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Appistry Awards Inaugural Pipeline Challenge Prize to the Shivanand R. Patil Cytogenetics and Molecular Laboratory

Proposed NGS quality control pipeline will reduce costs and lower turnaround times for common genetic tests.

by Appistry
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ST. LOUIS—October 6, 2014 - Appistry, Inc., a leading provider of tools, software, and services that bring the power of genomics to next-generation medicine, has selected the winner of its inaugural Appistry Pipeline Challenge. A project team led by Dr. Benjamin Darbro, director of the Shivanand R. Patil Cytogenetics and Molecular Laboratory at the University of Iowa Hospital and Clinics, will receive a complete hardware and software system from Appistry for developing and executing a unique pipeline intended to reduce the costs and turnaround times associated with next-generation sequencing (NGS)-based genomics testing.

The winning pipeline will integrate the results of a concurrently run NGS assay (i.e., whole exome sequencing) and a SNP containing chromosomal microarray (CMA) to calculate patient specific, genome-wide, NGS-performance metrics (e.g., sensitivity, specificity, positive and negative predictive value) for various types of genetic variations detectable by the CMA platform. These performance metrics are intended to alleviate the need for confirmatory assays using conventional Sanger sequencing.

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“Variant confirmation by conventional sequencing is currently one of the most costly drawbacks to clinical NGS testing,” said Darbro. “These additional assays add to the costs and lengthen the turnaround time for sequencing. A pipeline that helps reduce those costs will be especially important to clinical laboratories that are having difficulty being reimbursed for clinical molecular testing.”

The proposed pipeline will leverage standard NGS analysis tools provided by Appistry, specifically the Genome Analysis Toolkit (GATK), along with other commercial and open-source tools and a tool developed by the Cytogenetics and Molecular Laboratory called CNV-ROC. The Appistry tools are included as part of Appistry’s Ayrris On Ramp Program for NGS Analysis, which provides a developer workstation capable of processing 200 Gbases per day, Appistry’s Ayrris® software for developing and executing NGS pipelines, and preconfigured analysis tools and starter pipelines. Appistry is also providing a MacBook Air or iPad Air to Dr. Darbro to facilitate his personal research.

“Our goal in sponsoring the Appistry Pipeline Challenge was to inspire and support innovation that will advance the utility and impact of NGS in clinical labs,” said Dr. Rich Mazzarella, chief scientific officer at Appistry and chair of the judging panel for the Pipeline Challenge. “There is enormous promise in the pipeline proposed by Dr. Darbro, and we look forward to assisting in its development over the coming year.”

Part of the Carver College of Medicine and the Stead Family Department of Pediatrics, the Shivanand R. Patil Cytogenetics and Molecular Laboratory, within the Division of Medical Genetics, serves the University of Iowa Hospitals and Clinics, the University of Iowa Children’s Hospital, and several hospitals and healthcare practices across the state of Iowa. The laboratory is CAP accredited and CLIA certified and performs over 5,000 clinical tests per year using both conventional and high throughput genomic technologies for prenatal and postnatal genetics and molecular oncology diagnostics and prognostics.