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Thanks,
Tamar
~~~~~~~~
When the power of love overcomes the love of power,
the world will come to know peace.
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________________________________
From: Meir Weiss <[log in to unmask]>
To: [log in to unmask]
Sent: Wed, October 27, 2010 4:20:18 PM
Subject: FW: 1000 GENOMES PROJECT PUBLISHES ANALYSIS OF COMPLETED PILOT PHASE
-----Original Message-----
From: NIH news releases and news items [mailto:[log in to unmask]] On
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Sent: Wednesday, October 27, 2010 3:19 PM
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Subject: 1000 GENOMES PROJECT PUBLISHES ANALYSIS OF COMPLETED PILOT PHASE
U.S. Department of Health and Human Services
NATIONAL INSTITUTES OF HEALTH NIH News
National Human Genome Research Institute (NHGRI) <http://www.nhgri.nih.gov/>
For Immediate Release: Wednesday, October 27, 2010
CONTACTS:
Jeannine Mjoseth, NHGRI, 301-594-1045,<e-mail:[log in to unmask]>
Don Powell, Wellcome Trust Sanger Institute, +44 (0)1223 496928,
<e-mail:[log in to unmask]>
Nicole Davis, Broad Institute, 617-714-7152,
<e-mail:[log in to unmask]>
1000 GENOMES PROJECT PUBLISHES ANALYSIS OF COMPLETED PILOT PHASE
NIH-supported work produces tool for research into genetic contributors to
human disease
Small genetic differences between individuals help explain why some people
have a higher risk than others for developing illnesses such as diabetes or
cancer. Today in the journal Nature, the 1000 Genomes Project, an
international public-private consortium, published the most comprehensive
map of these genetic differences, called variations, estimated to contain
approximately 95 percent of the genetic variation of any person on Earth.
Researchers produced the map using next-generation DNA sequencing
technologies to systematically characterize human genetic variation in 180
people in three pilot studies. Moreover, the full scale-up from the pilots
is already under way, with data collected from more than 1,000 people.
"The pilot studies of the 1000 Genomes Project laid a critical foundation
for studying human genetic variation," said Richard Durbin, Ph.D., of the
Wellcome Trust Sanger Institute and co-chair of the consortium. "These
proof-of-principle studies are enabling consortium scientists to create a
comprehensive, publicly available map of genetic variation that will
ultimately collect sequence from 2,500 people from multiple populations
worldwide and underpin future genetics research."
Genetic variation between people refers to differences in the order of the
chemical units - called bases - that make up DNA in the human genome. These
differences can be as small as a single base being replaced by a different
one - which is called a single nucleotide polymorphism (abbreviated SNP) -
or is as large as whole sections of a chromosome being duplicated or
relocated to another place in the genome. Some of these variations are
common in the population and some are rare. By comparing many individuals
to one another and by comparing one population to other populations,
researchers can create a map of all types of genetic variation.
The 1000 Genomes Project's aim is to provide a comprehensive public resource
that supports researchers aiming to study all types of genetic variation
that might cause human disease. The project's approach goes beyond previous
efforts in capturing and integrating data on all types of variation, and by
studying samples from numerous human populations with informed consent
allowing free data release without restriction on use. Already, these data
have been used in studies of the genetic basis for disease.
"By making data from the project freely available to the research community,
it is already impacting research for both rare and common diseases," said
David Altshuler, M.D., Ph.D., deputy director of the Broad Institute of
Harvard and MIT, and a co-chair of the project. "Biotech companies have
developed genotyping products to test common variants from the project for a
role in disease. Every published study using next-generation sequencing to
find rare disease mutations, and those in cancer, used project data to
filter out variants that might obscure their results."
The project has studied populations with European, West African and East
Asian ancestry. Using the newest technologies for sequencing DNA, the
project's nine centers sequenced the whole genome of 179 people and the
protein-coding genes of 697 people. Each region was sequenced several
times, so that more than 4.5 terabases (4.5 million million base letters) of
DNA sequence were collected. A consortium involving academic centers on
multiple continents and technology companies that developed the sequencing
equipment carried out the work.
To process these data required many technical and computational innovations,
including standardized ways to organize, store, analyze and share DNA
sequencing data. Launched in 2008, the 1000 Genomes Project started with
three pilot projects to develop, evaluate and compare strategies for
producing a catalogue of genetic variations. Funded through numerous
mechanisms by foundations and national governments, the 1000 Genomes Project
will cost some $120 million over five years, ending in 2012.
When the work began, sequencing was very expensive, so the project began
with two approaches aimed at increasing efficiency: One strategy - called
"low pass" -- combines partial data from many people; the second only
focused on the part of the genome that encodes protein-coding genes. By
comparing these strategies to "gold standard" data produced at great
completeness and accuracy, the project was able to show that both the
alternative approaches work well and have complementary strengths.
Researchers will use both strategies in the full-scale project because,
although sequencing costs have decreased, it is still relatively expensive.
"We have shown for the first time that a new approach to sequencing - low
coverage of many samples - works efficiently and well," said Gil McVean,
Ph.D., professor of statistical genetics at the University of Oxford. "This
proof of principle is now being applied not only in the 1000 Genomes
Project, but in disease research, as well."
The resulting map of human genetic variation includes about 15 million SNPs,
1 million short insertion/deletion changes, and more than 20,000 structural
variations. Many of the genetic variants had previously been identified, but
more than half were new. The project's database contains more than 95
percent of the currently measurable variants found in any individual, and
continuing work will eventually identify more than 99 percent of human
variants.
Richard Gibbs, Ph.D., director of the Human Genome Sequencing Center at the
Baylor College of Medicine (one of the project's sequencing centers) said:
"What really excites me about this project is the focus on identifying
variants in the protein-coding genes that have functional consequences.
These will be extremely useful for studies of disease and evolution."
The improved map produced some surprises. For example, the researchers
discovered that on average, each person carries between 250 and 300 genetic
changes that would cause a gene to stop working normally, and that each
person also carried between 50 and 100 genetic variations that had
previously been associated with an inherited disease. No human carries a
perfect set of genes. Fortunately, because each person carries at least two
copies of every gene, individuals likely remain healthy, even while carrying
these defective genes, if the second copy works normally.
In addition to looking at variants that are shared among many people, the
researchers also investigated in detail the genomes of six people: two
mother-father-daughter nuclear families. By finding new variants present in
the daughter but not the parents, the team was able to observe the precise
rate of mutations in humans, showing that each person has approximately 60
new mutations that are not in either parent.
With the completion of the pilot phase, the 1000 Genomes Project has moved
into full-scale studies in which 2,500 samples from 27 populations will be
studied over the next two years. Data from the pilot studies and the
full-scale project are freely available on the project website,
<www.1000genomes.org>.
Researchers studying specific illnesses, such as heart disease or cancer,
use maps of genetic variation to help them identify genetic changes that may
contribute to the illnesses. Over the last five years, the first generation
of such studies (called genome-wide association studies or GWAS) have been
based on an earlier map of genetic variation called the HapMap. Built using
older technology, HapMap lacks the completeness and detail of the 1000
Genomes Project.
"The 1000 Genomes Project map fills in the gaps between the HapMap
landmarks, helping researchers identify all candidate genes in a region
associated with a disease," said Lisa Brooks, Ph.D., program director for
the Genetic Variation Program at the National Human Genome Research
Institute, a part of the National Institutes of Health. "Once a
disease-associated region of the genome is identified, experimental studies
must be done to identify which variants, genes and regulatory elements cause
the increased disease risk. With the new map, researchers can just look up
all the candidate genes and almost all of the variants in the database,
saving them many steps in finding the causes."
Organizations that committed major support to the project include: 454 Life
Sciences, a Roche company, Branford, Conn.; Life Technologies Corporation,
Carlsbad, Calif.; BGI-Shenzhen, Shenzhen, China; Illumina Inc., San Diego;
the Max Planck Institute for Molecular Genetics, Berlin, Germany; the
Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK; and the National
Human Genome Research Institute, Bethesda, Md., which supports the work
being done by Baylor College of Medicine, Houston, Texas; the Broad
Institute, Cambridge, Mass.; and Washington University, St. Louis, Missouri.
Researchers at many other institutions are also participating in the project
including groups in Barbados, Canada, China, Colombia, Finland, the Gambia,
India, Malawi, Pakistan, Peru, Puerto Rico, Spain, the UK, the US, and
Vietnam. Additional information about the project, including a list of all
participants and organizations, can be found at
<http://www.1000genomes.org/>.
The National Institutes of Health - "The Nation's Medical Research Agency" -
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, visit www.nih.gov.
The National Human Genome Research Institute is one of 27 institutes and
centers at National Institutes of Health, an agency of the Department of
Health and Human Services. NHGRI's Division of Extramural Research supports
grants for research and for training and career development. For more, visit
<www.genome.gov>.
The Wellcome Trust is a global charitable foundation dedicated to achieving
extraordinary improvements in human and animal health. It is independent of
both political and commercial interests. For information, go to
http://www.wellcome.ac.uk/.
The Wellcome Trust Sanger Institute, which receives the majority of its
funding from the Wellcome Trust, was founded in 1992. In October 2006, new
funding was awarded by the Wellcome Trust to exploit the wealth of genome
data now available to answer important questions about health and disease.
More information, go to <http://www.sanger.ac.uk/>.
The European Molecular Biology Laboratory is a basic research institute
funded by public research monies from 20 member countries and supports
research by approximately 85 independent groups covering the spectrum of
molecular biology. For more information, go to <http://www.embl.de>.
European Bioinformatics Institute (EBI) is part of the European Molecular
Biology Laboratory (EMBL) and is located on the Wellcome Trust Genome Campus
in Hinxton near Cambridge (UK). For more information, go to
<http://www.ebi.ac.uk>.
The Eli and Edythe L. Broad Institute of MIT and Harvard, founded in 2003 by
MIT, Harvard and its affiliated hospitals, and Los Angeles philanthropists
Eli and Edythe L. Broad, includes faculty, professional staff and students
from throughout the MIT and Harvard biomedical research communities and
beyond, with collaborations spanning over a hundred private and public
institutions in more than 40 countries worldwide. For further information,
go to <http://www.broadinstitute.org/>.
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>.
##
This NIH News Release is available online at:
<http://www.nih.gov/news/health/oct2010/nhgri-27.htm>.
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