It’s been a busy week for Fabric Genomics. During the annual meeting of the American Society for Human Genetics in Washington DC this week, the company announced deals with both Oxford Nanopore Technologies and DNAnexus that are aimed at supporting the use of genomic information in clinical contexts.
Fabric’s collaboration with Oxford Nanopore is focused on providing a joint solution for deployment in CLIA/CAP labs that supports the use of nanopore sequencing in neonatal and pediatric intensive care units. Specifically, the combined solution, which integrates Oxford Nanopore’s EPI2ME software with Fabric’s GEM solution, will help clinicians characterize genetic disorders in babies and children. Customers of the combined solution will be able to directly upload variant call files from EPI2ME directly into GEM. Clinicians will receive a ranked list of annotated variants and generate reports through an interactive interface.
The initial focus of this partnership is on testing cases in the NICU because of the higher frequencies of monogenic diseases—more than 40%—compared to 30% in outpatient cases. “For this incredibly high-risk patient population, speed and data-rich insights matter,” said Gordon Sanghera, PhD, CEO of Oxford Nanopore Technologies. “We are excited to team up with Fabric Genomics to develop an end-to-end analysis tool for the clinical reporting of nanopore sequencing data in pediatric care settings that will make it easier for healthcare providers to leverage genetic insights and, in the future, support the health and wellbeing of children and families.”
The company shared details of the combined solution and some initial results from their collaboration during ASHG in one of the CoLab sessions. Kamran Shazand, PhD, the Director of the Genomics Institute at Shriners Children’s Hospital, described a study involving adolescent idiopathic scoliosis—the most common form of the disease accounting for 80% of cases. According to Shazand, they collected 10 samples from patients and sequenced them using ONT sequencers followed by analysis with the combined software platform. For comparison, they sequenced the same samples with short read sequencing technology and analyzed the data using an internal pipeline.
Using ONT and Fabric technology, they observed three variants of interest in conditions like Noonan syndrome and chondrodysplasia, two of which were confirmed by short read sequencing and analysis, Shazand said. Specifically, the found variants in NF1, COL6A2, and EBP. The variants in NF1 and EBP were confirmed by analysis with short reads. However verification using short reads for the COL6A2 variant is pending.
The combined platform is available on a limited basis via an early access program to customers. It will be widely available in Q1 2024.
Fabric also announced a strategic collaboration with cloud-based data management company DNAnexus to provide tools that help hospitals, clinical laboratories, and academic centers rapidly access and analyze large-scale clinical whole genome data. Under the terms of the agreement. Fabric will integrate its genomic analysis tools and AI engine with DNAnexus’ Precision Health Cloud. According to Fabric, customers of the combined solution will be able to interpret genomic sequences, detect clinically meaningful variants, and generate comprehensive patient reports.
DNAnexus actively manages and supports more than 80 petabytes of complex clinical genomic, proteomic, and other multi-omic datasets on behalf of a growing network of collaborations with leading pharmaceutical, clinical diagnostic, academic research, biobank, and government organizations. Reports generated by Fabric not only pinpoint candidate genes, but also rank diagnoses based on a patient’s clinical information and probabilistic disease matching. This approach ensures that clinical teams can focus on the most plausible diagnoses to help optimize patient care.
Fabric’s platform is used in academic medical centers and commercial laboratories such as Rady Children’s Institute for Genomic medicine and the Broad Clinical Labs. “The technology advances and cost reduction in genomics sequencing is generating an even larger data management and analysis bottleneck for clinical genomics labs,” according to Martin Reese, PhD, Fabric’s CEO and co-founder. “Combining Fabric Genomics’ clinical expertise with the leading data management solution provided by DNAnexus, allows us to further clinical genomics.”