Affymetrix Commercializes Next-Generation Transcriptome Array for Large-Scale Clinical Studies
August 08 2011 - 4:57AM
Business Wire
Affymetrix, Inc. (NASDAQ:AFFX) today announced commercialization
of the next-generation human transcriptome array demonstrated by
Stanford University researchers to be superior to mRNA sequencing
(RNA-Seq) in gene expression profiling studies. In multiple
experiments using a clinically relevant transcriptome discovered by
deep sequencing, the research scientists compared the throughput
and performance of both profiling technologies and found the new
GeneChip® Human Transcriptome and Splice Junction Array
outperformed RNA-Seq in most all parameters when detecting exonic
changes implicated in human disease and genetic disorders.
According to results of Stanford’s recently published study, the
Human Transcriptome Array detected the same number of genes and two
times the number of exons, had lower variance over a wide range of
expression levels, improved the percentage of true-positive
detections in alternative splicing analysis, and measured more
non-coding RNA than RNA-Seq. With 99 percent coverage of human
genes and 95 percent coverage of transcript isoforms, researchers
determined that the high density microarray is a better profiling
array for clinical studies.
“With unparalleled sensitivity, reproducibility, and ease of
use, arrays of this type will be the platform of choice for patient
profiling in clinical trials,” said Stanford Professor of
Biochemistry and Genetics Ronald W. Davis, PhD, a pioneer in the
development and application of recombinant-DNA techniques and the
study’s lead researcher. “The power of next-generation sequencing
(NGS) harnessed into a clinically viable platform, like the
Affymetrix Human Transcriptome Array, will be what changes the face
of patient care.”
In typical large-scale studies of 5,000 samples, Stanford
researchers estimated it would take RNA-Seq 10 times longer to
analyze one percent of the number of genes processed by the new
array and 20 times longer to analyze one-half percent of exons.
Moreover, to achieve the same level of reproducibility as the new
array, RNA-Seq would require 150 million mappable reads for genes
and 200 million for exons (3711).1 Based on this level of power and
performance, the researchers concluded the Human Transcriptome
Array is more reproducible, faster, and cost-effective than RNA-Seq
for detecting and characterizing low-level expression changes of
clinically relevant transcripts.
“An emerging approach for large-scale clinical genomic studies
is to first use RNA-Seq to the sufficient depth of 200 million or
greater reads for the discovery of transcriptome elements relevant
to the disease process, followed by high-throughput and reliable
screening of these elements on thousands of patient samples using
custom designed arrays,” added Dr. Davis, winner of this year’s
Gruber Genetics Prize for distinguished contributions to genetics
research.
Until its worldwide rollout, Affymetrix is selling the Human
Transcriptome Array through an early-access program to
pharmaceutical and research institutions using microarrays or NGS
for basic discovery or whole transcriptome analyses. Designed in
collaboration with Stanford researchers, it has attracted worldwide
attention from pharmaceutical and research institutions seeking a
tool sensitive enough to reproducibly measure low abundance
transcripts in complex disease and reproducible enough to take
their de novo research to the clinical level—enabling them to
leverage the power of NGS in a clinical setting.
“Human transcript diversity has been well characterized—there
are more than 65 million expressed sequence tags now available in
public databases and during the last 15 years, they’ve been
instrumental in gene discovery and gene sequence determination,”
said Frank Witney, PhD, Affymetrix President and CEO. “Researchers
and clinicians are demanding solutions like our new array to go
beyond simply identifying transcripts, to actually measuring the
differences in their abundance in large clinical studies.”
The new array is the 6.9 million-feature Glue Grant Human
Transcriptome (GG-H) Array developed with Stanford as part of the
NIH Glue Grants program, a three-year multicenter effort to answer
clinical questions requiring a translational bench to bedside
strategy. Led by Stanford’s Genome Technology Center and Department
of Biochemistry research scientists, the performance of the GG-H
Array was examined and compared with RNA-Seq results over multiple
independent replicates of liver and muscle samples. The findings,
recently published in the journal of Proceedings of the National
Academy of Sciences (PNAS), determined “the GG-H Array was highly
reproducible in estimating gene and exon abundance and more
sensitive at the exon level” when compared with RNA-Seq of 46
million uniquely mappable reads per replicate (3707).
“Research like Stanford’s really demonstrates how to use
multiple technologies effectively in large scale clinical studies
where detection and measurement of low-abundance transcripts is
essential,” said Kevin Cannon, PhD, Vice President of Gene
Expression at Affymetrix. “These observations provide researchers
practical guidance on using the right technology at the right time;
first NGS for discovery, then high density next-generation
transcriptome microarrays for high volume profiling.”
Information regarding the early access program is available from
Affymetrix at GGH_Support@Affymetrix.com.
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
23,700 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, Asia,
and Latin America. 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, 2010, and other SEC reports for subsequent
quarterly periods.
NOTE: Affymetrix, the Affymetrix logo, and GeneChip are
trademarks or registered trademarks of Affymetrix, Inc.
1 Weihong Xu, et al.”Human transcriptome array for
high-throughput clinical studies.” Proceedings of the National Academy of Sciences
(PNAS), 108 (9) (2011):3707-3712.
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