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DAC GCAT

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This DAC controls 15 datasets

Dataset ID	Description	Technology	Samples
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	1
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
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