Whole-Exome Sequencing Used to Identify Novel Alport Syndrome Mutations
This article was part of a job application at a health news agency. Thought I might as well share it here if anyone is interested.
Whole-exome sequencing, a genetic screening technique that analyzes all protein producing regions of the genetic code, was used to identifyAlport syndrome (AS) mutations in three families. This study suggests that whole-exome sequencing may be an effective tool for improving AS diagnosis, particularly for patients with difficult-to-diagnose variants.
The study is titled “Alport syndrome cold cases: Missing mutations identified by exome sequencing and functional analysis”, and was published in PlosOne.
AS is a genetic condition that stems from mutations in the collagen IV protein. Three genes, named COL4A3, COL4A4, and COL4A5, can cause AS if mutated. While the genes involved in AS have been known since the 1990’s, identifying disease-causing mutations remains challenging. According to the study, 20% to 45% of AS patients lack a molecular diagnosis.
The authors emphasized the significance of a genetics-based diagnosis, stating “Unequivocal -and possibly early- molecular diagnosis is extremely important for prognostic assessment and genetic [counselling].” Whole-exome sequencing assists in molecular diagnosis as it offers a detailed picture of protein-coding DNA. This makes whole-exome sequencing practical for identifying genetic variants that are missed by conventional screening techniques.
This study looked at three AS-affected families that had previously not received a genetics-based diagnosis. An individual was selected from each family that had received an AS diagnosis on the basis of a kidney biopsy, family medical history, and AS-associated symptoms. The first individual was found to have a mutation in the COL4A5 gene. Subsequent in vitro testing showed that this mutation caused errors in reading the gene, leading to collagen IV protein abnormalities. This was the first time this mutation has been reported by scientists.
A different COL4A5 mutation was also found in the individual from the second family. In this case a novel point mutation was identified in a highly conserved region of the COL4A gene. When analyzed by computer, it was predicted that this mutation would lead to a serious structural defect in the protein.
The individual from the third family had a deletion in the COL4A3 gene in a region involved in signalling. Follow-up tests using a human cell culture found that this deletion disrupts proper protein secretion, which would lead to low protein concentration. This mutation had previously been found in AS patients.
Overall, this study was successful in showing that whole-exome sequencing is useful for assessing difficult-to-diagnose AS variants. They were also able “…to provide three AS families with a molecular diagnosis after years of inconclusive results, highlighting non-obvious pathogenic variants that escaped previous screenings” according to the authors.
To conclude, the researchers observed that whole-exome sequencing “…was fundamental for molecular diagnosis in 3 AS families, highlighting pathogenic variants that escaped previous screenings.”