How many genetic variants do we have?

When sequencing the entire human genome (whole genome sequencing), the average number of variants detected in one person is about 4 million. From whole exome sequencing, the number of genetic variants detected is very high too. So, how do we guess the clinical significance of all those variants?
The vast majority of genetic variants are polymorphisms, i.e. variants with high allele frequency in the general population, and they are simply the cause of our interpersonal phenotypic variability.
However, few variants may be pathogenic and, as such, (1) be the cause of a genetic disease in the patient and/or (2) determine the status of healthy carrier for an autosomal or X-linked recessive disorder (e.g. cystic fibrosis).

VUS: Variant of Uncertain Significance. What is that?

VUS, sometimes changed into (VOUS), stays for Variant Of Uncertain Significance. A VUS is a variant that, a priori, cannot be defined wither as neutral/benign or as pathogenic. This term is pretty much used in clinical diagnostics, i.e. when performing a genetic test on an affected patient.
A VUS is usually considered a variant of possible pathogenic relevance because (1) it has a very low allele frequency across populations, (2) it's falling in a gene where other mutations have been reported as pathogenic for a disorder similar to the one of the patient, (3) its biological features may indicate it's pathogenic (e.g. in silico predictions say that it might affect the protein structure in a damaging way, or it sits nearby the exon/intron junctions - hence possibly impacting the splicing process - or it falls at the same codon, or the same nucleotide position, where another variant has been confirmed to be pathogenic).

Why do we care about VUS?

VUS are a consistent proportion of the final results in genetic testing. Especially when doing large multigene panels, whole exome sequencing or whole genome sequencing, the quantity of VUS is absolutely impressive. In affected patients, in whom a clearly pathogenic variant cannot be detected, several VUS may come into play as possible, candidate pathogenic variants.
Each VUS is then evaluated for its possible relevance to the phenotype of the patient based on (1) genotype (is this VUS heterozygous or homozygous?) (2) specific gene mutational spectrum (is the VUS biological type described as pathogenic in this gene) and, most of all, (3) the relevance of gene to the clinical presentation of the patient.

How do we finally determine the real significance of a VUS?

Well, there aren't much ways, but something can be done and, sometimes, we can really shift the final interpretation to something certain. Especially in rare disorders, there are basically two ways:
(1) familial segregation studies: the VUS must be tested (usually by simple carrier testing with capillary electrophoresis - Sanger sequencing), to see if the variant has arisen de novo in the affected person (this is usually a very strong indicator for pathogenicity in isolated disorders) or to see if the variant appears only in affected family members and not in healthy members of the same family (this is also a very good indicator of pathogenicity);
(2) functional studies in-vitro: this is certainly the most complicated way, especially because a research assay must be designed from scratch and tested specifically for that variant. However, this may be the only accessible way, especially if other affected family members are not available (de novo disorder) or when it comes to verifying the real impact on the splicing of deep intronic variants.

VUS and preconception screenings

A common misconception regards the imaginative power of high-throughput sequencing (i.e. whole exome sequencing and whole genome sequencing) in preconception screenings. Some believe that doing whole exome or whole genome sequencing before having a baby will protect them from having a genetic disease at birth. This is absolutely not true and the reason is right the presence of VUS.

We're all healthy carrier of several genetic disorders, which can be transmitted in an autosomal recessive or X-linked recessive manner (i.e. disorders that can be transmitted to the progeny by two parents which are unaffected healthy carrier or by a mother who is unaffected healthy carrier and may conceive affected males). Because several pathogenic mutations for rare disorders have been deposited in the literature, we can isolate them in preconception screenings and consequently calculate the reproductive risk for those specific mutations. However, we'll always be carriers of additional pathogenic mutations which can't be defined pathogenic a priori, because they are VUS.


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Posted in Academia, Last Update, Medical Genetics, Mutations and tagged , .

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