EGAD00001007729
Sex, age at recruitment (2014-2018), and birthdate of GCAT Cohort individuals.
1
EGAD00001007730
First 20 principal components of 4988 genotyped GCAT Cohort individuals with Infinium Multi-Ethnic Global (MEGAEX2) array, with data for Cr1-22. Plink files with QC and imputed (SHAPEIT+IMPUTE).
1
EGAD00001007731
Disease diagnoses of GCAT Cohort participants obtained from electronic health records (EHR), mainly including the time period from 2012 to 2017. Disease diagnoses are codified in ICD-9, and the position of diagnosis refers to primary/secondary diagnoses (up to 14 secondary diagnoses per visit). The date and origin of the visit are also specified (AP: primary care, UGR: emergency, AH: hospital care, SMA: outpatient medical service, SMH: hospital medical service).
1
EGAD00001007774
This dataset contains genotypes (35.4M of SNVs, Indels and SVs), from 785 samples, after QC filtering, from the 808 WGS GCAT cohort.
1
EGAD00001008201
This dataset include FASTQ files of 808 samples from GCAT cohort. Technology used HiSeq 4000, read length 150 bp, inner mate distance 300 bp. For each sample the paired -ends are generated in separated files. Each FASTQ is splitted in multiple LANEs and grouped by the Multiplex index.
Illumina HiSeq 4000
12
EGAD00001008202
This dataset include BAM files of 808 samples from GCAT cohort. Technology used HiSeq 4000, read length 150 bp, inner mate distance 300 bp. For each sample the paired -ends are generated in separated files. Each FASTQ is splitted in multiple LANEs and grouped by the Multiplex index.
1
EGAD00001008210
This dataset contains raw genotypes ( SNVs, Indels and SVs), from 785 samples,without applying any filter, from the 808 WGS GCAT cohort.
1
EGAD00010001664
4988 samples issued from GCAT cohort, genotyped with MEGAex-Infinium Array, with data for Cr1-22. Plink files with QC and imputed (SHAPEIT+IMPUTE).
Illumina-Genotyping Array
4988
EGAD00010001665
4988 samples issued from GCAT cohort, genotyped with MEGAex-Infinium Array, with data for Cr1-22. Plink files with QC but not imputed.
Illumina-Genotyping Array
4988
EGAD00010002152
This resource contains the SV annotations using the AnnotSV tool. The description of annotations can be found in AnnotSV web page https://lbgi.fr/AnnotSV/ or GCAT-BSC web page: http://cg.bsc.es/GCAT_BSC_iberianpanel
Illumina HiSeq 4000
785
EGAD00010002153
This dataset includes the .hap, .legend and .sample files from the GCAT|Panel (Iberian reference panel), built from 785 samples, after QC, from the 808 WGS GCAT cohort, including 30.3M SNVs, 5M Indels and 89K SVs. This resource has been generated using Shapeit4 and WhatsHap software. Technology used HiSeq 4000, read length 150 bp, inner mate disatance 300 bp.
Illumina HiSeq 4000
785
EGAD00010002740
This dataset contains DNA methylation data from 400 individuals (200 Type 2 Diabetes cases and 200 controls) from the GCAT (Genomes for Life) cohort. The methylation profiling was performed using the Illumina Infinium MethylationEPIC v2.0 BeadChip, which offers comprehensive coverage of over 850,000 CpG sites. Data are provided in IDAT file format, enabling raw signal-level analysis and downstream processing.
Infinium MethylationEPIC v2.0
400
EGAD00010002749
4988 samples issued from GCAT cohort, genotyped with MEGAex-Infinium Array, with data for Cr1-23. Plink files with QC and imputed using TOPMed r2.
Illumina-Genotyping Array
4988
EGAD00010002758
2746 samples issued from GCAT cohort, genotyped with GSA Array, with data for Cr1-23. Plink files with QC and imputed using TOPMed.
Illumina-Genotyping Array
2746
EGAD00010002786
Proteomic expression analysis of 866 individuals assessing 92 inflammatory protein biomarkers using Olink® technology.
Olink
866
EGAD00010002814
Proteomic expression analysis of 171 individuals, in two time points, with confirmed SARS-CoV-2 infection, including 133 long COVID patients, assessed 1,395 protein biomarkers using Olink® technology.
Olink
171
EGAD00010002872
This dataset contains quality-controlled genome-wide genotype data from 18,728 individuals belonging to the GCAT (Genomes for Life) study, a population-based prospective cohort of adults recruited in Catalonia, Spain. Genotype data are provided in PLINK binary format (BED/BIM/FAM) alongside a metadata file containing phenotypic and ancestry covariates.
Genotyping was performed using the Illumina Global Clinical Research Array v.1.0. Raw genotype data underwent a comprehensive quality-control pipeline prior to release. At the variant level, sites with a genotype call rate below 98% were removed in two rounds, once across all samples and once restricted to the final clean sample set, and variants failing Hardy-Weinberg equilibrium (p < 1x106) or with a minor allele frequency below 1% were also excluded. At the sample level, individuals with a call rate below 95% or with heterozygosity deviating more than three standard deviations from the cohort mean were removed. Sex was verified by comparing reported sex against X-chromosome F-statistics and Y-chromosome coverage, and discordant samples were flagged and excluded.
Pairwise kinship was estimated using the KING estimator, and where an individual had been genotyped more than once, the highest-quality sample was retained, yielding exactly one sample per individual in the final dataset. All coordinates are on the GRCh38/hg38 reference genome. Imputation was carried out using TopMed R3.
The accompanying metadata file contains one row per individual. The fields age and sex correspond to age at recruitment (in years) and self-reported sex (1 = Male, 2 = Female), respectively. The field is_european is a binary flag (1/0) indicating whether the individual was classified as of European ancestry, based on a joint principal component analysis (PCA) with the 1000 Genomes Project and HGDP reference panels followed by Rye ancestry classification at a posterior probability threshold of 0.85. The field is_unrelated is a binary flag (1/0) indicating whether the individual has no second-degree or closer relative retained in the dataset (KING kinship coefficient < 0.0884).
The columns GlobalPC1-GlobalPC20 contain the first 20 principal components derived from the joint PCA with global reference panels, capturing broad ancestry structure and suitable for multi-ancestry analyses or cohort characterisation. The columns PC1-PC20 contain the first 20 within-European principal components, computed on unrelated European-ancestry individuals using FlashPCA and subsequently projected onto all European-ancestry individuals; these are intended as covariates for genome-wide association analyses to correct for fine-scale population stratification, and are set to NA for non-European individuals.
For European-restricted analyses, we recommend selecting individuals with is_european = 1 and including PC1-PC20, age, and sex as covariates. For analyses requiring independence between observations, additionally filtering on is_unrelated = 1 is advised. GlobalPC1-GlobalPC20 are recommended for multi-ancestry analyses or as an additional check on population structure.
Illumina-Genotyping Array
18728
EGAD50000001378
This dataset comprises targeted sequencing data of 52 genes previously implicated in severe COVID-19 outcomes. The study includes samples from 764 individuals with severe COVID-19 and 3,939 population-based controls from the GCAT cohort (Spain). Molecular Inversion Probes (MIPs) were utilized for cost-effective and precise sequencing of the selected genes.
The targeted genes include:
Inflammasome/IL-1/TNF Pathway: NLRP3, CASP1, CASP8, IL1B, TNF, RIPK1, RIPK3, MYD88, TNFRSF13B
SARS-CoV-2 Entry/Replication: ACE2, TMPRSS2, FURIN, SLC6A20, DDX1, DDX58, TLR4, FYCO1, CTSB, CTSL, ADAM17
Complement System: MBL2, CFH, CFI, CFB, ADAM10, CD46
Interferon Signaling: TLR3, IFIH1, IFITM3, TBK1, TLR7, IL10RB, IFNAR1, IFNAR2, SIGLEC1, MYD88, IFNGR1
Chemokine Receptor Signaling: CCR1, CCR3, CCR2, CCR9, IL8, CXCL3, CXCL10, CXCR6, XCR1, CCL2, CCL20
Immunodeficiency Genes: CASP8, CD46, CFB, CFH, CFI, IFNAR1, IFNAR2, IFNGR1, IFIH1, MYD88, NLRP3, RIPK1, TBK1, TLR3, TLR7
Illumina NovaSeq 6000
2294
EGAD50000002415
This dataset comprises targeted sequencing data from 191 participants of the GCAT cohort generated using the I2HCP custom hereditary cancer panel. The panel is based on a custom bait library covering 122 genes associated with hereditary cancer syndromes, including genes related to hereditary colorectal cancer, hereditary breast and ovarian cancer, neurofibromatosis, and related disorders.
Target enrichment was performed using a clinically validated design optimized for diagnostic accuracy. The panel and associated bioinformatic pipeline were previously validated, achieving analytical sensitivity and specificity greater than 99%. Sequencing data were processed using standardized alignment and variant calling procedures against the human reference genome.
The dataset includes raw sequencing reads (FASTQ format) and processed variant call files (VCF format). All samples were pseudonymized prior to submission in accordance with ethical approvals and participant consent. Data are available under controlled access.
Illumina MiSeq
194
