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Talkin’ ’bout my generation
April 2011
EDIT CONNECT
SHARING OPTIONS:
REDWOOD CITY, Calif.—With an eye on next-generation
sequencing (NGS) analysis, Ingenuity Systems has entered into a research collaboration
with Covance.
The companies will work together to develop new and novel
approaches
using Ingenuity's IPA software to obtain more actionable insights
from NGS data and to answer research questions in a relevant biological
context.
"We're delighted that Covance has selected IPA for its NGS
workflows," says Doug Bassett, chief scientific and
technology officer at
Ingenuity Systems. "We've been involved in several NGS collaborations recently,
and our partnership with Covance, a leading
drug development services company,
represents another powerful validation of IPA's value in the NGS space. It is
exciting to see IPA being used to
accelerate and inform so much groundbreaking
research."
Thomas Turi, vice president of science and technology
for
Covance Discovery and Translational Services, notes that this is the first
formal collaboration between the Covance Genomics Laboratory (CGL) and
Ingenuity Systems.
"Prior to its acquisition by Covance, CGL (formerly known as
Rosetta Inpharmatics) was a
significant user of Ingenuity's IPA software," he
says. "Additionally, there had previously been significant interactions between
key scientific
leaders at Covance and Ingenuity that facilitated this
collaboration."
Ingenuity Systems is a provider of
information solutions and
custom services for life-science researchers, computational biologists and
bioinformaticists and life science industry
suppliers.
According to Bassett, Covance proved to be a good fit for
this effort because of the company's
standing as a provider of genomics
solutions for the drug discovery and development industry and the fact that the
companies share many of the same
customers.
"Covance is also similarly forward-looking in how they are
thinking about next-generation
sequencing technologies," he says. "Both of our
companies recognize that without biological interpretation, the value and
potential in NGS
technologies will not be unlocked for our mutual customers.
Having Excel files of data or a list of variants or genes with associated statistics
is a
first step, but it does not get researchers to their end goal of answering
a scientific question."
The
collaboration, Turi points out, is aimed at providing
deeper insights and interpretation of biological pathways and networks from
genomic data.
"The key part of this collaboration is aimed specifically at
making sense of large volumes of
next-generation sequencing data to provide a
systematic and multi-dimensional view of human genetics and cover various data
types, e.g., gene
expression, genotyping, splice variation and methylation," he
says. "Integrating these various data types into coherent biological stories is
what
constitutes the most challenging step."
In the collaboration, Ingenuity and Covance are working
together to develop new methodologies to help pharmaceutical clients maximize
the value of their NGS investments and obtain more actionable insights
from NGS
data, including isoform-level biological interpretation for RNA-Seq studies
leveraging Ingenuity knowledgebase content, and helping customers
using
resequencing technology to get from a list of 3 million-plus variants down to
the less than 50 most compelling for follow-up.
"Ingenuity's Knowledge Base of expert-curated, structured
biomedical content provides the biological context necessary to
move past long
lists of genes, isoforms and variants, enabling researchers to more quickly
uncover those that are most critical to biology," Bassett
notes. "Using this
approach, Covance can more rapidly and confidently narrow in on what is
interesting or unique in a dataset and deliver more
meaningful results to their
customers."
Moreover, Bassett says the companies share a common
conviction that
analyzing data in the context of known biology—like pathways,
processes and diseases—is essential to uncovering novel insights and helping
researchers
quickly get to high-value outcomes like causal disease variants,
biomarker identification, target ID and validation, understanding drug
mechanism of
action and safety assessment.
According to Bassett, success of this collaboration can be
measured by the effectiveness and efficiency of their mutual customers.
"This partnership should enable
scientists to invest their
valuable time on the biological interpretation of their data—validating hypotheses,
assessing safety, prioritizing
biomarkers, identifying causal variants and so
on—not dealing with data processing issues, manually iterating through large
lists of variants or genes,
or struggling to place their data into the context
of previously published mutations and findings," he points out.
Being digital in
nature and due to its larger dynamic range
compared to microarrays, this technology helps in the identification of novel
genetic alterations, non-
coding RNAs and alternative splicing, in addition to
gene expression associated with various diseases.
"As more data becomes available, there is a growing need in
the industry to develop automated pipelines to integrate and mine complex
datasets for
better understanding of biological processes that impact drug
development," Turi explains. "Covance plans to use this collaboration to
further
develop its pipeline for analyzing complex datasets and aid
pharmaceutical and biotech partners to identify targets or biomarkers for their
drug
discovery programs. Covance will test these capabilities using a pilot
project with Institute of Systems Biology (ISB) targeting glioblastoma."
Additionally,
Turi says the collaboration will further
enhance Covance's offerings in the genomics arena.
"As next-generation sequencing rapidly becomes the
focus of
genomics, Covance realizes that in the near future the platforms will
significantly shift into the space of next-generation sequencing," he
says. Code: E041111 Back |
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