How to determine gender by homozygosity (rate?) in X chromosome?
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2.5 years ago
MatthewP ★ 1.0k

Hello, I am reading paper A tutorial on conducting genome‐wide association studies: Quality control and statistical analysis, this is link. At table1 it says:

Can indicate sample mix‐ups. If many subjects have this discrepancy, the data should be checked carefully. Males should have an X chromosome homozygosity estimate >0.8 and females should have a value <0.2.

My question is why thresholds 0.8 and 0.2, any data/paper supports? Thanks a lot!

snp X plink • 1.2k views
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Those are generic recommendations, which typically don't have specific papers to reference.

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Ok, I can image that male contains one X chromosome, so genotype would be 0/0 or 1/1 both can treated as homozygosity. But why female's value so low even though female has 2 X chromosome?

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It can't be over 1, 0.8 is 80%, which is pretty high given multimapping and such.

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5 months ago

Did you figure out those values?

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