGS are used to develop rapid molecular-based qPCR-tests that replace traditional cultures in detect- ing antibiotic-resistant genes . Together, these platforms are driving the grow- ing field of genetic testing, where specialized companies use a combi- nation of technologiesā€”NGS to dis- cover mutations, and qPCR or Sanger sequencing as an orthogonal valida- tion method . Cancer research, diagnosis, and treatment represent another contin- uum where multiple technologies play a role . In lung cancer research, NGS has enabled the discovery of import- ant information about the EGFR gene, including effects of its mutation and response to inhibitor treatment (read study) . This has helped scientists develop fast, highly specific multi- plex assays that detect EGFR muta- tion using qPCR, and digital PCR . Additionally, advances in software for Sanger sequencing now enable variant detection at the 5% level, which now makes Sanger sequencing platforms suitable for cancer research . Microarray technology was the first platform for broad gene expression analysis, and remains well-established in the field. With the rise of NGS RNA-Seq, the two technologies are now used in a complementary fash- ion. With their flexibility for whole transcriptome analysis and high throughput, arrays fill an important role when working with FFPE sam- ples and/or studies requiring large numbers of samples . After relevant variants or biomarkers are identified with NGS, microarray panels can be finely tailored for applications such as cancer profiling, transplantation, pharmacogenomics and pre-emptive genotyping . Microarrays, as well as high- throughput qPCR systems, are also making their way into the clinic for molecular diagnostic testing and phar- macogenomics screening, particularly because they are flexible, scalable, fast, and cost-effective . Microarrays are used for gene expression-based cancer diagnostic and prognostic tests, includ- ing the 510(k)-cleared Tissue of Origin test for metastatic cancers . In 2014, the FDA cleared a first-of-its kind postna- tal test for developmental delays and intellectual disabilities in children . This microarray-based test enables postnatal detection of DNA copy num- ber variants (CNV) in patients referred for chromosomal testing . Microarrays are also meeting the need of population biobanks that are undertaking large-scale genotyping studies . For example, the U . S . Depart- ment of Veterans Affairs' Million Vet- erans Program is using a customized microarray to study selected genetic variants (discovered with NGS) of up to one million veteran volunteers . The UK Biobank Genetics Analysis Proj- ect is using another customized array with more than 800,000 markers to genotype 500,000 samples . As we continue to move from basic research through the emerging field of precision medicine, multiple solutions will be required to achieve the goals of improved human health . And while new technologies may provide major advances, it is when they are combined with complementary, well-established and trusted platforms that a more complete solution often emerges . How New Technologies Reinvigorate the Old OP-ED Kim Kelderman Vice President and General Manager for Genetic Analysis Thermo Fisher Scientific

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