Comparing the 147 CKDGen Loci in CHRIS

dariushghasemi / kidneyInCHRIS

Genetic determinants of Kidney function in the CHRIS study

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Comparing the 147 CKDGen Loci in CHRIS #7

Closed dariushghasemi closed 1 year ago

dariushghasemi commented 1 year ago

Comparing the 147 CKDGen identified kidney-associated Loci for European ancestry in CHRIS study

Here we see the significance status of the entire 147 identified SNPs by the discovery study (CKDGen meta-GWAS; Wuttke et al. 2019) in our study.
Previously we have seen that we were able to replicate 10 out of these 147 Multi-A-specific kidney associated Loci in the CHRIS study.

dariushghasemi commented 1 year ago

The same process for aligning the effect allele in both studies should be done for this dataset. At the end, we will have the same effect allele for all 147 SNPs in replication and discovery studies.

dariushghasemi commented 1 year ago

We found that there was a bug in the positions.sh file, in a way that extraction.R script misses some of the 147 the CKDGen top SNPs which were significantly associated to log(eGFR) in CHRIS 10K.
We added the coordinates (CHR, POS38) of the CKDGen top SNP of PDILT (proxy locus to UMOD) to CHRIS proxy (LD>0.8) variants listed in test_convert_prepared.txt bed file.