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".

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:

pQTL and finemap in XXXX independent samples:

To be added very soon