Saturation mapping of MUTYH variant effects using DNA repair reporters DOI Creative Commons
Shelby L. Hemker, Ashley P.L. Marsh,

Felicia Hernandez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 6, 2025

Variants of uncertain significance (VUS) limit the actionability genetic testing. A prominent example is MUTYH , a base excision repair factor associated with polyposis and colorectal cancer, which has pathogenic variant carrier rate approaching 1 in 50 individuals some populations. To systematically interrogate function we coupled deep mutational scanning DNA reporter containing its lesion substrate, 8OG:A. Our variant-to-function map covers >97% all possible point variants (n=10,941) achieves 100% accuracy classifying pathogenicity known clinical (n=247). Leveraging large registry, observe significant associations polyps more severely impaired missense conferring greater risk. We recapitulate functional differences between founder alleles, highlight sites complete intolerance, including residues that intercalate coordinate essential Zn 2+ or Fe-S clusters. This provides resource to resolve 1,032 existing VUS 90 conflicting interpretations demonstrates scalable strategy other clinically relevant factors.

Language: Английский

Functional evaluation and clinical classification of BRCA2 variants DOI Creative Commons
Huaizhi Huang, Chunling Hu, Jie Na

et al.

Nature, Journal Year: 2025, Volume and Issue: unknown

Published: Jan. 8, 2025

Germline BRCA2 loss-of function variants, which can be identified through clinical genetic testing, predispose to several cancers1–5. However, variants of uncertain significance limit the utility test results. Thus, there is a need for functional characterization and classification all facilitate management individuals with these variants. Here we analysed possible single-nucleotide from exons 15 26 that encode DNA-binding domain hotspot pathogenic missense To enable this, used saturation genome editing CRISPR–Cas9-based knock-in endogenous targeting human haploid HAP1 cells6. The assay was calibrated relative nonsense silent validated using benign standards ClinVar results homology-directed repair assay7. Variants (6,959 out 6,960 evaluated) were assigned seven categories pathogenicity based on VarCall Bayesian model8. Single-nucleotide loss-of-function associated increased risks breast cancer ovarian cancer. integrated into models ClinGen, American College Medical Genetics Genomics, Association Molecular Pathology9 Using this approach, 91% classified as or likely benign. These improve variant. Results comprehensive evaluation particularly significance, provide useful resource who carry such

Language: Английский

Citations

2
Saturation mapping of MUTYH variant effects using DNA repair reporters DOI Creative Commons
Shelby L. Hemker, Ashley P.L. Marsh,

Felicia Hernandez

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2025, Volume and Issue: unknown

Published: March 6, 2025

Variants of uncertain significance (VUS) limit the actionability genetic testing. A prominent example is MUTYH , a base excision repair factor associated with polyposis and colorectal cancer, which has pathogenic variant carrier rate approaching 1 in 50 individuals some populations. To systematically interrogate function we coupled deep mutational scanning DNA reporter containing its lesion substrate, 8OG:A. Our variant-to-function map covers >97% all possible point variants (n=10,941) achieves 100% accuracy classifying pathogenicity known clinical (n=247). Leveraging large registry, observe significant associations polyps more severely impaired missense conferring greater risk. We recapitulate functional differences between founder alleles, highlight sites complete intolerance, including residues that intercalate coordinate essential Zn 2+ or Fe-S clusters. This provides resource to resolve 1,032 existing VUS 90 conflicting interpretations demonstrates scalable strategy other clinically relevant factors.

Language: Английский

Citations

0