# pQTL analysis

## FINNGEN PROTEOMICS SUMMARY STATISTICS

### General description

Compiled summary stats for proteomics QTL in imputed SNPs on FINNGEN. Two platforms are included, Olink (619 samples across 2925 proteins) and SomaScan (828 samples across 7596 proteins). 

* pQTL:  The association results are from PLINK2 and in unrelated samples only (Relatedness cutoff based on genotype correlation r > 0.0625 for HapMap3 SNPs).   Due to different sample size, the SNP set are not same between those two dataset.
* Finemap:  see [Fine-mapping ](https://finngen.gitbook.io/documentation/r11/methods/finemapping)page, we input the summary data from pQTL
* autoreporting: annotation of independent hits lead variants with e.g. gwas catalog, putative causal coding variants in credible set, gnomad allele frequencies

See the "Software" section for the software or pipeline we used. 

### Data

#### Folder structure

/Somascan: from Somascan V4.1 assay, 828 unrelated samples from R12 imputed genotype

/Olink: from Olink Explore 3072 library, 619 unrelated samples from R12 imputed genotype

```markup
/pQTL:  proteomics QTL via PLINK2 with pre-adjusted age, sex, batch variables and 5PCs, then rank-based inverse normal transformed.

    Files:  ${PROBE_NAME}.txt.gz, bgzipped summary statistics.

            ${PROBE_NAME}.txt.gz.tbi, tabix index without the header line.


/Finemap:  Finemap of the pQTL results above for SNPs with MAC > 8
    FINEMAP: finemapping results from FINEMAP
    - all: all results
    - filter: filtered results

    Susie: finemapping results from Susie
    - all: all results
    - filter: filtered results

/autoreporting:
    Filter and group genome-wide significant variants from FinnGen summary statistics
    Annotate the genome-wide significant variants using gnomAD and FinnGen annotations.
    - group_report: grouped results by phenotype
    - variant_report: results for each variant
```

#### Column descriptions for pQTL results

| Field     | Description                                                                                 |
| --------- | ------------------------------------------------------------------------------------------- |
| CHR       | chromosome for variants                                                                     |
| POS       | BP of the variants                                                                          |
| ID        | SNP name (CHR\_POS\_REF\_ALT)                                                               |
| REF       | reference allele provided in FINNGEN imputed data                                           |
| ALT       | alternative allele, this is the effect allele (aka. A1, effect allele, A0 in some software) |
| ALT\_FREQ | allele frequency of the alternative allele                                                  |
| BETA      | effect size in additive model                                                               |
| SE        | standard error of the effect size                                                           |
| T\_STAT   | t statistics from PLINK2                                                                    |
| P         | p-value in association test                                                                 |
| log10\_P  | -log10(P) keep extra precision when P < 10^-308                                             |
| N         | per-SNP sample size for the SNP                                                             |

#### Map the probes's name to gene symbol

File: all\_gene\_info.txt&#x20;

| Field    | Description                             |
| -------- | --------------------------------------- |
| Probe    | probe name in the data/results gene     |
| geneName | mapping to the gene name (GeneCode V43) |
| CHR      | gene CHR                                |
| start    | gene start position                     |
| end      | gene end position                       |
| strand   | gene strand                             |

* Olink: Other annotations from Olink as indicated by the column name.
* Somascan: Other annotations from SomaScan as indicated by the column name. Note: NA means no matching, but keep the probe in the data to be complete.

### Software

* Assocation: PLINK2 v2.00a3.3LM AVX2 Intel (3 Jun 2022)
* Finemap: FINNGEN/finemapping-pipeline, revised on R10, hash e0792ea
* Coloc: FINNGEN/colocalization, revised on R10, hash 2e0632c
* Autoreporting: FINNGEN/autoreporting, revised on hash 9dbea66


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