Date: May 18, 2012 Source: (
click here to go to the source)
SimulConsult,
a bioinformatics company based in Chestnut Hill, Mass., is
marketing a new software tool called the Genome
-
Phenome Analyzer, which lets
clinicians and research labs combine whole
-
ge
nome and whole
-
exome
sequencing data with clinical findings and phenotype information from the
scientific literature.
Lynn Feldma
n, CEO, explained to
BioInform
that SimulConsult developed the
software to automatically correlate patients' clinical findings
and bioinformatics
analysis results with phenotype information, a step that is usually done manually.
Genome
-
Phenome Analyzer, which was launched in March, enables clinicians to
assess and prioritize which gene variants are most likely to account for the
clinical findings, the company said.
It uses information from SimulConsult's curated phenome database, clinical
findings, and a table of associated variants generated by whole
-
exome
sequencing to compute a differential diagnosis for patients using propriet
ary
statistical pattern
-
matching algorithms.
The software reads information in the variant table generated by the initial
bioinformatics analysis of a patient's genomic information, and imports the
Human Genome Nomenclature Committee code for the gene, the
severity of
each variant, and the zygosity of the variant. This information is then matched
with the clinical findings for the patient as well as information culled from the
literature.
With this tool users can detect autosomal dominant and autosomal rece
ssive
diseases as well as deal with complex situations involving compound
heterozygosity, for instance. It can also be used to identify difficult
-
to
-
detect
genetic variants such as trinucleotide repeats and large copy number variants.
Clinicians can then t
ake the results generated by the system and run further
tests, such as additional Sanger sequencing, to obtain more information about a
variant in question, or they can check familial information in cases of inherited
diseases, Feldman said.
Genome
-
Phenome
Analyzer builds on medical decision
-
support software
previously developed by the company to enable clinicians to combine clinical and
laboratory findings to come up with a diagnosis for their patients.
The medical decision support system prioritizes disea
ses based on pertinent
positive and negative findings, as well as the onset and disappearance of each
finding, family history, and incidence of diseases.
That system also includes SimulConsult's database
—
focused primarily on
genetic neurological and meta
bolic diseases, although it is being expanded
—
which is populated by information from about 1,400 sources including
GeneReviews and GeneTests as well as several textbooks and articles.
Before public information is entered into the database, it is manually
curated by
medical specialists and sub
-
specialists, Feldman said. In addition to ensuring
that the information entering the repository is of good quality, the manual curation
step also ensures that clinical findings that may not be explicitly reported in
the
medical literature or that may be rare occurrences in patient populations are
captured and added to the database, she said.
Clinicians can contribute information about clinical findings and diseases to the
database, which is freely available. Contribut
ed information is subject to the
same curation process as public sources before it's entered into SimulConsult's
database.
Since the tool's initial debut at American College of Medical Genetics annual
meeting in March, Feldman said that it has received "co
nsiderable interest." So
far the company has signed one contract with a CLIA lab and is in the process of
signing additional contracts for evaluation pilots, although she could not disclose
who these groups are.
She said the company offers seat
-
based licen
ses for small research labs and site
licenses for larger CLIA labs but declined to provide pricing details.
SimulConsult was founded in 1998 by Michael Segal, a pediatric neurologist who
formerly worked at the Children's Hospital Boston and now serves as t
he
company's chairman and chief scientist. The firm launched its first product, a
database and the decision support software, in 2006.
Although the use of the database is free, that could change, Feldman said. The
company currently charges for integrating
its resource with physician order
-
entry
platforms, she said.
It is also working on integrating the system with an electronic health record
system in a clinic but Feldman could not disclose additional details.
Currently, the company has less than ten employ
ees and it plans to hire more
staff including a chief medical officer and a sales person in the next few months,
Feldman said.
The company also hires a large number of contractors to curate the information
that goes into its database, she said.
