Summary stats used from Bellenguez et al AD GWAS - stage 1 vs meta?

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Hi there,

I was looking at the results for a specific study - the 2022 AD GWAS by Bellenguez et al and noticed that one of the significant results from the stage 1 + stage 2 meta analysis wasn’t present (SORT1, on chromosome 1). This locus isn’t significant in stage 1 (figure 1 vs table 2 here: New insights into the genetic etiology of Alzheimer’s disease and related dementias | Nature Genetics ).

The paper provides summary stats for both stage 1 and for the stage 1+2 meta (Index of /pub/databases/gwas/summary_statistics/GCST90027001-GCST90028000/GCST90027158) so I wonder if the Open Targets results are just from stage 1? Would it be possible to add the summary stats from the meta to open targets?

Thanks!
Stephanie

2

Dear Stephanie,

Thanks for reaching out to us with your question.

The GWAS Catalog only hosts full summary statistics for the discovery stage (Stage I) from the Bellenguez publication. Their top hits results from the meta-analysis (stage1 + stage 2) are manually curated from the paper. This was confirmed to us by the GWAS Catalog team, but please also feel free to contact them directly. They may be able to ask the authors whether they are happy to share the meta-analysis sumstats as well.

Open Targets has integrated and fine-mapped their summary statistics from Stage I (as per our inclusion criteria), where the SORT1 variant you are referring to (rs141749679) has a sub-significant p-value and it was therefore not included amongst the loci to fine-map.

I hope this helps!

Best,

Annalisa

3

Hi Annalisa,

Thanks very much for your response and for looking into this! I see that the file labeled with “meta” on the download site doesn’t in fact contain meta analysis results. Unfortunate that they only share stage 1 results.

Best,
Stephanie

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