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GeneTerpret: a customizable multilayer approach to genomic variant prioritization and interpretation
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12920_2022_Article_1166.pdf
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2.21 MB
Format
Adobe PDF
Checksum (MD5)
c323d44f15f2b4f7e62a3f3e60363158
Author(s)
Manshaei, Roozbeh
DeLong, Sean
Andric, Veronica
Joshi, Esha
Okello, John B. A.
Dhir, Priya
Somerville, Cherith
Farncombe, Kirsten M.
Kalbfleisch, Kelsey
Jobling, Rebekah K.
Date Issued
February 18, 2022
Publisher
BioMed Central
Citation
BMC Medical Genomics. 2022 Feb 18;15(1):31
Version
Final published version
Abstract
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
.
Terms of Use
Creative Commons Attribution
Persistent DSpace Link
DOI of Published Version
https://doi.org/10.1186/s12920-022-01166-3
