heterozygous variant on the X chromosome

Question

[ashaneev07]

Hi, I have found a heterozygous variant on the X chromosome in the VCF file of a male sample. This variant is clinically significant and has high quality and depth. How should I proceed with further analysis? Any suggestions would be appreciated.

Answer 1

[benformatics]

You should start by checking if it is in the PAR region (homologous region with the Y) - https://en.wikipedia.org/wiki/Pseudoautosomal_region : this seems most likely

If not you should consider that there is potential mosaicism within the sample

Or it could be contamination

In a clinical context you would validate it via sanger sequencing just to be sure - and then if it's not in the PAR it would be assumed to be mosaic (or potentially subclonal if this is a cancer sample)

[benformatics]

also worth checking for general homology genome-wide - you can BLAT the reads in IGV (maybe its in a transposable element sequence)

[ashaneev07]

Thank you for the reply. In that VCF file, this is not the only case. All the genotypes for the X and Y chromosomes are represented as 0/1 or 1/1 instead of 0 or 1. Could this be an error in the variant calling pipeline, where the chromosomes were mistakenly treated as diploid?

[benformatics]

Probably not - by default they will all be represented as such and even for male patients (data uniformity is very important for processing pipelines).

You need to look at some of these variants in IGV. You need to calculate the homozygosity of X-chromosome if its 90% homozygous then it's probably just some noise in the data that you would understand better by visualization in IGV.

Calculate the ratio of homozygous to heterozygous variants across the X. Compare male samples to female samples and also to your sample. This will let you know if something is wrong with your sample.