Affymetrix Releases Comprehensive Validated Data from the Axiom™ Genomic Database
03 March 2011 - 7:00PM
Business Wire
Affymetrix, Inc. (NASDAQ: AFFX) today announced the release of a
complete data set of 5 million variants on its website. The
genotyping data set, part of the Axiom™ Genomic Database, is based
on extensive validation of genomic variants from the Single
Nucleotide Polymorphism Database (dbSNP), 1000 Genomes Project,
NHGRI Database of Published Associations, and collaborations that
have led to the discovery of novel SNPs and insertion/deletions
(indels). The data set includes genotyping data for more than 2
million validated rare and common genomic variants that Affymetrix
recently contributed to the 1000 Genomes Project, many of which
were not previously available from any source. The data will be
incorporated into the 1000 Genomes Project’s public data
repository.
"With the availability of millions of novel markers in more
diverse populations, along with the increasing capacity of our
microarray technology, we are providing researchers with more
resources to accelerate their disease association studies,” said
Kevin King, President and CEO of Affymetrix. “By releasing this
unparalleled data set, Affymetrix is giving clinical researchers
better access to valuable content and making it easier to optimize
their discovery and validation efforts.”
Affymetrix has ensured that all variants in the Axiom Genomic
Database are highly informative and reliable through a
comprehensive SNP screening and validation effort. This program is
critical because many SNP discovery sources contain only putative
SNPs, in which the minor allele frequency (MAF) is unknown or
observed infrequently in only two chromosomes. As a result, many of
these sources contain monomorphic SNPs that can yield a false
positive rate greater than 20 percent, or may not generate high
data quality in an assay. Competing arrays are often designed in
silico against putative SNPs, which requires the research community
to spend time and money validating the genomic content themselves.
By pre-screening all content against stringent performance metrics,
Affymetrix alleviates this burden for the researcher and ensures
each marker can be reliably genotyped for the rare allele in the
Axiom assay.
All variants were tested against a large, diverse sample set,
including 1,300 samples across 11 populations from the
International HapMap Project. The result is that all validated
markers offer a broader view of alleles across diverse populations.
Additionally, the data set offers a conversion rate of greater than
98 percent for all validated markers, which allows researchers to
quickly design and implement fully customizable Axiom™ myDesign™
Arrays without any gaps in genomic coverage or the need to optimize
the assay in their laboratories.
The Axiom myDesign Arrays enable researchers to create their own
customized genotyping arrays with up to 2.6 million markers for
candidate gene and genome-wide association studies by disease,
pathway, and population. Scientists can submit their own sequences
to design their arrays and leverage the Axiom Genomic Database,
which includes an unprecedented number of genetic variants in key
pathways, such as cardiovascular, cancer, drug metabolism, human
leukocyte antigen (HLA), and immunity/inflammation, as well as
other SNP classifications. The database also provides greater
support for meta-analysis through imputation.
The files, located at www.affymetrix.com/Axiomdatabase, contain
data on 5.4 million SNPs, including approximately 1.8 million from
HapMap and dbSNP, approximately 3 million from the 1000 Genomes
Project 2009 release, and an additional 0.6 million from
collaborative discovery projects. Almost all of the 1.8 million
SNPs from HapMap and dbSNP were genotyped on 11 populations
comprising more than 1,000 individuals, while the remaining 3.6
million SNPs were genotyped on the three HapMap populations
comprising roughly 270 individuals, including Utah residents with
European ancestry (CEU), Han Chinese in Beijing, China (CHB),
Japanese in Tokyo, Japan (JPT), and Yoruba in Ibadan, Nigeria
(YRI).
The Axiom Genomic Database and its genotyping data set is the
result of an ongoing screening pipeline that leverages the
company’s production-scale infrastructure and its capacity to
analyze billions of genotypes. Affymetrix continues to screen novel
putative SNPs to expand the Axiom Genomic Database and will
publicly release additional data sets throughout 2011 and
beyond.
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
2,000 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 Santa Clara, Cleveland, Ohio, and
Singapore. The company has about 900 employees worldwide and
maintains sales and distribution operations across Europe and Asia.
For more information about Affymetrix, please visit
http://www.affymetrix.com.
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, and myDesign are
trademarks or registered trademarks of Affymetrix Inc.
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