Three Sequencing Companies Join 1000
Biotech Innovators Will Contribute to International Effort to Produce
Most Detailed Map of Genetic Variation
Leaders of the 1000 Genomes Project announced today that three
firms that have pioneered development of new sequencing technologies
have joined the international effort to build the most detailed
map to date of human genetic variation as a tool for medical research.
The new participants are: 454 Life Sciences, a Roche company, Branford,
Conn.; Applied Biosystems, an Applera Corp. business, Foster City,
Calif.; and Illumina Inc., San Diego.
The 1000 Genomes Project, which was announced in January 2008,
is an international research consortium that is creating a new
map of the human genome that will provide a view of biomedically
relevant DNA variations at a resolution unmatched by current resources.
Organizations that have already committed major support to the
project are: the Beijing Genomics Institute, Shenzhen, China; the
Wellcome Trust Sanger Institute, Hinxton, Cambridge, U.K.; and
the National Human Genome Research Institute (NHGRI), part of the
National Institutes of Health. The NHGRI-supported work is being
done by the institute’s Large-Scale Sequencing Network, which includes
the Human Genome Sequencing Center at Baylor College of Medicine,
Houston; the Broad Institute of MIT and Harvard, Cambridge, Mass.;
and the Washington University Genome Sequencing Center at Washington
University School of Medicine, St. Louis.
"The additional sequencing capacity and expertise provided
by the three companies in the pilot phase will enable us to explore
the human genome with even greater depth and speed than we had
originally envisioned, and will help us to optimize the design
of the full study to follow," said Richard Durbin, Ph.D.,
of the Wellcome Trust Sanger Institute, who is co-chair of the
consortium. “It is a win-win arrangement for all involved. The
companies will gain an exciting opportunity to test their technologies
on hundreds of samples of human DNA, and the project will obtain
data and insight to achieve its goals in a more efficient and cost-effective
manner than we could without their help."
The genetic blueprints, or genomes, of any two humans are more
than 99 percent the same. Still, the small fraction of genetic
material that varies among people holds valuable clues to individual
differences in susceptibility to disease, response to drugs and
sensitivity to environmental factors.
The 1000 Genomes Project builds upon the International HapMap
Project, which produced a comprehensive catalog of human genetic
variation – variation that is organized into neighborhoods called
haplotypes. The HapMap catalog laid the foundation for the recent
explosion of genome-wide association studies that have identified
more than 130 genetic variants linked to a wide range of common
diseases, including type 2 diabetes, coronary artery disease, prostate
and breast cancers, rheumatoid arthritis, inflammatory bowel disease
and a number of mental illnesses.
The HapMap catalog, however, only identifies genetic variants
that are present at a frequency of 5 percent or greater. The catalog
produced by the 1000 Genomes Project will map many more details
of the human genome and how it varies among individuals, identifying
genetic variants that are present at a frequency of 1 percent across
most of the genome and down to 0.5 percent or lower within genes.
The 1000 Genomes Project’s high-resolution catalog will serve to
accelerate many future studies of people with specific illnesses.
"In some ways, this application of the new sequencing technologies
is like building bigger telescopes," said NHGRI Director Francis
S. Collins, M.D., Ph.D. "Just as astronomers see farther and
more clearly into the universe with bigger telescopes, the results
of the 1000 Genomes Project will give us greater resolution as
we view our own genetic blueprint. We’ll be able to see more things
more clearly than before and that will be important for understanding
the genetic contributions to health and illness."
The HapMap was based mainly on genotyping technology, in which
genetic markers were used to broadly scan the genome. In contrast,
the 1000 Genomes Project catalog will be built on sequencing technology,
in which the genome is examined at the level of individual DNA
letters, or bases. The increased resolution will enable the 1000
Genomes’ map to provide researchers with far more genomic context
than the HapMap, including more precise information about the genetic
variants that might directly contribute to disease.
"We find that there is a lot of value in participating in
international consortia; they produce large datasets that are valuable
to the scientific and medical communities while promoting the rapid
release of the data" said Illumina Vice President and Chief
Scientist David Bentley, Ph.D., who participated in the International
To enhance the production of the 1000 Genomes map, each of the
three biotech companies has agreed to sequence the equivalent of
75 billion DNA bases as part of the pilot phase. The human genome
contains about 3 billion bases. Consequently, each company will
contribute the equivalent of 25 human genomes over the next year,
and additional sequence data over the project’s expected three-year
timeline. In addition, Applied Biosystems will contribute an additional
200 billion bases of human sequence through its collaboration with
"This project is clearly the most ambitious and comprehensive
study to date of the human genome. Our participation continues
our commitment to partner with the scientific community to explore
the genetic factors involved in human disease," said Francisco
de la Vega, distinguished scientific fellow and vice president
for SOLiD System Applications and Bioinformatics at Applied Biosystems.
Michael Egholm, Ph.D., vice president of R&D at 454, said, "We
are proud to contribute to the 1000 Genomes Project as we further
our ongoing support of researchers worldwide and their goal of
deepening our understanding of human genome complexity. By applying
innovative technology to these complex challenges, this project
will deliver the highest standard of data quality and analysis."
In its first phase, expected to last about a year, the 1000 Genomes
Project is conducting three pilots that will be used to decide
the best strategies for achieving the goals of the full-scale effort.
The first pilot involves sequencing the genomes of six people (two
nuclear families) at high resolution; the second involves sequencing
the genomes of 180 people at lower resolution; and the third involves
sequencing the coding regions of 1,000 genes in about 1,000 people.
The full-scale project will involve sequencing the genomes of
at least 1,000 people, drawn from several populations around the
world. The project will use samples from donors who have given
informed consent for their DNA to be analyzed and placed in public
databases. Most of these samples have already been collected, and
any additional samples will come from specific populations. The
data will contain no medical or personal identifying information
about the donors.
Given the rapid pace of sequencing technology development, the
cost of the entire effort is difficult to estimate, but is expected
to be about $60 million. The sequence data provided by the three
companies are estimated to be worth approximately $700,000 for
the pilot phase, and the firms are expected to contribute much
more sequencing to the full project.
Already, the 1000 Genomes Project has generated such vast quantities
of data that the information is taxing the current capacity of
public research databases. Since the first phase was begun in late
January, project participants have produced and deposited some
240 billion bases of genetic information with the European Bioinformatics
Institute and the National Center for Biotechnology Information,
a part of the U.S. National Library of Medicine. Data generated
by the 1000 Genomes Project also will be distributed from a mirror
site at BGI Shenzhen.
Along with their contributions of sequencing capacity, the companies,
like all other project participants, have agreed to comply with
the open access policies established by the 1000 Genomes Project
Steering Committee. Those policies include rapid public release
of the data, including project participants having no early access
to the data; an intellectual property policy that precludes any
participants from controlling the information produced by the project;
regular progress reporting; and coordination of scientific publications
with the rest of the consortium.
Additional information about the project can be found at http://www.1000genomes.org/.
NHGRI is one of 27 institutes and centers at the NIH, an agency
of the Department of Health and Human Services. The NHGRI Division
of Extramural Research supports grants for research and for training
and career development at sites nationwide. Additional information
about NHGRI can be found at its Web site, www.genome.gov.
The National Institutes of Health (NIH) — The Nation's
Medical Research Agency — includes 27 Institutes and
Centers and is a component of the U.S. Department of Health and
Human Services. It is the primary federal agency for conducting
and supporting basic, clinical and translational medical research,
and it investigates the causes, treatments, and cures for both
common and rare diseases. For more information about NIH and
its programs, visit www.nih.gov.