MEDICAL: GENETICS : MEDICAL: PUBLICATIONS: 1000 Genomes Project Publishes Analysis of Completed Pilot Phase
David P. Dillard
.
MEDICAL: GENETICS :
MEDICAL: PUBLICATIONS:
1000 Genomes Project Publishes Analysis of Completed Pilot Phase
Date: Wed, 27 Oct 2010 15:19:11 -0400
From: "NIH OLIB (NIH/OD)" <ol...@od.nih.gov>
To: NIHP...@list.nih.gov
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
e-mail:
Don Powell, Wellcome Trust Sanger Institute
e-mail:
Nicole Davis, Broad Institute
e-mail:
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,
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
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
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
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
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
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
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
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
##
This NIH News Release is available online at:
http://www.nih.gov/news/health/oct2010/nhgri-27.htm
======================================
1000 Genomes Project Tutorial Videos
The 1000 Genomes Project has released the data sets for the pilot projects
and for more than 1000 samples for the full-scale project. A tutorial for
how to use the data was held at the 2010 American Society of Human
Genetics (ASHG) annual convention on November 3.
Videos for each of the tutorial sessions are now available. The tutorial
describes 1000 Genomes Project data, how to access it and how to use it.
Each of the speakers and their topics are listed below along with their
tutorial videos and PowerPoint slides.
A map of human genome variation from population-scale sequencing
The 1000 Genomes Project Consortium
Nature
Volume: 467,
Pages: 10611073
Date published:
(28 October 2010)
DOI:
doi:10.1038/nature09534
Received
20 July 2010
Accepted
30 September 2010
Published online
27 October 2010
http://www.nature.com/nature/journal/v467/n7319/full/nature09534.html
Introduction
Data generation, alignment and variant discovery
Power to detect variants
Genotype accuracy
Putative functional variants
Application to association studies
Mutation, recombination and natural selection
Discussion
Methods
References
Acknowledgements
Author information
Supplementary information
Comments
Sincerely,
David Dillard
Temple University
(215) 204 - 4584
jw...@temple.edu
http://daviddillard.businesscard2.com
Net-Gold
http://groups.yahoo.com/group/net-gold
Index: http://tinyurl.com/myxb4w
http://listserv.temple.edu/archives/net-gold.html
http://groups.google.com/group/net-gold?hl=en
General Internet & Print Resources
http://guides.temple.edu/general-internet
COUNTRIES
http://guides.temple.edu/general-country-info
EMPLOYMENT
http://guides.temple.edu/EMPLOYMENT
TOURISM
http://guides.temple.edu/tourism
DISABILITIES
http://guides.temple.edu/DISABILITIES
INDOOR GARDENING
http://tech.groups.yahoo.com/group/IndoorGardeningUrban/
Educator-Gold
http://groups.yahoo.com/group/Educator-Gold/
K12ADMINLIFE
http://groups.yahoo.com/group/K12AdminLIFE/
THE COLLEGE LEARNING CENTER
http://tinyurl.com/yae7w79
Nina Dillard's Photographs on Net-Gold
http://tinyurl.com/36qd2o
and also http://gallery.me.com/neemers1
http://www.flickr.com/photos/neemers/
Net-Gold Membership Required to View Photos
Twitter: davidpdillard
Bushell, R. & Sheldon, P. (eds),
Wellness and Tourism: Mind, Body, Spirit,
Place, New York: Cognizant Communication Books.
Wellness Tourism: Bibliographic and Webliographic Essay
David P. Dillard
http://tinyurl.com/p63whl
http://tinyurl.com/ou53aw
INDOOR GARDENING
Improve Your Chances for Indoor Gardening Success
http://tech.groups.yahoo.com/group/IndoorGardeningUrban/
http://groups.google.com/group/indoor-gardening-and-urban-gardening
SPORT-MED
https://www.jiscmail.ac.uk/lists/sport-med.html
http://groups.google.com/group/sport-med
http://groups.yahoo.com/group/sports-med/
http://listserv.temple.edu/archives/sport-med.html
HEALTH DIET FITNESS RECREATION SPORTS TOURISM
http://health.groups.yahoo.com/group/healthrecsport/
http://groups.google.com/group/healthrecsport
http://healthrecsport.jiglu.com/
http://listserv.temple.edu/archives/health-recreation-sports-tourism.html
Please Ignore All Links to JIGLU
in search results for Net-Gold and related lists.
The Net-Gold relationship with JIGLU has
been terminated by JIGLU and these are dead links.
http://groups.yahoo.com/group/Net-Gold/message/30664
http://health.groups.yahoo.com/group/healthrecsport/message/145
.