22 research outputs found
P619: Three years of newborn screening for MPS1 in Ontario: Challenges of screening for the severe end of a disease continuum
Incidence and risk factors of herniated lumbar intervertebral disc or sciatica leading to hospitalization
P169: Characterizing the phenotypic spectrum and estimated penetrance of families with pathogenic loss of function variants in the FLT4 gene
Comparison of survival among patients with breast cancer treated at First Teaching Hospital, Changchun, China, and Saint-Sacrement hospital, Quebec, Canada
GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation
Abstract
Background
Variant interpretation is the main bottleneck in medical genomic sequencing efforts. This usually involves genome analysts manually searching through a multitude of independent databases, often with the aid of several, mostly independent, computational tools. To streamline variant interpretation, we developed the GeneTerpret platform which collates data from current interpretation tools and databases, and applies a phenotype-driven query to categorize the variants identified in the genome(s). The platform assigns quantitative validity scores to genes by query and assembly of the genotype–phenotype data, sequence homology, molecular interactions, expression data, and animal models. It also uses the American College of Medical Genetics and Genomics (ACMG) criteria to categorize variants into five tiers of pathogenicity. The final output is a prioritized list of potentially causal variants/genes.
Results
We tested GeneTerpret by comparing its performance to expert-curated genes (ClinGen’s gene-validity database) and variant pathogenicity reports (DECIPHER database). Output from GeneTerpret was 97.2% and 83.5% concordant with the expert-curated sources, respectively. Additionally, similar concordance was observed when GeneTerpret’s performance was compared with our internal expert-interpreted clinical datasets.
Conclusions
GeneTerpret is a flexible platform designed to streamline the genome interpretation process, through a unique interface, with improved ease, speed and accuracy. This modular and customizable system allows the user to tailor the component-programs in the analysis process to their preference. GeneTerpret is available online at
https://geneterpret.com