Important:

I contacted AncestryDNA, but their support staff seemed to not understand the issue. Please let me know how to proceed here, if at all.

If you have any issues with this writeup or want to critique my methodology, feel free to correct me in the comments. I am just a amateur and am sure I made a mistake.

TLDR at the bottom

Hello everyone!

This is my write-up on a presumed error in my Promethease analysis of my AncestryDNA.txt SNP data, which can sometimes mark people with male genes as female.

First, the base stats of what I was analyzing. My AncestryDNA.txt file contains 434,837 SNPs. I marked myself as male on signup.

Initial Promethease result

gs145

Female Female.

Magnitude	4
2015-11-04	Geno modified

This was the result I got in my Promethease processing of my AncestryDNA data. I was very confused, so I had to teach myself a bit about genetics to be able to understand. And I think I have a decent grasp now.

I realize now I should have picked 23andme, as well.

Research/methodology (may be boring, skip if uninterested)

Checked for any markers mapped to the Y chromosome, denoted as 24 or Y. Found 0 results.
Checked the 47 specific X-chromosome SNPs listed on the gs145 snpedia page. Female criteria were 3 heterozygous calls among the markers.
- Extracted the target SNPs; they were entirely homozygous. (15,913 X SNPs counted, 0 Y SNPs)
- This is the expected biological profile for a male with only one X chromosome.
- 1 out of ~15,915 X-chromosome SNPs was heterozygous, maybe a standard array scan error (???), though this would be a very specific place for one
  - rs11541651 at position 114346258, reading as T C
Queried for SRYas well as sex-determining region Y rsIDs (like rs11575897). None existed.

Reasoning for my current hypothesis

My hypothesis is that AncestryDNA somehow completely excluded Chromosome 24 (Y) data from the export. Maybe something related to the export script. We will assume it is.

Promethease relies on an exclusionary check regarding sex: not(gs266) . This tests if male Y-DNA is absent. Because the Y-DNA was stripped by Ancestry, this evaluates to True, and so Promethease's logic defaults to gs145 "female", while ignoring contradictionary markers (notably that 15,915 X SNPs are perfectly homizygous/homozygous).

TLDR

Basics

>- In the Promethease analysis of my AncestryDNA data, I was falsely marked as genetically female
- I researched why by learning how we classify male/female genes, and processed my raw files

Hypothesis

>- AncestryDNA somehow completely excluded Chromosome 24 (Y) data from the export
- Promethease relies on an exclusionary check regarding sex: not(gs266)
- Because the Y-DNA was stripped by Ancestry, this evaluates to True
- Promethease's logic defaults to gs145 "female", while ignoring contradictionary markers
- This means that the false gs145 marker is likely a software artifact

Hope nobody here minds the long text post. A lot of effort and 2h of testing and writing went into this. Important:I contacted AncestryDNA, but their support staff seemed to not understand the issue. Please let me know how to proceed here, if at all.If you have any issues with this writeup or want to critique my methodology, feel free to correct me in the comments. I am just a amateur and am sure I made a mistake.

u/Lunatic155

Issues with Ancestry

955

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[Write-up] A investigation and potential theory behind gs145 mislabeling