Plasma proteomics in two Swedish Ovarian Cancer cohorts

Plasma samples of women with benign and malignant ovarian tumors were collected from either the U-CAN collection at Uppsala Biobank, Sweden or the Gynaecology tumor biobank Göteborg, Sweden. All samples from the biobanks were included based on surgical ovarian cancer diagnosis or patients that had been surgically diagnosed with benign conditions based on suspicion of ovarian cancer. Exclusion criteria were patients that had received neoadjuvant treatment prior to surgery or if the tumor was pathologically determined to be metastatic originating from other tissues. The samples from Uppsala were collected between 2012 and 2018. The samples from Göteborg were collected from 2016 to 2018. The tumors were examined by pathologist specialized in gynaecologic cancers for histology, grade, and stage according to International Federation of Gynaecology and Obstetrics (FIGO) standards. The samples used here have previously been analyzed with the proximity extension assay (PEA) Explore1536 assay (Gyllensten, U. et al. Next Generation Plasma Proteomics Identifies High-Precision Biomarker Candidates for Ovarian Cancer. Cancers (Basel) 14, 1757 (2022), Bueno Álvez, M. et al. Next generation pan-cancer blood proteome profiling using proximity extension assay. Nature Communications 14, 4308 (2023)) and was here complemented with the PEA Explore3072. The samples were randomized across seven 96 well plates. Protein concentrations are reported in NPX (normalised protein expression). The NPX data are on a log2 scale and in the logarithmic phase of the curve one increase of the NPX value corresponds to a doubling of the protein content. A high NPX value corresponds to a high protein concentration. Each of the measured proteins has a lower limit of detection (LOD) which is determined at run time. Here, each protein measure with NPX under LOD was replaced with the plate-specific LOD as indicated in the provided result file from the manufacturer. In total 2493 unique proteins were measured in up to 521 individuals. The study was approved by the Regional Ethics Committee in Uppsala (Dnr: 2016/145) and Göteborg (Dnr: 201-15) and informed written consent was obtained from all participants following the guidelines of the Declaration of Helsinki.