Simons Foundation and WuXi NextCODE Put World's
Largest Autism Dataset Online to Spur New Era of Massive Genomics Research
The Simons Simplex
Collection is now accessible in the cloud with WuXi NextCODE clinical discovery
analytics, uniting the genome and the internet for real-time queries and
collaboration
- Comprising 10,000 exomes from families with one child with an autism spectrum disorder, the SSC is the largest dataset ever to be made fully usable over an ordinary internet connection
- SSC data can instantly be used in tandem with other major datasets around the world, as a standard reference and the hub for autism genomics research of unprecedented scale
- Comprising 10,000 exomes from families with one child with an autism spectrum disorder, the SSC is the largest dataset ever to be made fully usable over an ordinary internet connection
- SSC data can instantly be used in tandem with other major datasets around the world, as a standard reference and the hub for autism genomics research of unprecedented scale
SHANGHAI and REYKJAVIK,
Iceland and CAMBRIDGE, Mass. and NEW YORK, March 10,
2016 /PRNewswire/ -- WuXi NextCODE,
the global genomic information and precision medicine company, and the Simons Foundation today announced that the Simons Simplex
Collection (SSC) is now accessible on WuXi NextCODE's
integrated cloud-based database, interpretation and discovery system, the WuXi
NextCODE Exchange. The WuXi NextCODE SSC portal has been inaugurated by autism
researchers from seventeen leading institutions from the US, Canada, China, France, Iceland, Austria, Ireland, Brazil and Qatar,
and from today will be open to researchers worldwide. Those interested can
apply for training and access via the WuXi NextCODE
SSC signup or by writing tocollections@simonsfoundation.org.
The SSC
comprises genomic sequence and detailed clinical phenotypic data from nearly
2,600 families with one child with an autism spectrum disorder (ASD) and
unaffected parents and siblings. It is a fundamental resource for advancing the
understanding of ASDs and one of the largest focused collections of genome
sequence data anywhere. The computational efficiency of WuXi NextCODE's
database architecture makes it possible to utilize data of this scale online.
SSC users can now directly interrogate individual genomes, families, or the
entire collection using WuXi NextCODE's integrated clinical discovery tools. They
can also tap into both GATK and FreeBayes variant calls for all samples; view
findings with always-on visualizations backed by normalized global reference
data; and collaborate with colleagues, all without having to move or download
the data files. The data is stored in WuXi NextCODE's elastically scalable,
HIPAA-compliant cloud powered by DNAnexus.
"The
SSC was conceived of and has succeeded as a large-scale, open-access discovery
engine. We are glad to now be partnering with WuXi NextCODE to realize this
next phase in the collection's potential by making it directly accessible to
the autism community worldwide," said Dr. Louis Reichardt, Director
of the Simons Foundation Autism Research Initiative (SFARI). "And because
it is now accessible online, the SSC can serve as the hub of a network of other
major autism datasets and virtual cohorts of ever greater power. We invite
everyone in the field to take advantage of this new resource."
"We
are thrilled and proud to be working with the Simons Foundation to inaugurate
what we see as a new era of global collaboration to better understand, diagnose
and address ASDs," said Hannes Smarason, COO of WuXi NextCODE.
"Putting the SSC on the Exchange is a landmark in creating a working
internet of DNA, and it is appropriate that it should address autism.
Unravelling its complexity demands the creation of truly vast datasets, and we
look forward to working with the Foundation and the autism community to refine
this resource, bring in whole genome data, and continue to expand the scale,
scope and reach of the SSC in pursuit of this goal."
"This
is a game-changer and we are already using the WuXi NextCODE SSC portal to
validate and extend new discoveries and confirm clinical diagnoses," said
Dr. Timothy Yu, a clinician and assistant professor of neurology at Boston
Children's Hospital. "This is the way the investment in big genomics is
going to deliver on its potential to accelerate our understanding of autism and
many other complex conditions. Since we and a growing number of our
collaborators have our research and diagnostic data in GOR format, we are
already seeing the impact of big virtual cohorts for rapidly advancing the
field and are inviting our collaborators to do the same."
The
SSC comprises whole-exome sequence data and more than 2000 phenotypic variables
for some 2,600 ASD probands and their parents and unaffected siblings. Among
the portal's features are:
·
All SFARIGene and
other major ASD gene and variants lists
·
All major public
reference datasets
·
Instant visualization
of raw BAM sequence reads
·
Variant aggregation to
power statistical association of rare variants
·
De novo, paralog
detection
·
Carrier analysis
·
Toggle filters for
predicted variant impact and allele frequencies
·
Histographic selectors
and report builders for phenotype definition
·
Import and merge
functionality to incorporate external datasets
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