Clinical genomics

Clinicians today are increasingly turning to clinical genomics applications to help identify and diagnose medical conditions at all stages of a patient’s life. Before conception, carrier screening can identify recessive genetic diseases in prospective parents, and newborn screening for common metabolic disorders and inherited diseases can now be performed via genomics, augmenting traditional biochemical means. As patients age, clinicians are frequently turning to genomics to diagnose rare genetic diseases and identify susceptibilities for diseases that aren’t manifested until later in life. And advances in cancer genomics have resulted in development of new targeted therapies associated with specific genetic biomarkers.

Adoption of clinical genomics applications has been driven by increasingly scalable genomic technologies. Higher-throughput approaches to genetic testing have resulted in increased diagnostic yields and discovery coupled with advances in bioinformatic analysis tools. Because of our increase in knowledge, the decreasing cost of sequencing, and diagnostic yield increasing with the number of genes tested, single-gene tests are now being replaced by multi-gene panels, whole-exome sequencing (WES), and whole-genome sequencing (WGS).

Fabric Genomics is the pioneer of AI-driven genomic interpretation

Clinical genomic applications produce huge amounts of data in a very short time, creating new challenges in data interpretation and analysis. Genomic interpretation has become the bottleneck in clinical genomics workflows. Geneticists must perform time-consuming reviews of annotation data, literature, phenotypic databases, and the patient’s clinical details to identify the gene variants that are most likely to cause the disease. For childhood diseases and time-sensitive medical conditions where delays in treatment can be life-changing, reducing time to diagnosis can significantly improve outcomes and quality of life.

Fabric Genomics pioneered the use of artificial intelligence (AI) in clinical genomics to reduce the effort of genomic interpretation and increase the clinical utility of DNA sequencing data. Fabric Genomics published its first algorithm, VAAST, in 2011 and released the first commercially available genome interpretation platform for clinical genomics in 2014. The company has continued to improve on this platform. Their bioinformatics platform, Fabric Enterprise, enables labs to achieve the highest diagnostic yield and fastest turnaround time of any genomic analysis platform.

Fabric Enterprise: A flexible, highly scalable genomic interpretation platform

Fabric Enterprise is designed to fit into any genomics workflow. The platform can be used for WGS and WES discovery applications as well as more targeted testing using multi-gene panels. This flexibility is useful across broad genomics applications, from prenatal and newborn screening and rare disease diagnostics in childhood to later-in-life applications like carrier screening and cancer detection.

Fabric Enterprise uses two application-specific algorithms to accelerate clinical reporting – Fabric GEM and ACE. Fabric GEM delivers near-instantaneous genomic interpretation for rare disease and neonatal and pediatric intensive care unit (NICU, PICU) testing using WGS and WES data. Fabric GEM combines deep phenotypic data with genotypic data using AI and machine learning to deliver near-instantaneous identification of disease-causing variants, significantly reducing genomic interpretation time. A recent retrospective study of whole-genome cases from the NICU showed how Fabric GEM provided very short candidate gene lists, including 100% of the previously reported disease genes and variants, with 98% present in the top 5 ranked genes, saving days of analysis time while providing industry-leading results.

Fabric ACE is used with targeted panels to deliver rapid gene variant reporting. ACE is an automated ACMG-compliant classification engine for accelerating interpretation of commonly used genetic testing panels, including inherited cancers, newborn screening and ACMG incidental findings. ACE has been extensively validated with over 100,000 variants.

Fabric Enterprise is a complete end-to-end genomic data analysis solution. The platform is capable of raw data analysis and delivery of rapid, comprehensive insights for high-throughout panels, exomes, and whole genomes.

Fabric Genomics in neonatal and childhood healthcare

Studies report that 34% of children’s hospital admissions had clear genetic underlying disorders that accounted for 50% of the total hospital charges for all admitted patients. If diagnosed rapidly, many genetic illnesses can be easily treated—sometimes with something as simple as a dietary modification—leading to improved patient outcomes and substantial savings in healthcare costs.

Fabric Hereditary Panels with ACE are purpose-built for rapid testing, whether for newborn screening or panel testing for conditions such as neurodevelopmental disorders, epilepsy, hearing loss and cardiology. Fabric Enterprise also delivers in WGS and WES testing, rapidly diagnosing rare genetic diseases in pediatric hospitals.

Rapid diagnosis was critical for Sebastiana, a patient at Rady Children’s Institute for Genomic Medicine in San Diego, CA who after experiencing frequent seizures was rushed to the NICU shortly after birth. Doctors at Rady relied on Fabric Enterprise to quickly identify Sebastiana’s rare KCNQ2 gene variant, accelerating diagnosis and significantly improving patient outcome compared to traditional standard of care.

Fabric Genomics for adult testing and carrier screening

Carrier screening with Fabric Enterprise is typically performed using a panel test ranging from a small number of genes to several hundred genes, to determine the risk of having a child with a genetic disorder. Labs are also deploying panel testing with Fabric Enterprise to identify susceptibility for genetic disease as well as to diagnose and treat diseases such as cancer. In cancer risk testing, Fabric can be quickly deployed in conjunction with out of the box assays such as the Illumina TruSight Hereditary Cancer panel.

In rare disease diagnostics, Fabric Genomics is a key partner of Genomics England’s 100,000 Genomes Project, a trailblazing population genome sequencing project to sequence 100,000 genomes for rare disease and cancer. In adults, rare disease cases have included neurological disorders, cardiovascular disorders, tumor syndromes, and more. In 1973 cases analyzed, Fabric identified causative disease variants in 49.8% of cases.

DNA is the fabric of humanity

Our shared experiences in life – birth, development, parenting, and aging – are what unite us as humans. Our ability to use clinical genomics has led to an abundance of information that holds the key to improved health and wellness. Fabric Genomics is deciphering this information faster and more completely than ever before, providing actionable, clinical reporting that is already improving the lives of children and adults across the world.

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