Researchers seek to accelerate genome interpretation
Written by Kirsty Oswald, Science Writer
Researchers have developed an all-in-one platform for genome interpretation to help accelerate the prioritisation of genomic variants, as reported in BMC Medical Genomics.
The team say their platform, known as GeneTerpret, can help cut the gene interpretation process down from hours to minutes and could help boost accuracy.
“GeneTerpret is a user-friendly visual analytics platform that utilizes information from a variety of databases and modules to assist speeding up the laborious process of genome variant interpretation,” write Roozbeh Manshaei from The Hospital for Sick Children in Toronto, and colleagues.
Testing speed and accuracy
The researchers showed that the time to investigate single nucleotide variants in a trio of genomes from family members took 3 to 10 hours using manual interpretation methods, and this was reduced to 15 to 20 minutes using GeneTerpret.
They also examined the accuracy of their platform, by comparing their results to established datasets. This showed an 83.5% concordance for pathogenic or likely pathogenic variants with the DECIPHER database and 97.2% concordance with ClinGen in identifying moderate or strong evidence for a gene-disease relationship.
Creating a new platform
The platform can analyse data from a single, trio or cohort of genomes and from this produces a prioritised list of single nucleotide variants that are of interest for the researcher to further investigate.
The team developed the platform by combining data and computational tools so that data gathering, comparison and filtration steps of gene variant interpretation can be automated.
They caution, however, that their platform does not obviate the need for a human interpreter, but can significantly reduce the time required by an interpreter to sift the data.
There are already packages available that, like theirs, offer phenotype-driven variant prioritisation. But the team believe theirs is more user-friendly and accessible for routine use.
A boost to concordance?
Gene variant interpretation can be a time consuming and tedious process and, although tools have been developed to help accelerate it, discordance commonly occurs between labs and groups. Therefore, the team say, creating a unified platform for variant interpretation could help standardise the process.
“Platforms like GeneTerpret can ultimately help to improve accuracy and reduce the interlab variability in variant interpretation,” they conclude in BMC Medical Genomics.
Image Credit: Canva
