GCAT | Genomes for life: cohort study of the genomes of Catalonia

Study ID	Alternative Stable ID	Type
EGAS00001003018		Other

Study ID

Alternative Stable ID

Type

EGAS00001003018

Other

Study Description

The GCAT Study have recruited 20 000 participants aged 40–65 years. Participants who agreed to take part in the study completed a self-administered computer-driven questionnaire, and underwent blood pressure, cardiac frequency and anthropometry measurements. For each participant, blood plasma, blood serum and white blood cells are collected at baseline. A total of 5459 genomic profiles have been characterised by comprehensive genotyping. Genome-wide genotypes have been generated using Illumina Infinium SNP-bead array technology. We chose the Multi-Ethnic Global (MEGAEX, V.2) consortium array, a multipurpose, multiethnic genotyping array with two million selected markers (including previously described germline mutations, insertions-deletions (InDels) and SNPs).We have strictly followed the standard manufacturer recommended automated protocol for the Infinium HTS Assay scanned with a HiScan confocal scanner (Illumina, San Diego, California, USA). Genome Studio V.2011.1 has been used for raw data analysis. Genotyping was performed at the Genomics and Bioinformatics Unit of the ... (Show More)

Dataset ID	Description	Technology	Samples
EGAD00001007729	Sex, age at recruitment (2014-2018), and birthdate of GCAT Cohort individuals. Sex, age at recruitment (2014-2018), and birthdate of GCAT Cohort individuals.		19329
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). 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).		4988
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). 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).		17155
EGAD00001007774	This dataset contains genotypes (35.4M of SNVs, Indels and SVs), from 785 samples, after QC filtering, from the 808 WGS GCAT cohort. This dataset contains genotypes (35.4M of SNVs, Indels and SVs), from 785 samples, after QC filtering, from the 808 WGS GCAT cohort.		785
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. 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	808
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. 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.		808
EGAD00001008210	This dataset contains raw genotypes ( SNVs, Indels and SVs), from 785 samples,without applying any filter, from the 808 WGS GCAT cohort. This dataset contains raw genotypes ( SNVs, Indels and SVs), from 785 samples,without applying any filter, from the 808 WGS GCAT cohort.		785
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). 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. 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 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. 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

Dataset ID

Description

Technology

Samples

EGAD00001007729

Sex, age at recruitment (2014-2018), and birthdate of GCAT Cohort individuals.

19329

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).

4988

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).

17155

EGAD00001007774

This dataset contains genotypes (35.4M of SNVs, Indels and SVs), from 785 samples, after QC filtering, from the 808 WGS GCAT cohort.

785

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

808

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.

808

EGAD00001008210

This dataset contains raw genotypes ( SNVs, Indels and SVs), from 785 samples,without applying any filter, from the 808 WGS GCAT cohort.

785

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

Study

Study Description

Study Datasets 11 datasets.

Who archives the data?

Publications

Citations

The European Genome-phenome Archive (EGA) is part of the ELIXIR infrastructure.