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","availabilityStatus":"The data is not available for download directly via DataverseNL but is available on request if the request is compliant with the Terms of Access. ","contactForAccess":"Please fill out the request form.","fileAccessRequest":true,"metadataBlocks":{"citation":{"displayName":"Citation Metadata","name":"citation","fields":[{"typeName":"title","multiple":false,"typeClass":"primitive","value":"Diminished plasma serotonin and taurine levels are a metabolic feature of age-related macular degeneration"},{"typeName":"subtitle","multiple":false,"typeClass":"primitive","value":"Dataset and scripts"},{"typeName":"author","multiple":true,"typeClass":"compound","value":[{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Rijken, Rianne"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"},"authorIdentifierScheme":{"typeName":"authorIdentifierScheme","multiple":false,"typeClass":"controlledVocabulary","value":"ORCID"},"authorIdentifier":{"typeName":"authorIdentifier","multiple":false,"typeClass":"primitive","value":"0000-0002-0873-6368"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Gerritsen, Bram"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Stehouwer, Marilette"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"St. Antonius Ziekenhuis Nieuwegein"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Pameijer, Els M."},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Hiddingh, Sanne"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Lintelmann, Jutta"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"https://ror.org/00cfam450","expandedvalue":{"scheme":"http://www.grid.ac/ontology/","@type":"https://schema.org/Organization"}}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Cecil, Alexander"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"https://ror.org/00cfam450","expandedvalue":{"scheme":"http://www.grid.ac/ontology/","@type":"https://schema.org/Organization"}}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Meester-Smoor, Magda"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"https://ror.org/018906e22","expandedvalue":{"scheme":"http://www.grid.ac/ontology/","termName":"Erasmus MC","@type":"https://schema.org/Organization"}}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"de Boer, Joke H."},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Imhof, Saskia M."},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"van Leeuwen, Redmer"},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"authorName":{"typeName":"authorName","multiple":false,"typeClass":"primitive","value":"Kuiper, Jonas J.W."},"authorAffiliation":{"typeName":"authorAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}}]},{"typeName":"datasetContact","multiple":true,"typeClass":"compound","value":[{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"Rijken, Rianne"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"DHS Datamanagement"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}},{"datasetContactName":{"typeName":"datasetContactName","multiple":false,"typeClass":"primitive","value":"Kuiper, Jonas"},"datasetContactAffiliation":{"typeName":"datasetContactAffiliation","multiple":false,"typeClass":"primitive","value":"UMC Utrecht"}}]},{"typeName":"dsDescription","multiple":true,"typeClass":"compound","value":[{"dsDescriptionValue":{"typeName":"dsDescriptionValue","multiple":false,"typeClass":"primitive","value":"\n\n

This dataset contains metabolomics data from samples collected from patients with Age-Related Macular Degeneration (AMD) and control participants. The data includes processed metabolomic measurements, clinical data, and genetic risk scores (GRS) for each sample, as well as allele scores for 52 single nucleotide polymorphisms (SNPs) associated with AMD.

\n\n

Information about the data:

\n\n

The dataset contains 99 samples, which are organized as follows:

\n\n\nOne AMD sample (I-AMD 041) and one control sample (I-AMD HC 021) were excluded from the analysis. These samples remain in the dataset but were not included in the analysis due to diagnoses of unrelated disease conditions after sampling that did not meet the study's inclusion criteria.\n\n

Data restrictions:

\n\n

Due to hospital data protection policies and privacy regulations, the data and metadata underlying this study are made available under restrictions. Researchers may request access through the PI and data manager. Please fill out the \n\nrequest form or via de Contact Owner button (top right of this page).

\n\n

Information about the uploaded dataset files:

\n

A complete overview of all data files is described in README.

\n\n

Go to the Files tab and click on \"Change view to Tree\" to view the folder structure. \n\n\n\nThe dataset consists of the following main parts:

\n\n\n

All folders have been organized and uploaded in a way that aligns with the structure of an R project. If you download all the files at once, you can directly load the dataset into an R environment, and the folder structure will be preserved, allowing you to use the project seamlessly without any further setup.

\n\n

The Metadata folder:

\n\n

The metadata for the study consists of clinical and genetic information. The `clinicaldata.csv` file contains clinical details for all participants, such as sex, age, smoking status, AMD stage, and medication usage. The `GRS_df.csv` file includes genetic risk scores (GRS-52) and allele scores for 52 SNPs associated with AMD risk. These two files were merged into `participant_info.csv` using the `R/01_metadata_processing.R` script, which combined the metadata for analysis.

\n\n\n

The Data folder:

\n\n

The raw data for the metabolomics analysis is provided in the `Results_P-21050.zip` archive, which contains the experimental results. Additionally, the `Quant_500_Metabolic_Indicators.csv` file provides metabolic indicators used in the analysis, including formulas and identifiers. These raw data files are processed using the `R/02_data_processing.R` script, which performs preprocessing of the data for further analysis.

\n

The processed data includes multiple versions of the metabolomics data after various processing steps, including normalization, filtering, Box-Cox transformation, and standardization relative to controls. The following files are included:

\n\n\n\n"},"dsDescriptionDate":{"typeName":"dsDescriptionDate","multiple":false,"typeClass":"primitive","value":"2025-01-14"}}]},{"typeName":"subject","multiple":true,"typeClass":"controlledVocabulary","value":["Medicine, Health and Life Sciences"]},{"typeName":"keyword","multiple":true,"typeClass":"compound","value":[{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"Age-related macular degeneration"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"targeted plasma metabolomics"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"GRS-52"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"serotonin"}},{"keywordValue":{"typeName":"keywordValue","multiple":false,"typeClass":"primitive","value":"taurine"}}]},{"typeName":"publication","multiple":true,"typeClass":"compound","value":[{"publicationCitation":{"typeName":"publicationCitation","multiple":false,"typeClass":"primitive","value":"Gerritsen, Bram and Rijken, Rianne and Stehouwer, Marilette and Pameijer, Els M. and Hiddingh, Sanne and Lintelmann, Jutta and Cecil, Alexander and Meester-Smoor, Magda and de Boer, Joke H. and Imhof, Saskia M. and van Leeuwen, Redmer and Kuiper, Jonas, Diminished Plasma Serotonin and Taurine Levels are a Metabolic Feature of Age-Related Macular Degeneration."},"publicationIDType":{"typeName":"publicationIDType","multiple":false,"typeClass":"controlledVocabulary","value":"doi"},"publicationURL":{"typeName":"publicationURL","multiple":false,"typeClass":"primitive","value":"http://dx.doi.org/10.2139/ssrn.5095122"}}]},{"typeName":"notesText","multiple":false,"typeClass":"primitive","value":"Age-related macular degeneration (AMD) is a leading cause of vision loss in older adults, but its precise pathogenic mechanisms remain incompletely understood. The emerging evidence suggests that metabolic alterations contribute to AMD, but this has not been exhaustively investigated and may provide new insights into the disease's pathophysiology. This study compares the metabolic profiles of peripheral blood plasma of early and late AMD patients with controls without AMD. Peripheral blood plasma was profiled with a 622-plex targeted metabolomic array using liquid chromatography–mass spectrometry in patients with early AMD (n = 21), late AMD (n = 39), and control participants without AMD (n = 39). The study participants underwent ophthalmological examinations and imaging and were classified as AMD according to the criteria of the Age-Related Eye Disease Study (AREDS). The AMD Genetic Risk Score (GRS-52) was calculated using genotype data obtained from the custom SNP assay. No metabolites were significantly associated with the GRS-52 (or individual risk variants). Using a regression model correcting for age, sex, and smoking status, we identified significant changes in 3 small molecules, 5 lipids, and 5 metabolic indicators between late AMD patients (n = 39) and controls (n = 39). The plasma levels of these metabolites increased or decreased incrementally from control, to early, to late AMD, following the disease's clinical course. A strong decrease in plasma serotonin (P = 1.03 × 10-13) and taurine (P = 2.36 × 10-9) were the most significant metabolic changes detected. The decrease of serotonin in AMD patients could not be attributed to serotonin reuptake inhibitors (SRIs) use. Analysis of predefined sums and ratios of metabolites (metaboINDICATOR™ analysis) confirmed a strong reduction in serotonin and taurine synthesis in late AMD (P = 4.41 × 10-14; P = 2.3 × 10-29). These findings suggest that AMD is characterized by metabolic changes in peripheral blood plasma, including a strong and clinically progressive depletion of plasma serotonin and taurine levels."},{"typeName":"depositor","multiple":false,"typeClass":"primitive","value":"Rijken, Rianne"},{"typeName":"dateOfDeposit","multiple":false,"typeClass":"primitive","value":"2026-02-16"},{"typeName":"timePeriodCovered","multiple":true,"typeClass":"compound","value":[{"timePeriodCoveredStart":{"typeName":"timePeriodCoveredStart","multiple":false,"typeClass":"primitive","value":"2020-10-01"},"timePeriodCoveredEnd":{"typeName":"timePeriodCoveredEnd","multiple":false,"typeClass":"primitive","value":"2021-12-01"}}]},{"typeName":"dateOfCollection","multiple":true,"typeClass":"compound","value":[{"dateOfCollectionStart":{"typeName":"dateOfCollectionStart","multiple":false,"typeClass":"primitive","value":"2022-06-01"},"dateOfCollectionEnd":{"typeName":"dateOfCollectionEnd","multiple":false,"typeClass":"primitive","value":"2025-01-14"}}]},{"typeName":"software","multiple":true,"typeClass":"compound","value":[{"softwareName":{"typeName":"softwareName","multiple":false,"typeClass":"primitive","value":"R"},"softwareVersion":{"typeName":"softwareVersion","multiple":false,"typeClass":"primitive","value":"4·4.2 (2024-10-31)"}}]}]},"dansDataVaultMetadata":{"displayName":"Data Vault Metadata","name":"dansDataVaultMetadata","fields":[{"typeName":"dansDataversePid","multiple":false,"typeClass":"primitive","value":"doi:10.34894/J9MZRO"},{"typeName":"dansDataversePidVersion","multiple":false,"typeClass":"primitive","value":"2.0"},{"typeName":"dansBagId","multiple":false,"typeClass":"primitive","value":"urn:uuid:c8a6653e-1e7b-4a39-85b0-5e90f91d8f64"},{"typeName":"dansNbn","multiple":false,"typeClass":"primitive","value":"urn:nbn:nl:ui:13-c96f69a9-33bd-4f0c-a72e-da4e6376411f"}]}},"files":[{"description":"Contains helper functions used for the processing of the data and metadata, and for the analysis `paper_analysis.Rmd`.","label":"00_functions.R","restricted":false,"directoryLabel":"Rproject_METABOL_DV/R","version":2,"datasetVersionId":34103,"dataFile":{"id":607630,"persistentId":"","filename":"00_functions.R","contentType":"type/x-r-syntax","friendlyType":"R Syntax","filesize":25885,"description":"Contains helper functions used for the processing of the data and metadata, and for the analysis `paper_analysis.Rmd`.","storageIdentifier":"surf://store:19c5da192fc-840960985953","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"296f883b3cb871c1381e6fabaf7e4dd2582348a7"},"tabularData":false,"creationDate":"2026-02-14","publicationDate":"2026-02-16","directoryLabel":"Rproject_METABOL_DV/R","lastUpdateTime":"2026-03-05T10:39:12Z","fileAccessRequest":true}},{"description":"Processes metadata, including the cleaning and preparation of participant data before analysis.","label":"01_metadata_processing.R","restricted":false,"directoryLabel":"Rproject_METABOL_DV/R","version":2,"datasetVersionId":34103,"dataFile":{"id":607639,"persistentId":"","filename":"01_metadata_processing.R","contentType":"type/x-r-syntax","friendlyType":"R Syntax","filesize":2690,"description":"Processes metadata, including the cleaning and preparation of participant data before analysis.","storageIdentifier":"surf://store:19c5da192f6-f82c40513afb","rootDataFileId":-1,"checksum":{"type":"SHA-1","value":"172a3df082d459698f041357ce13b69ac150035c"},"tabularData":false,"creationDate":"2026-02-14","publicationDate":"2026-02-16","directoryLabel":"Rproject_METABOL_DV/R","lastUpdateTime":"2026-03-05T10:39:12Z","fileAccessRequest":true}},{"description":"Script for processing the raw metabolomics data before analysis. 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