PRS-cs ancestry assignment seems wrong

[Gechang Yu]

Hi,

When I use the PennPRS to calculate trans-ancestry PRS by PRS-cs, I found a problem that even if I specified the ancestry of reference panel as East Asian, the PennPRS would always automatically specified it as European.

I tried twice but got the same error. The job IDs are 7ec72e5a-3355-4eb7-aa39-1432df27c8ea and eab805ec-5ac7-4c21-a66d-5439a7069aee

I checked the log file, which also showed that it specified the ancestry as EUR.

$methods
[1] "PRS-CS-auto"

$trait
[1] "T2DGGI_All_1KG_EAS_Penn"

$ancestry
[1] "EUR"

$LDrefpanel
[1] "1kg"

$phi
[1] 0.01

$coef_shrink
[1] 1

$allow_jump_sign
[1] TRUE

$use_MLE
[1] TRUE

$ensemble
[1] FALSE

Could you please help me check this issue? Thank you very much!

Gechang Yu

The Chinese University of Hong Kong

[Jin, Jin]

Hi Gechang,

 

Thank you for reporting the issue. Our team is working on it and will keep you posted.

 

Best,

Jin

 

From: pen...@googlegroups.com <pen...@googlegroups.com> on behalf of Gechang Yu <gecha...@gmail.com>
Date: Friday, December 5, 2025 at 4:51 AM
To: PennPRS <pen...@googlegroups.com>
Subject: [External] PRS-cs ancestry assignment seems wrong

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