<p>I have a tab-separated file (the columns are rsID CHROM POS GENOTYPE) generated by Diganomics with Illumina GSAMD (v2.2) from male DNA, and there are a few hundred loci within X or Y chromosome that contain two alleles, even heterozygous, e.g.</p>
<p>[cut]</p>
<pre><code>rs28463388  X   191998  TT
rs28669107  X   195014  GC
rs6655397   X   201935  GG
rs7890186   X   202458  TG
</code></pre>
<p>[skipped]</p>
<pre><code>rs1016793029    Y   8619592 GA
</code></pre>
<p>[skipped]</p>
<pre><code>rs527288580 Y   8771750 GA
</code></pre>
<p>[skipped]</p>
<pre><code>rs917158084 Y   14871973    TG
</code></pre>
<p>[…etc]</p>
<p>There are 1270 such double alleles (7 in Y chromosome and 1163 in the X chromosome) from a total of 734162 number of lines, or 0.17%. What is remarkable is that these 1163 doubles within the X chromosome tend to be clustered, i.e. come consequently one after another mostly, but the 7 in the Y were sparse single lines.</p>

CC BY-SA 4.0
2020-08-23T07:39:07.880Z
Do you have a link to the manual for the Illumina caller you used? I searched a bit for it but couldn't find anything.
user438383
CC BY-SA 4.0
2020-08-24T03:45:59.533Z
Could it be related to the pseudoautosomal regions of the chromosomes?
James Schinner
CC BY-SA 4.0
2020-08-24T17:47:00.907Z
@JamesSchinner It seems that you are right. For example, rs28463388 is in the PLCXD1 gene which is a pseudoautosomal gene.
Maxim Masiutin
CC BY-SA 4.0
2020-08-24T17:53:40.343Z
@JamesSchinner, here is a relevant reply: https://www.snpedia.com/index.php/Talk:Gs266
Maxim Masiutin
CC BY-SA 4.0
2020-08-25T06:08:18.923Z
Nice, first time my Biomedical Science degree has been useful!
James Schinner
<genotyping>
Male DNA genotyped with Illumina GSAMD gives two alleles for certain loci within sex chromosomes
# Male DNA genotyped with Illumina GSAMD gives two alleles for certain loci within sex chromosomes

(Asked by: username_0 on 2020-08-22)

I have a tab-separated file (the columns are rsID CHROM POS GENOTYPE) generated by Diganomics with Illumina GSAMD (v2.2) from male DNA, and there are a few hundred loci within X or Y chromosome that contain two alleles, even heterozygous, e.g.
[cut]
rs28463388  X   191998  TT
rs28669107  X   195014  GC
rs6655397   X   201935  GG
rs7890186   X   202458  TG

[skipped]
rs1016793029    Y   8619592 GA

[skipped]
rs527288580 Y   8771750 GA

[skipped]
rs917158084 Y   14871973    TG

[…etc]
There are 1270 such double alleles (7 in Y chromosome and 1163 in the X chromosome) from a total of 734162 number of lines, or 0.17%. What is remarkable is that these 1163 doubles within the X chromosome tend to be clustered, i.e. come consequently one after another mostly, but the 7 in the Y were sparse single lines.

**Tags:** genotyping
> **Comments:**
> **username_1**: Do you have a link to the manual for the Illumina caller you used? I searched a bit for it but couldn't find anything.  
> **username_2**: Could it be related to the pseudoautosomal regions of the chromosomes?  
> **username_0**: @JamesSchinner It seems that you are right. For example, rs28463388 is in the PLCXD1 gene which is a pseudoautosomal gene.  
> **username_0**: @JamesSchinner, here is a relevant reply: https://www.snpedia.com/index.php/Talk:Gs266  
> **username_2**: Nice, first time my Biomedical Science degree has been useful!  

---

## 0 answers

