feature
NEXT GENERATION
SEQUENCING:
STORIES FROM
THE FIELD
by Nancy Maddox, MPH, writer
In 1965, Gordon Moore, co-founder of Intel Corporation, foresaw a stunning pace of
change in computer power: so-called Moore’s Law posits a doubling in the number of
transistors in computer chips every two years.
Yet, Gregory Armstrong, MD, director of CDC’s Office of Advanced Molecular Detection,
said the rate of technological improvement in the field of genomics has surpassed even
this lofty, biennial benchmark.
T
he revolution in next generation sequencing (NGS)—also known as high-throughput, deep or massively parallel sequencing—
took off in about 2006-2007, after the introduction of pyrosequencing and other computer-based technologies that far surpass
the first-generation Sanger sequencing method in terms of speed, throughput and affordability.
Today, a next-gen platform such as Illumina’s popular benchtop MiSeq can handle 8 to 48 samples per run (depending on the
pathogen) and generate over a billion bases of output in about 55 hours. The instrument costs on the order of $100,000.
But despite the allure of the new technology, public health laboratories (PHLs) have been slow to join the next-gen revolution. In 2010,
for example, virtually no state PHL had NGS capability.
“Both here at CDC and a lot of public health agencies, there was a feeling, especially in laboratories, that public health was missing the
boat,” said Armstrong. “This revolution in technology was providing some real opportunities, and we were not taking advantage
of those.”
In 2011, CDC convened a Bioinformatics Blue Ribbon Panel to assess the agency’s bioinformatics capabilities, and the panel released
a damning report. That report, said Armstrong, “went up as far as Congress and the executive branch in Washington, DC.” The upshot
of the effort, which had broadened to include the bioinformatics-dependent NGS technologies, was the creation of CDC’s Advanced
Molecular Detection (AMD) program in October 2013.
Genome sequencing machine with a 96-channel selection size robot for genomic library construction
PublicHealthLabs
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Summer 2016 LAB MATTERS
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