Left to right: – Senior Research Scientist Silvia Casadei, MD-PhD Student Moez Dawood, and PhD Student Shawn Fayer
BBI will be well-represented at the upcoming conference of the Impact of Genomic Variation on Function, (IGVF), September 21 through 23, with presentations by three researchers.
The three – Senior Research Scientist Silvia Casadei, MD-PhD Student Moez Dawood, and PhD Student Shawn Fayer – will discuss their work on variants of unknown significance and saturation genome editing.
“This conference is an opportunity to spotlight three of BBI’s rising stars in genome science,” said Dr. Lea Starita, assistant professor and co-director of the BBI Advanced Technology Lab.
IGVF was established in 2021 by the National Human Genome Research Institute (NHGRI). It is a national collaborative effort focused on exploring how genomic variation alters genome function, and influences human health and disease.
Here are summaries of the three scientists’ presentations:
Silvia Casadei: Saturation genome editing (SGE) is an important and promising tool for measuring massive numbers of variants in clinically actionable genes. It is critical for the interpretation of genetic variants identified through clinical sequencing. Single nucleotide variants are edited directly into the genome to measure the effects on the survival of cells and to distinguish functionally normal from functionally abnormal variants. The assay lends itself to standardization and at-scale production and, since its original development, SGE today is more accurate and scalable through advances in optimizing workflows and increased production.
“Ultimately, we hope that comprehensive functional datasets of variant effect in clinically relevant genes will inform medical management and meaningfully impact patients’ diagnostic course, from early prevention to targeted treatment, fulfilling the promise of precision medicine,” said Casadei.
Moez Dawood: Partner and Localizer of BRCA2 (PALB2) functions in homology-directed repair of double-stranded DNA breaks, promotes nuclear localization and stability of BRCA2, and enables cell cycle checkpoint functions. Pathogenic variants in PALB2 have been implicated in breast, ovarian, and pancreatic cancer. In 2021, PALB2 was elevated to the 73 medically-actionable genes by the American College of Medical Genetics and mandated that secondary findings be reported to patient providers.
However, with 99 percent of more than 1,875 PALB2 missense single nucleotide variant (SNV) alleles classified as variants of uncertain significance (VUS) in ClinVar, the majority of variants in PALB2 still remain uninterpretable and, thus, are not practically implementable for guiding disease management. Saturation Genome Editing was used to investigate the effect of all possible 10,683 SNVs in PALB2 on cell survival. Within the N and C terminal functional domains required for binding RAD51, BRCA1, and BRCA2, 12 percent of missense SNV alleles result in decreased PALB2 function that compromises cellular viability.
“We have demonstrated SGE functional scores are poised to have a major impact on clinical variant interpretation for PALB2,” said Dawood.
Shawn Fayer: The clinical utility of genetic testing is limited by the inability to predict the consequence of most missense variants on the function of a gene. As a result, most missense variants interpreted clinically are variants of uncertain significance (VUSs), or genetic variants whose ability to cause disease is unknown. Thus, these VUSs are not used in guiding medical decision making. Multiplexed assays of variant effect (MAVEs) represent an emerging technology aimed at reducing the number of VUSs in clinical genetic testing. Thousands of missense variant effects are simultaneously measured experimentally, providing evidence that can help resolve VUSs.
To quantify the impact of the multiplexed functional data generated regarding clinical variant interpretation, we systematically integrated previously published BRCA1, TP53, and PTEN multiplexed functional data with 324 VUS interpretations from a single clinical genetic testing laboratory. Multiplexed functional data were effective in driving variant reclassification when combined with clinical data, eliminating 49 percent of VUSs for BRCA1, 69 percent for TP53, and 15 percent for PTEN.
“Collaboration among key stakeholders, including diagnostic laboratories, variant curation expert panels, population database curators/biobanks, and functional assay developers, will be necessary to increase the number of pathogenic and benign variants for assay validation,” Fayer said. “Addressing this challenge will significantly improve evidence strength achievable by MAVEs, improving their utility in clinical variant interpretation.”
