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Bionano Genomics, Inc. (NASDAQ: BNGO), pioneer of optical genome mapping (OGM) solutions on the Saphyr® system and provider of NxClinical™, the leading software solution for visualization, interpretation and reporting of genomic data, today announced the first publication demonstrating OGM as an alternative to karyotyping (KT) for products of conception (POC) sample analysis.
Chromosomal abnormalities are the most common cause of early pregnancy loss and at least 5% of women trying to conceive face recurrent pregnancy loss with two or more consecutive miscarriages. According to current medical guidelines, KT and chromosomal microarray (CMA) can be performed on POC to determine the etiology of a loss and identify potential inherited causes. However, KT requires cultured cells, which are difficult to obtain with POC samples, and as a result, KT test failures are frequent. In addition to failing to culture, POC samples are highly heterogeneous and frequently contaminated with maternal cells, making any cytogenetic or molecular analysis challenging.
In this preliminary study, published as a preprint in medRXiv, researchers devised a novel workflow that eliminated the need for tissue culture by using OGM as an alternative to KT for comprehensive SV analysis, thereby circumventing the most common failure mode of POC analysis. Previous studies have demonstrated that OGM is highly concordant with KT, and because of its higher resolution, OGM often identifies additional genetic aberrations missed by other methods. The study workflow also describes a way to rescue samples that are contaminated with maternal cells through a combination of microdissection of formalin-fixed, paraffin-embedded (FFPE) POC samples followed by microarray analysis. OGM was not tested on the microdissected FFPE samples.
Overall, the preliminary study results showed that the new workflow using both OGM and CMA provided results in 93% of cases vs. 9.6% for workflows using KT and CMA, and identified genetic aberrations in 45.1% of samples compared to only 6.4% of samples with KT and CMA.
“POC samples are some of the most challenging samples I have ever dealt with in the lab. It’s frustrating and emotionally draining not to be able to get results to families asking why they had a pregnancy loss,” remarked Alka Chaubey, PhD, FACMG, Chief Medical Officer of Bionano. “It fills me with hope when I see indications of how OGM and other advanced molecular methods can significantly improve test success rates, and I am very proud to have worked on this approach with Dr. Kolhe and his team at Augusta University.”
Erik Holmlin, PhD, president and chief executive officer of Bionano commented, “This study shows early-stage work in an area that we believe may prove to be very helpful to hopeful parents struggling with pregnancy loss. There is more work to do, but Dr. Kolhe and his team have brought a pioneering spirit to devising and testing this new method and the data show it may have a dramatic impact on analytical success rates as compared to standard workflows. We are eagerly awaiting their results as they extend this work to include more subjects and different iterations of the workflow.”
This publication is available at: https://www.medrxiv.org/content/10.1101/2022.02.03.22269494v1
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