New Gene Screening Method, Whole-Exome Sequencing, Seen to Help in Diagnosing Alport Syndrome

Genetic screening helps in diagnosing Alport syndrome, a difficult-to-diagnose disease, although its rate of success is still far from ideal and mutations in at least one-fifth of all patients are not identified. But state-of-the-art genetic screen techniques, such as whole-exome sequencing, seem to offer better chances of success, according to a study published in PlosOne that used the newer technique on three families.

Genetic mutations in three genes, COL4A3, COL4A4, and COL4A5, are known to cause Alport syndrome, an inherited progressive renal disease. These genes encode important structural proteins that are essential for the normal workings of a part (glomerular basement membrane) of the kidney, as well as that of the cochlea (auditory portion of the inner ear) and the eye.

So far, more than 900 different mutations have been detected on these genes. This represents significant variability among patients and their family members, making it much harder to identify and diagnose the disease. In addition, this genetic variability is translates into a variety of symptoms, with grades of severity depending on the genetic alterations that the patient carries.

Genetic screening techniques have allowed clinicians to identify several genetic conditions, including AS. In Alport, however, such identification has an efficiency that ranges from 55% to 80%, meaning that a significant number of patients never receive a proper genetic diagnosis, important to both treating the disease and offering genetic counseling

In the study titled “Alport syndrome cold cases: Missing mutations identified by exome sequencing and functional analysis,” researchers used a new genetic screen technique — whole-exome sequencing — to evaluate the genetic status of three Italian families. Whole-exome sequencing (WES) is a technique that sequences all the expressed genes, or genes that result in a protein, in a person’s genome (the complete genetic material of an organism).

Despite clear clinical manifestations and a familial history of AS, previous genetic analysis of COL4A genes in these three families came back with negative results, failing to allow for a molecular, or genetic, diagnosis. But by using whole-exome sequencing, and combining its results with functional tests, researchers were able to identify two mutations that had never been reported or associated with Alport syndrome.

One of the variants, identified as c.2245-40A>G, was found to interfere with the normal structure of the COL4A5 gene. A more detailed in vitro analysis of the effects of this mutation showed that it induces the production of an abnormal protein, explaining the AS-like symptoms presented by the patient. A second mutation on COL4A5 gene sequence, identified as p.Gly491Asp, was found to disrupt a normally highly conserved DNA sequence.

The third family presented a genetic variant of the COL4A3 gene, in which part of the sequence had been deleted. This could lead to abnormal protein secretion and subsequent low protein concentration, which was confirmed by the researchers through in vitro assays. This last mutation has previously been associated with Alport syndrome.

“We demonstrated how a diligent application of exome-sequencing data analysis combined with an accurate experimental validation are critical to solve elusive cases in the molecular genetic diagnosis of AS,” the researchers wrote.

“This concept is valid for most human genetic diseases and is becoming increasingly important in the P4 (Personalized, Predictive, Preventive, Participatory) medicine era,” they added.