On the alternate allele frequency

[jinshanmu]

I have a question on the number of alternate allele frequency (AF) / effect allele frequency (EAF) in the IEU OpenGWAS. Take rs12562034 in the ieu-a-1013 data for example, it has AF = 0.895 for the alternate allele A. However, when querying PhenoScanner or GRCh37 Ensembl, the A allele has a frequency of 0.09 in the European population. Is there a confusion between alternate allele and reference allele in the data curation process?

[mightyphil2000]

Hi Jinshanmu Thanks for bringing this to our attention. There is a metadata error in dataset ieu-a-1013. The effect allele columns are mislabelled. The effect allele (ea) is actually the non-effect allele (nea) and effect allele frequency (eaf) actually refers to the non-effect allele (nea).

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________________________________ From: jinshanmu ***@***.***> Sent: 16 July 2023 03:36 To: MRCIEU/TwoSampleMR ***@***.***> Cc: Subscribed ***@***.***> Subject: [MRCIEU/TwoSampleMR] On the alternate allele frequency (Discussion #429) I have a question on the number of alternate allele frequency (AF) / effect allele frequency (EAF) in the IEU OpenGWAS. Take rs12562034 in the ieu-a-1013 data for example, it has AF = 0.895 for the alternate allele A. However, when querying PhenoScanner or GRCh37 Ensembl, the A allele has a frequency of 0.09 in the European population. Is there a confusion between alternate allele and reference allele in the data curation process? — Reply to this email directly, view it on GitHub<#429>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/ACSDAPWRHLJLOEMY3X2DDCLXQNHRLANCNFSM6AAAAAA2LUQRKM>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[jinshanmu]

Thank you for the clarification!