Clinical OMICs - Issue 3 - (Page 17)
What to Look for in a Clinical
Next-Generation Sequencer
Shawn C. Baker, Ph.D.
N
ext-generation sequencing (NGS) has been making tremendous
strides in the research market and with Illumina's recent launch
of the HiSeq X Ten, we've essentially reached the $1,000 genome
(notwithstanding quibbles over what exactly should be accounted
for in the $1,000). With these advancements, the pull to adapt NGS
for the clinical market has gotten stronger. The first examples of how
this technology will transform medicine are already showing up.
The press has been filled with stories, sometimes heart-warming and sometimes gut wrenching, of NGS being used in the diagnosis of late-stage cancers
and rare childhood diseases. But while these examples show how NGS can be
used to treat patients, they aren't really examples of clinical sequencing. These
are still research projects, each one requiring the attention of multiple experts
poring over the data to come up with hypotheses of how to treat the underlying malady. In order for NGS to be considered a true clinical tool, it will have to
be used on a routine basis, replacing older genetic-based tests. This transition
is starting to happen for prenatal testing and cancer diagnostics.
The High-Throughput Trend
In the infancy of the NGS market, early adopters really only
cared about two things: how much raw output the new
machines could generate and how quickly the price per
base could drop. Secondary to these two drivers was the
pressure to increase the read length back up to the standard
of Sanger sequencing, the mainstay that NGS was displacing. These driving goals, combined with the intense competitive pressure seen in the market between 454, Illumina,
Life Technologies, and Complete Genomics, led to incredible
output gains and an equally incredible drop in price, with
Illumina's flagship HiSeq X generating nearly 2 Tb of data
over 3 days at a cost of only $7 per Gb.
(continued on next page)
www.clinicalomics.com
SHAWN C. BAKER, Ph.D.
is the CSO and co-founder of AllSeq.
Having received his Ph.D. at the University
of California - Davis, he started his career
as a research scientist at Illumina. After
spending several years at the bench
developing gene expression array products,
he transitioned to product marketing
where he led a team in charge of Illumina's expression and
regulation sequencing portfolio. In 2013 Dr. Baker cofounded AllSeq (www.allseq.com), the only true sequencing
marketplace that helps researchers pick the best provider for
their needs. He can be reached at shawn@allseq.com
May 15, 2014 Clinical OMICs
17
http://www.allseq.com
http://www.clinicalomics.com
Table of Contents for the Digital Edition of Clinical OMICs - Issue 3
Contents
Clinical OMICs - Issue 3
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol3iss9
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol3iss8
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol3iss7
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol3iss6
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol3iss5
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol3iss4
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol3iss3
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol3iss2
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol3iss1
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss12
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss11
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss10
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss9
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss8
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss7
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss6
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss5
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss4
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss3
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss2
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_vol2iss1
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue15
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue14
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue13
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue12
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue11
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue10
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue9
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue8
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue7
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue6
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue5
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue4
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue3
https://www.nxtbook.com/nxtbooks/gen/clinical_omics_issue2
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