cathynes
commented
17 hours ago Hi Jaehyun,
The presence of heterozygosity on the X chromosome in males may indicate the existence of SNPs on the X chromosome that have homologous counterparts on autosomal chromosomes. In such cases, the SNP on the X chromosome might mistakenly be targeting its homologous SNP on the autosome, leading to observed heterozygosity in males.
During imputation, this misassignment can propagate, resulting in surrounding SNPs also exhibiting heterozygosity in males. If the rate of heterozygosity in males is particularly high, it calls into question the reliability of results from the array. To address this, it is advisable to identify and exclude SNPs with a high probability of homology, as well as all other SNPs with elevated heterozygosity rates in males, before re-performing the imputation and subsequent analysis.
Hope this help
Hello, I would like to ask a question about the chrX analysis plan.
I am sorry that this question may be too basic, but I would like to know how we should interpret and apply the results of heterozygosity test.
I understood that the heterozygosity in X chromosome in males indicate possible errors, but I wonder how we should apply the results. We may exclude all variants with at least one heterozygous subject or remove all subjects with any heterozygosity in X chromosome, but I do not think these processes would be proper. Thus, I would like to ask how we could filter the data based on the heterozygosity test results.
I would appreciate it if someone could give me an answer.
Thank you.