Systematically and proactively testing variant effects for AIRE and SOD1

Despite the potential for personalized genomic medicine, clinical geneticists are often unable to determine the pathogenicity of rare variants in disease-associated genes. Under current guidelines, one of the strongest forms of evidence for variant annotation comes from (often cell-based) functional assays of variant impacts. One-at-a-time variant functional assays are the current standard, where results often lag months or years after a rare variant has first been detected in a patient. Variant effect ‘maps’ are ‘look-up tables’ which have recently been made possible by advances in cellular engineering and next-generation sequencing. Variant effect maps present proactive functional evidence for nearly all possible rare variants– even for those that have not yet been seen in the clinic. I led the generation, validation, characterization variant effect maps for two disease-associated genes: 1) the autoimmune regulator (AIRE), which is implicated in autoimmune polyendocrine syndrome type 1 (APS-1); and 2) superoxide dismutase 1 (SOD1), which is implicated in amyotrophic lateral sclerosis (ALS). The resulting variant effect map of AIRE missense variants, using an insulin promoter-driven reporter assay, agrees with previously reported biochemical expectations and current pathogenicity annotations, identifies novel gain-of-function variants, and generates proactive evidence to inform variant interpretation. Two variant effect maps were produced for SOD1, based on both a human-cell based abundance and yeast-based enzymatic activity assay. The abundance map is concordant with biochemical expectations and reveals novel sequence-structure findings. Validated variant effect maps of AIRE and SOD1 have promise to provide proactive evidence with the potential to improve patient outcomes by providing more rapid and definitive genetic diagnoses of APS-1 and ALS.

Department dc:contributor.department

Molecular Genetics

Year dc:date.issued

2024

Author dc:creator

• Axakova, Anna

Advisor dc:contributor.advisor

• Roth, Frederick

• functional genomics
• variant effect mapping

Statement dc:rights

• Attribution 4.0 International

Licence dc:rights.uri

• http://creativecommons.org/licenses/by/4.0/

Handle dc:identifier.uri

https://hdl.handle.net/1807/142823

OAI identifier oai:identifier

oai:utoronto.scholaris.ca:1807/142823