GeneTalk: an expert exchange platform for assessing rare sequence variants in personal genomes

Abstract

Summary: Next-generation sequencing has become a powerful tool in personalized medicine. Exomes or even whole genomes of patients suffering from rare diseases are screened for sequence variants. After filtering out common polymorphisms, the assessment and interpretation of detected personal variants in the clinical context is an often time-consuming effort. We have developed GeneTalk, a web-based platform that serves as an expert exchange network for the assessment of personal and potentially disease-relevant sequence variants. GeneTalk assists a clinical geneticist who is searching for information about specific sequence variants and connects this user to other users with expertise for the same sequence variant.Availability: GeneTalk is available at www.gene-talk.de. Users can login without registering in a demo account.Contact: peter.krawitz@gene-talk.de

Whole exome sequencing identifiesFGF16nonsense mutations as the cause of X-linked recessive metacarpal 4/5 fusion

“…Each exome contained more than 130 000 variant calls and allowed for high quality calls for over 90% of the human consensus coding sequence. We filtered the trio by applying homozygous, compound heterozygous, and de novo filters in GeneTalk 15. The numbers of detected variants were as follows: two for homozygous, five for compound heterozygous, and four for de novo models of filtering.…”

Whole exome sequencing identified a novel zinc-finger geneZNF141associated with autosomal recessive postaxial polydactyly type A

“…Single nucleotide variants and short insertions and deletion were detected with SAMtools 16. All variants were annotated with annovar17 and filtered using GeneTalk 18. The filtered variants were validated by routine Sanger Sequencing in all family members with ABI Prism BigDye terminator cycle sequencing reaction kit (Applied Biosystems, Foster City, California, USA) on ABI3730 Genetic Analyser (Applied Biosystems).…”

Key features and clinical variability of COG6-CDG

“…Variants were detected with GATK toolkit version 2.6 [13] and the exome genotyping accuracy was estimated to be above 0.9999 based on the variant calls [14]. Variants were detected with SAMtools, annotated with ANNOVAR and finally analyzed using the Gene-Talk platform [15,16]. Variant analysis was restricted to all genes known at the time of analysis to cause CDG.…”