Inflammation proteomics datasets in the ALSPAC cohort

Abstract

Proteomics is the identification, detection and quantification of proteins within a biological sample. The complete set of proteins expressed by an organism is known as the proteome. The availability of new high-throughput proteomic technologies, such as Olink Proteomic Proximity Extension Assay (PEA) technology has enabled detailed investigation of the circulating proteome in large-scale epidemiological studies. In particular, the Olink® Target 96 inflammatory panel allows the measurement of 92 circulating inflammatory proteins. The Avon Longitudinal Study of Parents and Children (ALSPAC) is a prospective population-based cohort study which recruited pregnant women in 1991-1992 and has followed these women, their partners, and their offspring ever since. In this data note, we describe the proteomic data available in ALSPAC. Ninety-two proteins were analysed in 9000 blood plasma samples using the Olink® Target 96 inflammatory panel. Samples were derived from 2968 fasted mothers (mean age 47.5; Focus on Mothers 1 (FOM1)), 3005 non-fasted offspring at age 9 (Focus@9) and 3027 fasted offspring at age 24 (Focus@24). Post sample filtering, 1834 offspring have data at both timepoints and 1119 of those have data from their mother available. We performed quality control analyses using a standardised data processing workflow (metaboprep) to produce a filtered dataset of 8983 samples for researchers to use in future analyses. Initial validation analyses indicate that IL-6 measured using the Olink® Target 96 inflammatory panel is highly correlated with IL-6 previously measured by clinical chemistry (Pearson’s correlation = 0.77) and we are able to reproduce the reported positive correlation between body mass index (BMI) and IL-6. The pre-processing and validation analyses indicate a rich proteomic dataset to further characterise the role of inflammation in health and disease.

Inflammation Proteomic Profiling of Psychosis in Young Adults: findings from the ALSPAC birth cohort

“…Data were returned in Normalised Protein eXpression (NPX) values on a log 2 scale, which are calculated from protein concentrations (cycle threshold [Ct] values) with normalization to minimize intra- and inter-assay variation (Olink Proteomics, 2021). Further details on the proteins assayed and quality control procedures applied have been previously reported (see data note by Goulding et al, 2024).…”

“…Samples that did not pass Olink’s quality control were excluded from the analysis. Proteins with ≥50% values below the limit of detection (LOD) were excluded (based on values reported in the relevant ALSPAC data note (Goulding et al, 2024); namely ARTN, Beta-NGF, FGF-23, FGF-5, GDNF, IL-1 alpha, IL-10RA, IL-13, IL-15RA, IL-17A, IL-2, IL-20, IL-20RA, IL-22 RA1, IL-24, IL-2RB, IL-33, IL-4, IL-5, LIF, NRT, NT-3, SIRT2, SLAMF1, TSLP), leaving 67 proteins to be used as outcomes in the analyses ( Table S1 ). NPX values beyond 5 standard deviations (SD) from the mean were recoded as missing.…”

Blood Immuno-metabolic Biomarker Signatures of Depression and Affective Symptoms in Young Adults

“…These included immune proteins measured by the Olink Target 96 Inflammation Panel 19 , blood cell counts, lipids, hormones and metabolites measured at age 24 ( Supplementary Table 1 ). See Supplementary Methods for full details on sample processing.…”

Relationship between Polyunsaturated Fatty Acids and Inflammation: evidence from cohort and Mendelian randomization analyses

“…The samples were collected when the participansts were 24 years old. Full dtails regarding sample processing, NMR analysis, and data processing have been provided elsewhere 60–62 . GlycA levels ranged from 0.84 to 2.25 mmol/L, and IL-6 levels ranged from 1.82 to 10.60 Normalized Protein eXpression (NPX) Log2 scale.…”

“…The samples were collected when the participansts were 24 years old. Full dtails regarding sample processing, NMR analysis, and data processing have been provided elsewhere [60][61][62] . and measures outside this were removed.…”