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Release Date: January 29, 2008
Publication: In Sequence: The Inside
Read on Genome Sequencing, Vol. 2, No.5
Author: Julia Karow
The National Heart, Lung, and Blood Institute and the
National Human Genome Research Institute have set aside
$12 million in grants to help reduce at least tenfold
the cost of whole-genome exon sequencing methods and
enable future genome-wide exon resequencing studies
that will focus on specific diseases.
The new technology grant program, which plans to make
up to four awards this fall totaling $12 million over
two years, as well as disease studies NHLBI has planned
for the future, complement the 1,000 Genomes Project
that the NHGRI, the Wellcome Trust Sanger Institute,
and the Beijing Genomics Institute announced last week.
Unlike that project, which aims to catalog genetic variations
in human populations unbiased for disease, the resequencing
technology program is geared towards studies that will
correlate sequence variations with disease phenotypes.
“We built a consensus, through informal and some
formal meetings we convened, that the time was right
to take the next-generation technologies that are being
developed and implemented and build the kind of pipeline
that would be required for large-scale production sequencing”
of thousands of samples from disease-specific collections
maintained by NHLBI, Alan Michelson, associate director
for basic research at NHLBI, told In Sequence earlier
this month.
The goal is to develop inexpensive methods for capturing
and sequencing all exons, which make up between 1 percent
and 2 percent of the human genome. Other functional
regions, such as microRNAs and regulatory elements,
might also be included, according to the grant announcement.
These methods would fill a technical void for studies
that neither seek to resequence entire genomes nor to
resequence a single candidate gene, according to Weiniu
Gan, a program director in the genetics, genomics, and
advanced technologies program of the division of lung
diseases at NHLBI.
“We think this is a gap [and] we want to see if
we can fill that,” he said.
Exon Marks the Spot
At the moment, sequencing an individual’s exome,
or about 60 megabases of DNA, at high quality —
including all costs such as personnel, reagents, instrument
amortization, and facilities — costs “multiple
tens of thousands of dollars,” according to Adam
Felsenfeld, program director of the large-scale sequencing
program at NHGRI. “Right now, that’s too
expensive to do routinely,” he said. The aim of
the program is to reduce this cost to about $1,000 per
sample.
To reach this goal, researchers awarded the two-year
grants will combine new technologies and methods for
sample preparation, target capture, sequencing, and
data management and analysis into an “integrated
re-sequencing pipeline,” according to the grant
solicitation.
According to Felsenfeld, developing new capture methods
and integrating them with different sequencing platforms
will be among the main technical challenges researchers
need to overcome.
“Although there are some very encouraging capture
methods, I think the field is not settled yet,”
he said. “There are some early successes, but
I think there is a long way to go and a lot of opportunity
out there.”
Last year, several research groups published studies
that coupled new DNA capture methods with new sequencing
technologies, such as NimbleGen microarrays with 454’s
sequencer, NimbleGen arrays with Illumina’s Genome
Analyzer, and an Agilent oligo-based PCR-like approach
with Illumina’s sequencer (see In
Sequence 11/6/2007).
But these will likely not remain the only methods for
exon sequencing. “Things won’t settle for
some time because new and better techniques are going
to constantly be dropped into the mix for some time,
and people are going to look at those in combination
with their other technologies and see what’s best,”
Felsenfeld said. He added that several successful combinations
of capture and sequencing might emerge in the end.
According to the funding announcement, the research
will probably take place in two phases. During an initial
“optimization phase,” scientists will develop
and fine-tune their methods and put them into a production
pipeline using DNA samples that have already been characterized
in genome-wide genotyping or sequencing studies, such
as the HapMap samples, which are unbiased for disease.
Fewer than 20 DNA samples per investigator “may
be sufficient” for this phase of the project.
In the second, scale-up phase, scientists will run hundreds
of DNA samples to see if their re-sequencing pipeline
is suitable for sequencing all exons in thousands of
DNA samples in later studies.
Technologies developed under the NHLBI/NHGRI’s
program might also benefit the 1,000 Genomes Project.
Under one of its pilot projects, participating sequencing
centers will sequence exons of about 1,000 genes in
about 1,000 individuals.
Last week, Elaine Mardis, co-director of the Genome
Sequencing Center at Washington University, told In
Sequence that her center has not yet decided which capture
method to use in that pilot study, but it will consider
both an in-house method and approaches based on Agilent
and NimbleGen technology (In
Sequence 1/22/2008).
Date Posted: February 2, 2008
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