This page contains information about the PGS Catalog downloads and FTP.
| PGS Scoring Files & Metadata | View PGS Score Directories (FTP) |
| PGS Catalog Metadata | Bulk Metadata Downloads.xlsx |
| PGS Catalog REST API | REST API endpoint descriptions |
The PGS Catalog FTP allows for consistent access to the bulk downloads, and is indexed by Polygenic Score (PGS) ID to allow programmatic access to score level data. The following diagram illustrates the FTP structure:
ftp://ftp.ebi.ac.uk/pub/databases/spot/pgs ├── metadata/ │ ├── pgs_all_metadata.xlsx │ ├── pgs_all_metadata_[sheet_name].csv (6 files) │ ├── pgs_all_metadata.tar.gz (xlsx + csv files) │ └── previous_releases/ └── scores/ ├── PGS000001/ │ ├── Metadata/ │ │ ├── PGS000001_metadata.xlsx │ │ ├── PGS000001_metadata_[sheet_name].csv (6 files) │ │ ├── PGS000001_metadata.tar.gz (xlsx + csv files) │ │ └── archived_versions/ │ └── ScoringFiles/ │ ├── PGS000001.txt.gz │ └── archived_versions/ ├── PGS000002/ · ├─ ··· · └─ ··· · └── PGS000.../ ├─ ··· └─ ···
Each scoring file (variant information, effect alleles/weights) is formatted to be a gzipped tab-delimited text file, labelled by its PGS Catalog Score ID (e.g. PGS000001.txt.gz).
Here is a description of the PGS Scoring Files header:
### PGS CATALOG SCORING FILE - see www.pgscatalog.org/downloads/#dl_ftp for additional information ## POLYGENIC SCORE (PGS) INFORMATION # PGS ID = PGS idenfier, e.g. 'PGS000001' # PGS Name = PGS name, e.g. 'PRS77_BC' - optional # Reported Trait = trait, e.g. 'Breast Cancer' # Original Genome Build = Genome build/assembly, e.g. 'GRCh38' # Number of Variants = Number of variants listed in the PGS ## SOURCE INFORMATION # PGP ID = PGS publication idenfier, e.g. 'PGP000001' # Citation = Information about the publication # LICENSE = License and terms of PGS use/distribution - refers to the EMBL-EBI Terms of Use by default rsIDchr_namechr_positioneffect_allelereference_allele...
It also has been edited to have consistent column headings based on the following schema:
| Column Header | Field Name | Field Description | Field Requirement |
|---|---|---|---|
| rsID | dbSNP Accession ID (rsID) | The SNP’s rs ID | Optional - unless both the chr_name and chr_position columns are absent |
| chr_name | Location - Chromosome | Chromosome name/number associated with the variant | Required - may be optional if an rsID for the variant is provided |
| chr_position | Location - Position within the Chromosome | Chromosomal position associated with the variant | Required - may be optional if an rsID for the variant is provided |
| effect_allele | Effect Allele | The allele that's dosage is counted (e.g. {0, 1, 2}) and multiplied by the variant's weight ('effect_weight') when calculating score. The effect allele is also known as the 'risk allele'. | Required |
| reference_allele | Reference Allele | The other allele(s) at the loci | Optional - but strongly recommended |
| effect_weight | Variant Weight | Value of the effect that is multiplied by the dosage of the effect allele ('effect_allele') when calculating the score. | Required |
| locus_name | Locus Name | This is kept in for loci where the variant may be referenced by the gene (APOE e4). It is also common (usually in smaller PGS) to see the variants named according to the genes they impact. | Optional |
| weight_type | Type of Weight | Whether the author supplied Variant Weight is a: beta (effect size), or something like an OR/HR (odds/hazard ratio) | Optional |
| allelefrequency_effect | Effect Allele Frequency | Reported effect allele frequency, if the associated locus is a haplotype then haplotype frequency will be extracted. | Optional |
| is_interaction | FLAG: Interaction | This is a TRUE/FALSE variable that flags whether the weight should be multiplied with the dosage of more than one variant. Interactions are demarcated with a _x_ between entries for each of the variants present in the interaction. | Optional |
| is_recessive | FLAG: Recessive Inheritance Model | This is a TRUE/FALSE variable that flags whether the weight should be added to the PGS sum only if there are 2 copies of the effect allele (e.g. it is a recessive allele). | Optional |
| is_haplotype is_diplotype | FLAG: Haplotype or Diplotype | This is a TRUE/FALSE variable that flags whether the effect allele is a haplotype/diplotype rather than a single SNP. Constituent SNPs in the haplotype are semi-colon separated. | Optional |
| imputation_method | Imputation Method | This described whether the variant was specifically called with a specific imputation or variant calling method. This is mostly kept to describe HLA-genotyping methods (e.g. flag SNP2HLA, HLA*IMP) that gives alleles that are not referenced by genomic position. | Optional |
| variant_description | Variant Description | This field describes any extra information about the variant (e.g. how it is genotyped or scored) that cannot be captured by the other fields. | Optional |
| inclusion_criteria | Score Inclusion Criteria | Explanation of when this variant gets included into the PGS (e.g. if it depends on the results from other variants). | Optional |
| Extra columns: | |||
| OR HR | Odds Ratio [OR], Hazard Ratio [HR] | Author-reported effect sizes can be supplied to the Catalog. If no other effect_weight is given the weight is calculated using the log(OR) or log(HR). | Optional |
| allelefrequency_effect_Ancestry | Population-specific effect allele frequency | Reported effect allele frequency in a specific population (described by the authors). | Optional |
Bulk download of the entire PGS Catalog's metadata, describing all PGS in terms of their publication source, samples used for development/evaluation, and related performance metrics. Download Metadata file.xlsx
The bulk download contains a single Excel file with multiple sheets describing each of the data types. The sheets are also provided as individual .csv files for easier import in analysis tools, and are provided on the FTP in the metadata/ folder.