The Geneyx Analysis platform enables out-of-the-box phenotype-driven interpretation of any genetic data, including structural variations (SVs), copy number variations (CNVs) and repeat regions. In a small pilot project in a Gastroenterology department in Israel, 5 families with no previous findings in gene panels were whole genome sequenced and were all diagnosed rapidly and successfully using the platform.​

The Geneyx Analysis platform enables out-of-the-box phenotype-driven interpretation of any genetic data, including structural variations (SVs), copy number variations (CNVs) and repeat regions. In a small pilot project in a Gastroenterology department in Israel, 5 families with no previous findings in gene panels were whole genome sequenced and were all diagnosed rapidly and successfully using the platform.

Top pediatric hospitals around the world are using Geneyx Analysis to analyze thousands of rare genetic disorder cases annually. Recently, exome sequencing and even whole genome sequencing (WGS) are beginning to see adoption in additional fields of medicine such as cardiology, neurology, cancer predisposition and others. Clinicians in these areas rarely have access to the same infrastructure and expert teams, but wish to similarly apply genetic sequencing for the diagnosis and identification of causal variants in their patients.

From gene panels to Exome-Seq to WGS

Prof. Kariv from the Department of Gastroenterology, Tel-Aviv Sourasky Medical Center (TSMC) in Israel routinely meets patients presenting with early polyposis of the gastro-intestinal tract which can lead, if not treated, to cancer. When presented early in life or when found in several members of a family, this condition is assumed to have strong genetic background. Accordingly, such patients and their families are typically tested using a dedicated gene panel. However, only ~30% end up with a clear diagnosis, i.e. identifying the genetic mutation that causes predisposition to polyposis. Such diagnosis is critical as it can lead to more personalized treatment for the patient and can even be used for future family planning.

Feeling that 30% diagnostic yield for clear genetic polyposis cases cannot be acceptable in the era of low-cost, highly available genetic sequencing, Prof Kariv launched a small pilot program, with 5 families presenting early hamartomatous polyposis. These families would be whole genome sequenced, and deep analysis of all genetic variants across their 3 billion bases of their DNA would be used to try to identify the genetic cause of their early predisposition to the disease.

Seamless WGS analysis and interpretation

The GI department at TSMC has neither bioinformatics team that can handle the raw sequencing data, nor the experience in analyzing the thousands of genetic variants resulting from such an operation.

As of the completion of the sequencing by their sequencing provider, Geneyx Analysis automatically downloaded the raw genetic data, ran the rapid DRAGEN primary and secondary pipelines and quality control processes, including structural variation and CNV calling, and prepared fully annotated cases for analysis and interpretation by Dr. Kariv and her team. All that remained was to enter the phenotypes of the patients.

Remarkably, the genetic culprit was detected in all 5 cases, presenting the subsequently validated causal events at the highest ranks, out of tens of thousands of called variants. This included a loss-of-function SNV in BMPR1A (for this proband the suspected gene was SMAD4 for which Sanger sequencing produced no clinically significant finding) and three SV events – two distinct cases of inversions, one affecting BMPR1A and the other affecting STK11, and a deletion in BMPR1A identified in two unrelated probands of a common ethnic origin, a possible founder mutation.

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