Diagnostics Leveraging Next-Generation Sequencing Become Mainstream for Cancer and Rare Diseases

August 1, 2017
Diagnostics Leveraging Next-Generation Sequencing Become Mainstream for Cancer and Rare Diseases
Source: Bainscou / Wickimedia Commons

Chris Anderson, Editor in Chief

It has been roughly nine years since next-generation sequencing (NGS) methods made their appearance in research labs. Largely led—at least initially—by sequencing heavyweight Illumina, the new technologies allowed researchers and molecular biologists in clinical labs to move from sequencing single genes to today where it is routinely used to analyze panels of hundreds of genes in a single run.

The steady migration of NGS from the research lab to a diagnostic tool in the clinical lab is the result of the combined effects of dramatically decreasing costs, improvements in the accuracy and specificity of NGS platforms, and the application of data from sequencing experiments that have unlocked our understanding of the genetic underpinnings of disease.

Yet, amid these positive developments, NGS first had to prove itself against existing and established technologies.

“Initially, (using NGS) was all about ‘can I match what I get with PCR,’ or ‘can I match what I get with FISH,’ or something else,” said Joydeep Goswami, Ph.D., president, clinical NGS and oncology with Thermo Fisher Scientific. “Today, we are seeing those concerns melt away. Clinicians are comfortable and pathologists are comfortable enough with the NGS readout that they don’t need to do confirmatory studies every time they get a result.”

According to Geoff Otto, Ph.D., vice president of clinical product development and strategy at Foundation Medicine, NGS first started making its bones as a diagnostics platform to detect germline mutations. This led to the development of noninvasive prenatal testing, tests for single genes known to be associated with disease such as cystic fibrosis, and also some limited cancer tests.

“Around seven or eight years ago, NGS reached a point where it started to generate the kind of information required to inform what was going on in human genomics—at the necessary scale, throughput, and accuracy for these tests,” Dr. Otto said. “That was the backdrop. But it was not entirely clear you could apply that to the detection of somatic events on the one hand, and on the other whether you could actually build a test that was capable of interrogating the different classes of genomic alterations all at once.”

 

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