Affymetrix to Provide Data Set of Millions of Genotypes to 1000 Genomes Project
November 03 2010 - 7:00AM
Business Wire
Affymetrix, Inc. (NASDAQ:AFFX) today announced that it will
contribute genotyping data for a large set of validated rare and
common genomic variants to the 1000 Genomes Project. This powerful
data consists of genotyping information from more than 2 million
single nucleotide polymorphisms (SNPs), and insertions/deletions
(indels), many of which were not previously available from any
source. The release includes common and rare variants genotyped on
the four major HapMap populations: Caucasian (CEU), Yoruba/African
(YRI), Chinese (CHB), and Japanese (JPT), as well as on the larger
HapMap Phase 3 sample-set. The data will be incorporated into the
1000 Genomes public data repository and will be freely
available.
“The 1000 Genomes Project is pleased to have Affymetrix join the
project and contribute this large data set to complement existing
genotyping data in the public domain,” said Dr. David Altshuler,
M.D., PhD, and Co-Chair of the 1000 Genomes Project. “The genotypes
that they have generated will be of interest to the project’s
participants, as well as to the broader research community,” Dr.
Altshuler noted.
In addition, Affymetrix will release a larger data set of
approximately 5 million variants on its website,
www.Affymetrix.com, before the end of 2010. The new data includes
approximately 3 million human SNPs discovered by the 1000 Genomes
Project that were not found in the HapMap Project or the NCBI’s
Single Nucleotide Polymorphism Database (dbSNP, release 130). This
information, which was generated by Affymetrix using the Axiom™
Genotyping Solution, will allow scientists to create customized
Axiom Genotyping Arrays containing 50,000 to as many as 2.6 million
markers. The entire Axiom Genomic Database provides an extensive
selection of ready-to-use variants for custom array designs and
enables an unprecedented level of success in assay conversion.
“This vast resource is a valuable supplement to existing data
sets and represents a new haplotype map which will provide further
insights into human genetic diversity and population
sub-structure,” said Carlos Bustamante, PhD, Professor of Genetics
at Stanford University. “Our ongoing work at Stanford in enabling
multi- and trans-ethnic genome-wide association and medical
resequencing studies will benefit greatly from this substantial
data set in particular and from Affymetrix’ screening capabilities
in general,” Dr. Bustamante added.
The Affymetrix Axiom Genome Screening Service allows researchers
to screen their populations and cohorts of interest against
approximately 5 million of these validated Axiom markers. For
studies focused on previously underserved ethnic groups, for which
public information is often limited, this service is invaluable for
its ability to inform SNP selection and array design.
“The release of these data sets strengthens our longstanding
tradition of partnering with the scientific community and is aimed
at characterizing human genetic variation, its link to disease, and
its importance in improving human health,” said Affymetrix
President and CEO Kevin King. “With these unprecedented data sets,
the scientific community has access to new tools to design custom
genotyping arrays for a wide range of studies by disease and
population, as well as the support they require for meta-analysis
through imputation. Moreover, the Axiom platform makes it easily
accessible and flexible to use.”
In addition to genotype information, the Affymetrix-hosted data
set also contains comprehensive minor allele frequency information
and can inform haplotype structure, which will enable more guided
genotyping study designs. The data set has been genotyped in 270
HapMap reference samples and portions have also been genotyped in
the HapMap Phase 3 set of 1,301 samples.
To create the data set, Affymetrix leveraged the Axiom
Genotyping Solution’s production-scale infrastructure to screen
millions of genomic variants from phases 1 to 3 of the
International HapMap Project and SNPs from pilots 1 and 2 of the
1000 Genomes Project. The database contains only those markers
determined to be polymorphic in the respective population and those
that meet Affymetrix’ stringent data quality metrics.
About Affymetrix
Affymetrix technology is used by the world's top pharmaceutical,
diagnostic, and biotechnology companies, as well as leading
academic, government, and nonprofit research institutes. More than
1,900 systems have been shipped around the world and more than
22,000 peer-reviewed papers have been published using the
technology.
Affymetrix is headquartered in Santa Clara, Calif., and has
manufacturing facilities in Cleveland, Ohio, and Singapore. The
company has about 1,000 employees worldwide and maintains sales and
distribution operations across Europe and Asia. For more
information about Affymetrix, please visit
http://www.affymetrix.com.
Disclaimer
The information stated above was prepared by Affymetrix, Inc.
and reflects solely the opinion of Affymetrix, Inc. Nothing in this
statement shall be construed to imply any support or endorsement of
Affymetrix, Inc., or any of its products, by Stanford University,
its officers, agents and employees.
Forward-looking statements
All statements in this press release that are not historical are
"forward-looking statements" within the meaning of Section 21E of
the Securities Exchange Act as amended, including statements
regarding Affymetrix' "expectations," "beliefs," "hopes,"
"intentions," "strategies," or the like. Such statements are
subject to risks and uncertainties that could cause actual results
to differ materially for Affymetrix from those projected. These and
other risk factors are discussed in Affymetrix' Form 10-K for the
year ended December 31, 2009, and other SEC reports for subsequent
quarterly periods.
NOTE: Affymetrix, the Affymetrix logo, Axiom, myDesign, are
trademarks or registered trademarks of Affymetrix Inc.
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