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

Issue link:

Contents of this Issue


Page 12 of 47 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

Articles in this issue

Links on this page

Archives of this issue

view archives of Clinical OMICS - MAR-APR 2017