> For the complete documentation index, see [llms.txt](https://docs.finngen.fi/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://docs.finngen.fi/finngen-data-specifics/red-library-data-individual-level-data/omics-data/proteomics/finngen-3-proteomics-data/batch-1+2-harmonized-data.md).

# Batch 1+2 harmonized data

The harmonised and QCd Olink dataset combines batches 1 and 2 (n=4,415) of 5.4k proteins. A detailed file was circulated with the data release, with the necessary details on how the merging was done. The file can also be found in FinnGen Teams/Data release announcements/Shared/Proteomics with the name ["DATA\_RELEASE\_NOTE\_FG3\_CrossBatch\_Harmonised\_March2026"](https://helsinkifi.sharepoint.com/:b:/s/FinnGen150-Datareleaseannouncements/IQDo_kGrTaptRZY0-y0Rk5LzASQeUZuFipz1sdm701JjmKQ?e=vdo4QB).

**You can find the data in**

`library-red/omics/proteomics/olink_genewiz_batch1_and_2_harmonized_QCd_2026_16_03`

**pQTL analysis**

The data and full documentation are available at: `/finngen/library-green/omics/proteomics/olink_genewiz_batch1_and_2_QCd_2026_01_05/`

In addition to the fine-mapped results, we have released the pQTL summary statistics and LDSC-formatted pre-munge summary statistics. The release note also details a formal comparison of the FG3 fine-mapping output against two benchmark cohorts: FinnGen Olink Batch 01 and UKB-PPP.

Upstream proteomics normalization, covariate adjustment, and kinship filtering remain as described in the previous release. For details on upstream processing, please consult the March 2026 (v1.1) documentation: DATA\_RELEASE\_NOTE\_FG3\_CrossBatch\_Harmonised\_v01\_1.pdf in `/finngen/library-red/omics/proteomics/olink_genewiz_batch1_and_2_harmonized_QCd_2026_16_03`

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