28 May 2015

Cypher Genomics and Clinic for Special Children Collaborate on Rare Disease Study

Cypher’s Mantis™ software to provide genomic interpretation of Amish and Mennonite population

SAN DIEGO – May 28, 2015 – Cypher Genomics, Inc., the leading genome informatics company, and the Clinic for Special Children today announced a collaboration in which Cypher’s automated genomic interpretation tools will be utilized for the diagnosis of rare genetic diseases among a unique population. Located in Strasburg, Pennsylvania, the Clinic for Special Children (CSC) serves many Amish and Mennonite patients, a founder population with a relatively high incidence of genetic disease.

“We are very excited to partner with such a distinctive and highly regarded organization,” said Ashley Van Zeeland, Ph.D., co-founder and CEO of Cypher Genomics. “In this unique setting, it will be critical to account for population-specific genetic variation in order to obtain an accurate interpretation for each patient. This is precisely why we designed Mantis to be flexible and adaptable to each of our partner’s needs, and we look forward to demonstrating the value of incorporating local reference data into our interpretation system.”

“A validated automated solution to interpret our genomic data will enable us to return results to more patients than we otherwise could with our current methods, which are both time and labor intensive,” said Dr. Erik Puffenberger, Laboratory Director, Clinic for Special Children. “Because the software will be tailored to our patient population, we also expect to have an increased level of confidence that we are getting to the correct answers.”

The collaborative study will be both retrospective and prospective. In the retrospective arm, Cypher will apply its Mantis™ software platform to validate its fully automated interpretation against CSC patients with a confirmed diagnosis. These cases consist of single genome, trio (patient plus parents), and large family analysis. The aim of this phase of the project will be to establish a baseline sensitivity and specificity profile before refining the software to account for allelic frequencies specific to CSC’s patient population, which the clinic can then apply to analyze new cases in a prospective study arm. In both arms, Cypher’s software will be utilized to interpret all categories of variants commonly observed in human genomes, including SNPs (single nucleotide polymorphisms), indels (insertions and deletions) and CNVs (copy number variations).

“It is well known from population studies that genetic variant frequencies vary widely across different global and founder populations, which can affect interpretation,” said Van Zeeland. “A general working assumption is that variants that are frequent in a population are likely to be harmless, whereas rare variants are considered more likely to be potentially disease-causing.”

This assumption can be compromised, however, if an individual’s genome is compared to and interpreted against a reference genome from a population with different characteristics. For example, genomes from African individuals contain variants not seen in genomes from European or Asian individuals. Interpreting a genome from an African individual against a European reference would mark many variants as rare, simply because they are absent from the reference, when in fact they can be quite common and harmless in the relevant population.

“These types of false positives have been a problem for us,” said Dr. Puffenberger. “When you are trying to get to the root cause of a disorder you have never seen before so you can recommend an appropriate therapy, you don’t want to lose valuable time.”

About Cypher Genomics

Cypher Genomics is a leading genome informatics company offering a highly accurate, rapid and robust interpretation software solution for users of human genome sequencing. The proprietary, automated genomic interpretation platform allows clinical laboratories to tune Cypher Genomics’ market leading sensitivity and specificity profiles to develop molecular tests for diagnostic and prognostic use and pharmaceutical companies to discover biomarkers from whole genome sequence data in sample sizes typical of early stage drug development studies. Through MantisTM, the genome interpretation software as a service offering, and CoralTM, a biomarker discovery service, Cypher Genomics can improve health care and reduce costs by facilitating improved diagnostic accuracy and earlier interventions, optimizing therapeutic approaches and reducing adverse drug reactions. Cypher Genomics is located in San Diego, California.

About the Clinic for Special Children

The Clinic for Special Children is a non-profit medical service predominantly for Amish and Mennonite children with genetic disorders. The clinic serves children by translating advances in genetics into timely diagnoses and accessible, comprehensive medical care, and by developing better understanding of heritable diseases. For more information, please visit: https://clinicforspecialchildren.org.