Sex Chromosomes Aneuploidy Detection

[ghost]

Hi Have you got any ideas to add SCAs detection (XO, XXY, XYY and XXX) to wisecondor? Or at least an algorithm/pipeline for this diagnosis test? I'd be thankful if you give a clue for SCAs. I'd like to develop a program for detecting these kind of aneuploidies.

Best AG

[rstraver]

Hi, We intentionally ignored those chromosomes for ethical reasons but I believe this fork originally started with the intent to include them: https://github.com/CenterForMedicalGeneticsGhent/WisecondorX Perhaps their project is helpful to you?

[ghost]

Hi, Strange to me! Why ethical reasons?, I think sex detection could be arguable, but a SCA like Klinefelter's syndrome which increases the risk of infertility, should be detected. No, In WisecondorX, there is no option for detecting SCAs, but they have developed a new tool called PREFACE that is designed for estimating FF, but as a side calculation, SCAs detection is available internally, but they didn't implemented the calculation as a feature in the R code. I opened a new issue at their repo, @leraman answered the issue, but I'm waiting for some more information. I hope @leraman helps to add the feature to the code.

[rstraver]

Well I might misremember, it's been a while. But yeah, while the ethical reason may sound weird, the thing is that to determine those kind of syndromes we pretty much need to determine the sex as well, can't say something is off otherwise, and our clinicians at the time really wanted to stay away from that discussion in general (including any semi-blind ways to test without telling). Might have had something to do with some laws and whatnot as well, combined with the extra challenges it poses compared to the autosomes, it was a rather logical decision for us to not look into it too much.

But if WisecondorX does test this internally, I'd expect they would like to provide results to users should they wish to test for these syndromes, so I just hope they'll respond soon.

[ghost]

Thanks for your reply. Interesting, but I think this over sensitivity about detecting sex is not really good, the cost that the community should pay for these aneuploidies will be really high, for example the treatments that people pay for infertility or the mental problems which occures for them.

I think it's better to detect SCAs. And we, the people who research or work in this area, should talk and publish papers about the importance of these kind of prenatal aneuploidies detection.

I hope so, and I'll try to find a way to detect these aneuploidies.