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The Molecular Epidemiology group at MD DHMH. (Left to right) Terence Moore, Eric Keller, Julie Haendiges, Jonathan Johnston, Jinshui Fan
Traditional NBS assays look for downstream functional
markers that are indicative of enzyme deficiencies or
other congenital disorders. NGS, on the other hand, looks
upstream for the genetic source of NBS disorders
Even though the NGS option is more costly, Baker says it is also more cost-effective
in terms of the per mutation price. Thus, the state chose to make the pilot assay its
routine second-tier CF screen.
Yet, despite a good outcome, Baker remains cautious about incorporating additional
NGS assays in the Wisconsin NBS program, and especially about using such assays as
first-tier screens.
Traditional NBS assays look for downstream biochemical markers—such as elevated
phenylalanine in the case of phenylketonuria—that are indicative of enzyme
deficiencies or other congenital disorders. NGS, on the other hand, looks upstream
for the genetic source of NBS disorders. The problem is that not all disease-causing
mutations are known. In addition, the clinical significance of a particular mutation is
not always well understood.
Baker said NGS is “complementary with traditional metabolite detection methods.” She
said, “You have to consider the utility. I want us to do this carefully.”
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Even though NGS might still be considered an emerging PHL technology,
CDC’s Armstrong said early investments in the technology are already
resulting in public health advances. As one example, he said, a CDC-developed
infrastructure for sequencing dengue and chikungunya virus was readily
adapted to Zika virus after that microbe prompted large-scale outbreaks in
Latin America.
The next big boost for NGS will likely come from metagenomics—a field
focused on the recovery of genetic material directly from environmental or
clinical samples, such as a gut swab or water sample. Metagenomic shortcuts
would eliminate the need to do extra sequencing to tease out bugs of interest
from microbial communities containing many species.
In the meantime, Boxrud said he expects the new AMD funding to be a
“game-changer.”
He said, “I think that one year from now, things are going to look really
different. I think NGS is going to be the norm within the next year; not for all
laboratories, but a significant number.”
Summer 2016 LAB MATTERS
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