FinnGen Handbook

Proteomics results

Data locations in the green library:

  • gs://finngen-production-library-green/omics/proteomics/release_2023_10_11/

  • gs://finngen-production-library-green/omics/proteomics/release_2023_03_02/

Colocalization between pQTLs and all genome wide significant hits in releases:

General description

Compiled summary stats and fine-mapping results for proteomics QTL (See below for data locations) in imputed SNPs on FINNGEN. Two platforms are included, Olink and SomaScan. The association results are from PLINK2 and in unrelated samples only. Due to different sample sizes, the SNP sets are not the same between those two datasets.

Data

Results from Somascan and Olink are in their own subdirectories in common format as below.

Column descriptions for pQTL results

  • CHR: chromosome for variants

  • POS: BP of the variant

  • 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 N: per- SNP sample size for the SNP

Map the probes's name to gene symbol

File: probe_map.tsv

  • Olink: geneName is the gene symbol which is also the probe name in Olink, other columns are chr (chromosome), start and end of the gene from Gencode V43

  • Somascan: AptName is the probe name in Somascan, other columns are geneName (gene symbol), start and end of the gene from Gencode V43

software

  • Assocation: PLINK2 v2.00a3.3LM AVX2 Intel (3 Jun 2022)

  • Finemap: FINNGEN/finemapping-pipeline, revised on R10, hash e0792ea

  • Autoreporting: FINNGEN/autoreporting, revised on hash 9dbea66

Data location in the green library:

  • gs://finngen-production-library-green/omics/proteomics/release_2023_10_11/

  • gs://finngen-production-library-green/omics/proteomics/release_2023_03_02/

Colocalization between pQTLs and all genome wide significant hits in releases:

  • Data location in the green library:

    • gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/colocalization/

    • gs://finngen-production-library-green/finngen_R10/finngen_R10_analysis_data/colocalization/

  • The results are browsable in FinnGen browser (e.g. https://results.finngen.fi/region/H7_AMD/1:196510779-196910779, scroll down for colocalization table)

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