Selection of genetic instruments (original) (raw)
Protocol for “Selection of genetic instruments”
Three classes of FDA-approved lipid-lowering drugs were includedas exposures in this study: HMGCR inhibitors, PCSK9 inhibitors, and NPC1L1 inhibitors. We used the expression of drug targetgenes and the level of LDL cholesterol mediated by these drug target genes to proxy the exposure.
Firstly, available eQTLsfor drugs targetgenes (i.e., HMGCR,PCSK9, NPC1L1) were selected as the genetic instruments for the expression of the drug's target gene. The eQTLs summary-level data was retrieved from eQTLGen Consortium (https://www.eqtlgen.org/) for HMGCR, or GTEx Consortium V8 (https://gtexportal.org/) for PCSK9 and NPC1L1.
Selection criteria are shown below:
1. Cis-eQTLs ;
2. P<5.0 × 10-8 ;
3. Minor allele frequency >1% ;
4. Whole blood eQTLs for HMGCR or PCSK9,adipose subcutaneous tissueeQTLs for NPC1L1 (as there are no eQTLs in blood or other tissues available at a significance level for NPC1L1).
Secondly, SNPs within 100 kb windows from the target gene of each drug that was significantly associated with LDL cholesterol level were further selected as genetic instruments for LDL cholesterol level mediated by the drug target genes. GWAS summary data of LDL cholesterol levelswas retrieved from the GlobalLipids Genetics Consortium (GLGC), which can be downloaded from http://csg.sph.umich.edu/willer/public/lipids2013/, or retrieved from IEU open GWAS project (https://gwas.mrcieu.ac.uk/) by using GWAS ID number “ieu-a-300”. Selection criteria are shown below:
1. Within 100 kb windows from drug target genes (Details are present in Table 1) ;
2. P<5.0 × 10-8 ;
3. Minor allele frequency >1% ;
4. Weak linkage disequilibrium: r2 <0.30 within 100kb.
Details of selected SNPs have been uploaded at the Github:
https://github.com/WH57/lipid_covid19. And the path of files is shown in Table 2.
Table 1. Details of genetic instruments for LDL cholesterol level mediated by the drug target genes.
| Gene name | Gene ID | Gene chromosome | Gene region | Region of selected SNPs |
|---|---|---|---|---|
| HMGCR | 3156 | 5 | 74632993 -74657941 | 74532993-74757941 |
| PCSK9 | 255738 | 1 | 55505221 -55530525 | 55405221-55630525 |
| NPC1L1 | 29881 | 7 | 44552134 -44580929 | 44680929-44680929 |
*Gene information was obtained from https://www.ncbi.nlm.nih.gov/gene/ .
Table 2. Path of files with detailed genetic instruments
| Gene name | File path |
|---|---|
| Genetic instruments for expression of the drug target genes | |
| HMGCR | lipid_covid19/SMR/blood_eqtl.besd, blood_eqtl.epi, blood_eqtl.esi |
| PCSK9 | lipid_covid19/SMR/blood_eqtl.besd, blood_eqtl.epi, blood_eqtl.esi |
| NPC1L1 | lipid_covid19/SMR/Adipose_Subcutaneous_eqtl.besd,Adipose_Subcutaneous_eqtl.epi, Adipose_Subcutaneous_eqtl.esi |
| Genetic instruments for LDL cholesterol level mediated by the drug target genes | |
| HMGCR | lipid_covid19/IVW_MR/HMGCR_gwas.txt |
| PCSK9 | lipid_covid19/IVW_MR/PCSK9_gwas.txt |
| NPC1L1 | lipid_covid19/IVW_MR/NPC1L1_gwas.txt |
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How to cite：
Readers should cite both the Bio-protocol preprint and the original research article where this protocol was used:
- Huang, W, Xiao, J, Ji, J and Chen, L(2022). Selection of genetic instruments. Bio-protocol Preprint. bio-protocol.org/prep1557.
- Huang, W., Xiao, J., Ji, J. and Chen, L.(2021). Association of lipid-lowering drugs with COVID-19 outcomes from a Mendelian randomization study. eLife. DOI: 10.7554/eLife.73873