Benzinga | Jan 10, 2022 08:32AM EST

Bionano Genomics Announces Publication Of Interim Readout From Consortium Conducting Postnatal Clinical Trial Intended To Support Establishing Optical Genome Mapping As Part Of Standard Of Care In Genetic Disease Diagnosis

Bionano Genomics, Inc. (BNGO), pioneer of optical genome mapping (OGM) solutions on the Saphyr(r) system and provider of NxClinical(tm), the leading software solutions for visualization, interpretation and reporting of genomic data, today announced the publication of the first readout from the ongoing clinical trial designed to support establishing OGM as part of standard of care (SOC) in diagnosis of genetic disease for postnatal patients. This publication reports on the postnatal genetic disease diagnostic arm of Bionano's study to evaluate OGM as an alternative to SOC workflows in four key clinical areas: prenatal and postnatal genetic diseases, hematologic malignancies and solid tumors. The studies will compare OGM to SOC, including concordance, reproducibility, technical success rates, turnaround time (TAT), diagnostic yield, health economics and patient outcomes. This first interim readout is designed to evaluate endpoints connected to analytical performance in key areas of technical performance and reproducibility of OGM.

"The process of establishing a trial program with a consortium like this one is made possible by capable principal investigators and leading sites," commented Alka Chaubey, PhD, FACMG, chief medical officer of Bionano. "We believe the trial is off to a terrific start, with a total of 813 subjects enrolled to date and as the interim readout of 202 subjects and 331 sample runs shows, OGM has performed well. We look forward to the investigators proceeding with the remaining samples and evaluating other critical endpoints like comparative diagnostic yields, turnaround times and health economic impacts."

Study Design

The study is an Institutional Review Board-approved, multicenter, double-blinded trial with 202 clinical research subjects analyzed in a total of 331 sample runs. All samples had been previously tested with traditional methods like karyotyping, fluorescence in situ hybridization (FISH) and chromosomal microarray (CMA). The samples were from cases with a genetic diagnosis (152), cases without a genetic diagnosis (6) and controls (44).

The sites conducting the study and their principal investigators are as follows:

* University of Rochester Medical Center (Dr. M. Anwar Iqbal)

* Medical College of Wisconsin (Dr. Ulrich Broeckel)

* Columbia University Medical Center (Dr. Brynn Levy)

* Greenwood Genetic Center (Dr. Roger Stevenson)

* Medical College of Georgia, Augusta University (Dr. Ravindra Kolhe)

* Praxis Genomics (Dr. Peter L. Nagy)

* University of Iowa Health Clinics (Dr. Aaron Bossler)

Key Findings

This publication describes OGM performance metrics like first pass success rate and reproducibility from site-to-site, operator-to-operator and run-to-run for the first time ever and for the largest number of samples investigated with OGM to date.

Key findings for the technical endpoints were reported as follows:

* Concordance with SOC -- 97.7% [214 out of 219 samples]

* Partially concordant with SOC -- 2.3% [5 out of 219 samples]

* Concordance with SOC for pathogenic variant calls -- 100% [219 out of 219 samples]

* Concordance with CMA -- 100% [103 out of 103 samples]

* First-pass success rate for OGM -- 94% [311 out of 331 samples]

* Reproducibility of analytical QC from site-to-site -- 98.8% [171 out of 173 replicates]

* Reproducibility of pathogenic variant calls from site-to-site -- 100% [173 out of 173 replicates]

Key Takeaways

The publication concluded that these results demonstrate high technical performance of the OGM workflow from DNA isolation through data analysis. The authors reported that replicate run performance demonstrates reproducibility of OGM, suggesting it can be adapted and validated. The authors further pointed out that OGM is not limited to copy number variation analysis alone, but can also resolve balanced structural rearrangements, size repeat expansions like FMR1 and repeat contractions like D4Z4. In summary, the authors concluded that a single approach, like OGM, can allow genetic laboratories to provide rapid results with a cost-effective solution, which can benefit both the lab and the affected individuals.

"The OGM community is evaluating the whole workflow. The performance we have seen matches our expectations and we are happy with this publication announcing that OGM is performing well across multiple sites," commented Erik Holmlin, PhD, president and chief executive officer of Bionano. "Congratulations to this team for getting this paper published in 2021 and congratulations to Dr. Chaubey on the progress of her program. I am eager to see the outcome for all trial subjects across the remaining endpoints. We believe we can change the standard of care in genetic testing with OGM and these studies can provide important supporting data."

The full publication can be found online at https://www.medrxiv.org/content/10.1101/2021.12.27.21268432v1