Expansion Area 5 proteomics data

The EA5 pilot was done in collaboration with the Blood Service Biobank, and the samples were collected from blood donors who were heterozygous or homozygous carriers of specific genetic variants of interest. The list of those variants of interest was suggested and approved by the Steering Committee at the beginning of the study and can be found here.

The data were generated as part of the FinnGen 2 Expansion Area 5 (EA5) pilot. For the analysis, we used Olink Explore 3072 and SomaScan 7K platforms.

Olink

Olink batches 1, 2, and 3

• Total number of samples is 1,990 and it contains the data and analysis of the Olink batches 1, 2 and 3.

  • Batch 1: Rare variant carriers (healthy blood donors)

  • Batch 2.1: Rare variant carriers (healthy blood donors)

  • Batch 2.2: Twins (selected from Twingen)

  • Batch 3: Rare variant carriers (GeneRisk cohort)

• The raw data:

  • Batch 1: finngen/library-red/EA5/proteomics/olink/first_batch/original_data/

  • Batch 2.1: finngen/library-red/EA5/proteomics/olink/second_batch/

  • Batch 2.2: To be added

  • Batch 3: finngen/library-red/EA5/proteomics/olink/third_batch/original_data/

• QCed data: finngen/library-red/EA5/proteomics/olink/third_batch/QCd/proteomics_QC_all.txt

• pqtl, finemap and auto reporting results are at gs://finngen-production-library-green/omics/proteomics/release_2023_10_11/

Olink batch 1 and 2

• Total number of samples is 1,534 and it contains the data and analysis from the batches 1 (n=813) and 2 (n=721).

• After QC and ID mapping the number of individuals in the analysis is 1,243.

• Raw proteomics data of batch 2 and combined batch 1+2:

  • finngen/library-red/EA5/proteomics/olink/second_batch/

• pQTL and finemapping results:

  • library-green/omics/proteomics/release_2023_08_08/data/Olink/Finemap/

  • library-green/omics/proteomics/release_2023_08_08/data/Olink/pQTL/

• Colocalization results:

• gs://finngen-production-library-green/finngen_R11/finngen_R11_analysis_data/colocalization/data/fg_r11_Olink_batch1_and_2.txt.gz

• Explanation of the result columns can be found from ​Olink data

SomaScan

• Total number of samples analyzed with SomaScan is 1,000 individuals. These are the same individuals from which metabolomics data was also generated.

• Raw data:

  • library-red/EA5/proteomics/soma/second_batch/QCd/SOMA_batch_1_2_QC_all_v2.txt

• pQTL and finemapping results:

  • library-green/omics/proteomics/release_2023_08_08/data/Somascan/Finemap/

  • library-green/omics/proteomics/release_2023_08_08/data/Somascan/pQTL/

• Colocalization results:

  • library-green/finngen_R11/finngen_R11_analysis_data/colocalization/data/fg_r11_Soma_v2.txt.gz

• Readme:

  • gs://finngen-production-library-green/omics/proteomics/release_2023_08_08/readme.txt

Link to explanation of result file SomaScan data