> 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/second-batch.md).

# Second 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).

### Below is a description of how the different sample sets included in this batch:

**Kidney diseases (n=684):**

* Start from N=232,237 QC+ individuals with KANTA eGFR decline information
* Plasma quality: frozen (or processed) within 6 hrs and no reported hemolysis
* Plasma collected before eGFR baseline (previously <2 years after baseline) and at least 3 months before 25% eGFR decline
* Individual exclusion criteria
  * At baseline, eGFR > 25 and no prior dialysis or kidney transplant
  * No cancer or liver cirrhosis before 1 year after 25% eGFR decline
  * Initial eGFR decline < 55%
  * Not already in the first plasma batch
  * Individual availability for follow-up
  * Alive as of the current end of follow-up
  * Age at current end of follow-up <= 90
  * At least 3 months of follow-up after 25% eGFR decline

**Rheumatic diseases (n=276):**

* Samples with autoantibody testing were taken regardless of the result
* Diagnoses include seropositive RA, MCTD, Sjögren’s syndrome, SLE, and systemic sclerosis
* Mostly cross-sectional, primarily pre-disease-onset samples
* No cancer dx 5 years before the sample collection date, no oral corticosteroid purchases 1 year before the sample collection date

**Metabolic disease (n=133):**

* Longitudinal before/after GLP1 initiation samples with BMI and HbA1c measurements available

**Parkinson's (n=335):**

Cross-sectional samples from:

1. Mild cognitive impairment, fast and slow progressors, and controls;
2. patients with device-assisted treatment.

**Pulmonary diseases (n=46):**

All available before-and-after diagnosis paired samples from ILD

**Eye diseases: (n=162):**

wAMD cases with plasma samples taken before diagnosis +​ 120 dAMD cases

**Rare variant carriers - Blood donors and GeneRisk cohort mainly (n=500):**

Samples were selected from individuals who carry rare Finnish-enriched coding variants of interest

**Chromosomal abnormalities (n=153):**

Samples were selected from individuals with the following conditions XO, XXX, XXY, XYY

**Gender identity disorders (n=61):**

* Diagnosis of F64.0 in inpatient or outpatient register (HILMO)
* Age 18-40 years old at diagnosis
* Alive and living in Finland based on info from FinnGen R12
* Samples stored <10 years
* Samples need to be frozen within 8 hours.

**Younger individuals (n=53):**

* Age 2-16 years old at sample collection
* Alive and living in Finland based on info from FinnGen R12
* Without diagnosis of congenital malformations (Q17\_CONGEN\_MALFO\_DEFORMAT\_CHROMOSOMAL\_ABNORMALITI), dialysis (DIALYSIS), CKD (N14\_CHRONKIDNEYDIS), and renal failure (N14\_RENFAIL) before sample collection
* Samples stored <10 years
* For individuals between <13 years old, the samples do not necessarily need to be frozen within 8 hours. For individuals between 13 and 16 years, samples need to be frozen within 8 hours."

### **Data availability:**

**QCed data:** currently available in the Sandbox (n=2600) `library-red/omics/proteomics/olink_genewiz_batch2_QCd_2025_23_12`

A detailed release note is available in the same location in Sandbox and in [Teams here](https://helsinkifi.sharepoint.com/:b:/s/FinnGen150-Datareleaseannouncements/IQCvIMZB3wbRSY3YW-cLmSKSAaeDZupxj-ZC1KnO1RR0M9g?e=aiFDbB):