# First batch

For information about the individual/sample selection criteria, please check the file in FinnGen Teams/Task Forces/Shared/General with the name ["FinnGen\_proteomics\_summary\_table.xlsx"](https://helsinkifi.sharepoint.com/:x:/s/FinnGen150/IQArIK0q7dtnSKumgXgo2oqBARTe-gaAmpgk9NI8N4En1Dw?e=PFWQB6).

In the first batch, the following sample selections were included:

* **Healthy controls** (blood donors), n=1,608
* **Kidney Task Force:** 261 CKD individuals were selected based on whether they had a sustained >=25% decline in eGFR. A minimum of 4 eGFR time points (\~4 weeks apart) was required to identify these individuals. The baseline measure is composed of two measures, and eGFR decline is defined by a sustained 25% eGFR decline for at least 2 time points.
  * The FGIDs list for these individuals can be found here: `library-red/omics/proteomics/olink_genewiz_batch1_31_12_24/metadata/Kidney_first_batch.txt`
* For additional information, please contact the Kidney TF co-leads:
  * Rodos Rodosthenous (<rodos.rodosthenous@helsinki.fi>)
  * Karol Estrada (<kestrada@mazetx.com>)
* **IBD Task Force:** a total of 268 individuals were selected based on the use of IBD-related medication and selecting samples 0-5 years before diagnosis (n=214). A small number of IBD patients with existing paired before-after diagnosis samples was also included (n=27x2).
  * The FGIDs list for these individuals can be found here:
    * `library-red/omics/proteomics/olink_genewiz_batch1_31_12_24/metadata/IBD_plasma_before_dx_samples_cutoff_2010_2024_04_10.tsv`
    * `library-red/omics/proteomics/olink_genewiz_batch1_31_12_24/metadata/IBD_plasma_serial_samples_cutoff_2005_2024_04_10.tsv`
    *
* For additional info, please contact the IBD TF co-leads:
  * Elisa Lahtela (<laura.lahtela@helsinki.fi>)
  * Jukka Koskela (<jukka.koskela@helsinki.fi>)
  * Mark Daly (<mark.daly@helsinki.fi>)

**Data availability:**

**The raw data:** currently available in the Sandbox `library-red/omics/proteomics/olink_genewiz_batch1_31_12_24/`

**QCed data:** currently available in the Sandbox (n=2094) `library-red/omics/proteomics/olink_genewiz_batch1_QCd_2025_28_02/`

**pQTL and finemap in 1,829 independent samples of the above:**

`gs://finngen-production-library-green/omics/proteomics/olink_genewiz_batch1_QCd_2025_28_02/`

**Sample timestamps for IBD, Kidney, and Control samples in Batch 1:**

* `library-red/omics/proteomics/olink_genewiz_batch1_31_12_24/metadata/sample_collection_times.txt`

**Sample timestamps from healthy blood donors:** In case a sample timestamp is needed for the blood donor's data (i.e., when the sample was collected), you can use the files below to screen for your samples.

* `/finngen/library-red/ EA5/omics_metadata/20250204_EA5_Plasma_Metadata_All.csv`

  `/finngen/library-red/EA5/omics_metadata/`[`20250204_EA5_Plasma_Metadata_Readme.md`](https://urldefense.com/v3/__http:/20250204_EA5_Plasma_Metadata_Readme.md__;!!H9nueQsQ!48BpnWXYE5YCnO93PXnwlx93bkDCAF3BJvdUp1OQ2yzLFIfQN4zuYrxO8gk4Flt8MQwNUkcTL1xZkTM8voX6Q8nTR18UzvwX$)
* \*\*\*Please note that the data provided at this point is original data from our Olink provider GeneWiz without any additional quality control applied. It is not recommended to use the data without first performing appropriate quality control as needed for your analysis.


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