Functional Assessment of Variants in Organisms of Research (FAVOR) - Profiling Canonical Human Genes and their Variants through Disease Model Phenotyping. - Project Summary / Abstract
Genome wide DNA sequencing is now being adopted in clinical practice and an increasing number of variants
are identified in epilepsy-associated genes, yet the clinical interpretation of the new variants is challenging.
Some of the variants are known to be either pathological or benign, yet a majority of the gene variations remain
unknown for their functional consequence. A large number of Variant of Uncertain Significance (VUS) are
becoming commonplace in genes for human diseases, providing a significant barrier in making diagnoses and
implementing therapies. Bioinformatic approaches can provide some insight into pathogenic probability of VUS
alleles, but functional studies in animal model systems are often needed to make definitive of pathogenicity
assignments. The expense and long timelines of mouse model production make the use of alternative small
animal models attractive. In this proposal, the C. elegansnematode is used as an alternative model capable of
fast high-throughput production and screening. Human genes are installed as gene-swap replacements of the
native disease-gene homologs. In preliminary work, gene-swap humanization of STXBP1 in the unc-18locus
rescued severe locomotion and behavior defects present in the gene knock-out animals. Pathogenic variants
into the STXBP1gene-swap loci leads to significant disruption of activity. In this proposal, significant and novel
improvements are made to our existing pipeline for the functional analysis of variants in vivo. In Aim 1, the
relevance and extensibility of the C. elegans model system for studying human disease is improved through
simultaneous humanization of multiple related loci. In Aim 2, new methods are developed for molecular
phenotyping, improving the resolution of inputs pathogenicity determination algorithms, and yielding
mechanism-of-action level readouts to variant manipulations. In Aim 3, the improvements to the pipeline are
tested to quantify gains in pathogenicity determination on a test set of variants.
