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OmniTier's CompStor™ Brings De Novo Analytics to Genomics

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Researchers in joint study cut time for de novo global assembly to
under two hours with CompStor's tiered-memory architecture; higher
accuracy and a faster path to precision medicine

OmniTier
Inc.
, an application-specific, high performance solutions company,
announced that in a joint study with researchers at the Mayo Clinic's
Center for Individualized Medicine, the company successfully
demonstrated human DNA variant calling using de novo global
assembly techniques with breakthrough performance and cost. Using the
well-characterized NA12878 short-read sequenced genome dataset, the
CompStor™ compute cluster completed variant-caller-ready assembly of a
50x coverage genome in less than two hours. The solution scales to 800x
sequence coverage, a dataset size previously considered too large for de
novo
techniques but necessary to reliably identify new and
infrequent variants.

The joint study builds upon OmniTier's previously
announced result
of assembling a human genome in 8 minutes. It shows
that de novo global assembling can be routinely applied to whole
genome sequencing, even with high coverage sequenced genomes where
accuracy is paramount. The joint study also shows that de novo
analytics no longer requires supercomputing-level resources, but instead
can be completed on application-specific bioinformatics platforms based
on standard, low-cost servers with next-generation software and memory –
opening the door to hundreds of institutions globally that are eager to
leverage next-generation sequencing techniques.

"De novo sequence assembly for better variant discovery and
characterization has remained elusive due to the exceedingly long
assembly times and resources requirement of existing assemblers.
CompStor holds the promise to change that paradigm," said Dr. Alexej
Abyzov, computational genomicist and biologist, senior associate
consultant and assistant professor of biomedical informatics at the Mayo
Clinic in Rochester, MN.

"In benchmarking, CompStor has enabled us with fast, robust, accurate,
and unbiased analysis of individualized high coverage whole genome
sequencing data. We expect to apply CompStor's unique capabilities to
analyzing point nucleotide substitutions as well as larger structural
variants and indels in several future studies," Dr. Abyzov continued.
Technical observations of the CompStor system will be published in a
forthcoming peer-reviewed paper, jointly produced by Dr. Abyzov's
laboratory and OmniTier scientists.

Whole genome sequencing (WGS) has emerged as the central approach in
characterizing human variation and disease states on a population scale,
but it demands new computational bioinformatics solutions. Current
variant-calling methods are based on alignment of the sequenced reads
against a known reference genome – a single reference approach that
introduces biases and leads to missed variants. This inherent bias
limits the quality of whole genome sequencing and other Next Generation
Sequencing (NGS) applications. The de novo global assembly
methodology avoids the use of a reference and, therefore, enables
complex variant calling with haplotype (phased) resolution. However,
current de novo implementations are too slow and expensive for
mass deployment.

CompStor's implementation addresses the demand for higher quality in WGS
by delivering high computational efficiency and low cost. Its
tiered-memory architecture utilizes DRAM and flash memory resources in a
novel cluster configuration to overcome the limitations of the existing de
novo
assembly implementations. By using standard, low-cost x86
(Intel processor) servers with software designed around expansive
computational memory, supercomputer-like results are possible. CompStor
clusters have optimized data ingress and egress – for example, ingesting
raw genome sequence datasets at up to 10 GB/s from suitable external
sources. The solution seamlessly integrates with existing genomics
workflows and provides command line, API, and web-based job control
mechanisms. Users can choose from industry-standard or built-in variant
callers.

"CompStor is bringing the de novo analytics era to genomics,"
said Dr. Hemant Thapar, founder and CEO of OmniTier. "Existing solutions
are severely limiting in the use of de novo assembly, especially
for high coverage genomes – yet in CompStor we have an approach that can
be deployed pervasively. Our current results in the joint study with the
Mayo Clinic highlight the potential to integrate de novo assembly
methodology in genomic medicine and achieve higher accuracy and shorter
assembly times on affordable cloud or on-premise infrastructure. Our
CompStor platform side-steps fundamental data transfer problems to
remote compute facilities and applies tiered memory innovations that can
expedite the path to personalized medicine."

CompStor is currently in beta testing and will be generally available in
the fourth quarter of 2018. For more information on ways that whole
genome sequencing providers can partner with OmniTier, please email sales@omnitier.com.

About OmniTier Inc.

OmniTier develops software for bioinformatics, scientific computing, and
web services applications. Its integrated software solutions accelerate
data-intensive infrastructure applications, including genomic workflows,
high performance object (K-V) caching, and scientific analysis for
machine learning and AI. Founded in February 2015, the company has R&D
operations in Milpitas, CA and Rochester, MN. The OmniTier R&D team has
a proven track record of previously delivering "industry-first"
technology and products.

CompStor is a trademark of OmniTier, Inc.

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