Fabric Genomics Inc.
Democratizing Genomics with AI

Fabric Genomics was founded in 2009 with the vision of generating meaningful clinical insights through genomic analysis. It is a company that focuses on precision medicine powered by genomics. In a recent interview with Francisco De La Vega Ph.D., SVP of Genomics at the company, we talk about the increasing use of genomics in clinical diagnostics and how Fabric’s technologies enable rapid and accurate analysis and interpretation of genomic data.

What are the challenges that customers face in the industry and how do you address them?

There are some major challenges for those who are trying to implement and scale clinical-based sequencing. First, there is a complexity problem. For those sequencing exomes or genomes, there are tens of thousands or even millions of genetic variants identified, most of which are not relevant to the patient’s disease. The variants need to be augmented with the prior knowledge that exists in biomedical variant databases to enable accurate analysis. This annotation is time-consuming and requires pulling data from many different sources, thus to be scalable and fast this process needs to be fully automated. In addition, experts trained in clinical genome interpretation are very hard to come by, and the interpretation of this data is laborious—reviewing the different variants in detail is time-consuming and a major driver of the cost of the test.

Given these issues, an ideal informatics solution aims to reduce the time clinicians spend looking at each case. Since Fabric Genomics’ founding, we have focused on AI-based techniques that eliminate most of the non-relevant variants from the process, so clinicians can focus on a short list of variants most likely responsible for the disease. We have also built a highly scalable platform that consolidates up-to-date information from more than 90 different public and private databases and manages the clinical interpretation workflow in an easy to use interface. Our AI approach has led to a huge reduction in cost as well as a much better turnaround time.

Can you tell us about Fabric Genomics and what the company does?

The focus of Fabric is to solve one of the most challenging problems in genome medicine: accurately analyzing and interpreting genomes at scale to inform diagnostics and enable precision medicine. Since its inception, Fabric Genomics has been focused on applying machine learning, and in general Artificial Intelligence techniques, to enable rapid, accurate analysis. The company started in the genetic diseases area, with analysis of whole genomes, exomes as well as gene panel tests. We have recently expanded to cancer testing, including identifying approved therapies and clinical trials based on genomic markers, so we now provide a single analysis and interpretation platform for all next-generation sequencing based testing.

The company is based in Oakland, California, in the heart of Silicon Valley which is a hub of software and biotech innovation.

Can you tell us about Fabric Enterprise?

Fabric Enterprise is our clinical-grade software platform for interpretation and clinical reporting, where we have embedded our AI methodologies. It is a single platform that supports multiple applications and incorporates associated algorithms for different use cases. For example, an application can be diagnostic odysseys—where a child has been sick but the disease has gone undiagnosed for years, and where the child has had different diagnostic tests with multiple care providers. The child might have a rare genetic disease; however, because they may have only had biochemical or single gene panel testing, the child’s disease goes undiagnosed. If the child gets exome testing, a clinical lab can utilize our platform and its AI algorithms to quickly identify the most likely diseased genes in about 50 percent of the cases (up from 30 percent industry average), then complete interpretation of this data and generate a meaningful report all within our software.

Another example is gene panel testing which may be used when a patient is concerned about their hereditary cancer risk. With Fabric Enterprise, a clinical lab can quickly analyze the data, identify pathogenic variants, and report on the test results from either a targeted panel assay or an “in silico” panel derived from whole genome or exome data, for a specific set of genes associated with hereditary cancer risk.

Fabric Enterprise was built with the needs of the clinical lab in mind, including configurable standard operating procedures within the software, audit capabilities, robust API for integration with LIMS and EMR, and enterprise security features.

Can you provide a case study that highlights Fabric Genomics’ solution?

One of our customers—Rady Children’s Hospital in San Diego—pioneered the idea that babies in the ICU could be diagnosed using next-generation sequencing as a first line test. Every day spent in the ICU is expensive, and every day without a diagnosis increases the risk of mortality and impacts the baby’s long-term outcome. So Rady developed a fast, whole genome sequencing protocol where they can deliver clinical insights to the physician in an average of three days and in some cases in as little as 20 hours–where previously results could take weeks or even months. This fast methodology includes a convergence of technologies: the sequencing instrument is run in fast-mode, while Fabric provides a “STAT” analysis product that guarantees annotation for whole-genome data in less than an hour. Fabric’s algorithms take the phenotype information from the child and the genomic information, and merges this data in a probabilistic fashion using our proprietary AI algorithms, then displays the results in an easy-to-use interface and workflow that enables the clinical lab to analyze and classify the variants relevant to the patient using clinical guidelines from the American College of Medical Genetics. Through the Fabric platform, Rady was able to fulfill their main requirement—rapid turnaround time for whole genome testing.

What does the future look like for Fabric Genomics?

Fabric Genomics is excited by the adoption of next-generation sequencing for diagnostic use in the clinic, and we are continuing to advance our platform to ensure more clinics can make efficient use of genomic sequencing for disease diagnosis, prevention, and treatment. One of our core value propositions is automation and speed with high accuracy. We continue to invest in improving our AI methods to automate more reports and reduce clinician time, and plan to announce some exciting developments for panel testing in early 2019. This will include enhanced capabilities for our classified variant database, a repository of variants previously reported in the system. From a customer perspective, we are seeing growth in clinical reference labs and hospital labs, as well as country sequencing programs. We will continue to expand our offering to support the enterprise requirements of these organizations.