PGS Catalog - Download Information

Downloads

This page contains information about the PGS Catalog downloads and FTP.

Available PGS Catalog downloads

PGS Scoring Files & Metadata Individual PGS variants scoring and metadata files	View PGS Score Directories (FTP)
PGS Catalog Metadata Available PGS global metadata files	Bulk Metadata Downloads.xlsx
PGS Catalog REST API Programmatic access to the PGS Catalog metadata	REST API endpoint documentation

PGS Catalog FTP structure

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
├── pgs_scores_list.txt (list of Polygenic Score IDs)
├── metadata/
│   ├── pgs_all_metadata.xlsx
│   ├── pgs_all_metadata_[sheet_name].csv (7 files)
│   ├── pgs_all_metadata.tar.gz (xlsx + csv files)
│   ├── publications/ (metadata for large studies)
│   └── previous_releases/
└── scores/
  ├── PGS000001/
  │   ├── Metadata/
  │   │   ├── PGS000001_metadata.xlsx
  │   │   ├── PGS000001_metadata_[sheet_name].csv (7 files)
  │   │   ├── PGS000001_metadata.tar.gz (xlsx + csv files)
  │   │   └── archived_versions/
  │   └── ScoringFiles/
  │       ├── PGS000001.txt.gz
  │       └── archived_versions/
  ├── PGS000002/
  ·	├─ ···
  ·	└─ ···
  ·
  └── PGS00..../
      ├─ ···
      └─ ···

PGS Scoring Files

Format: 2.0

Header— Columns— Format changes— Previous formats

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). The current PGS

Note: These files are composed of author-reported variants and annotations, and have only been consistently formatted to have the same column headings and data types within each column. We are currently working on methods to provide harmonized versions of each PGS in different genome builds (GRCh37 and GRCh38), ensuring each variant has a chromosomal position (either by adding it based on rsID or using liftover), and flagging potentially problematic variants (e.g. palindromic SNPs) or those that are inconsistent with the current genome build (e.g. strand flips, and variants not found in the Ensembl Variation databases).

PGS Scoring Files — Header

Here is a description of the PGS Scoring Files header:

###PGS CATALOG SCORING FILE - see https://www.pgscatalog.org/downloads/#dl_ftp_scoring for additional information
#format_version=Version of the scoring file format, e.g. '2.0'
##POLYGENIC SCORE (PGS) INFORMATION
#pgs_id=PGS identifier, e.g. 'PGS000001'
#pgs_name=PGS name, e.g. 'PRS77_BC' - optional
#trait_reported=trait, e.g. 'Breast Cancer'
#trait_mapped=Ontology trait name, e.g. 'breast carcinoma'
#trait_efo=Ontology trait ID (EFO), e.g. 'EFO_0000305'
#genome_build=Genome build/assembly, e.g. 'GRCh38'
#variants_number=Number of variants listed in the PGS
#weight_type=Variant weight type, e.g. 'beta', 'OR/HR' (default 'NR')
##SOURCE INFORMATION
#pgp_id=PGS publication identifier, 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_alleleother_alleleeffect_weight...

Note: The "#trait_mapped" and "#trait_efo" metadata can be composed of more than one value (separated by a | "pipe"), e.g.:

#trait_mapped=Ischemic stroke|stroke
#trait_efo=HP_0002140|EFO_0000712

Example of PGS Scoring Files header

###PGS CATALOG SCORING FILE - see https://www.pgscatalog.org/downloads/#dl_ftp_scoring for additional information
#format_version=2.0
##POLYGENIC SCORE (PGS) INFORMATION
#pgs_id=PGS000348
#pgs_name=PRS_PrCa
#trait_reported=Prostate cancer
#trait_mapped=prostate carcinoma
#trait_efo=EFO_0001663
#genome_build=GRCh37
#variants_number=72
#weight_type=log(OR)
##SOURCE INFORMATION
#pgp_id=PGP000113
#citation=Black M et al. Prostate (2020). doi:10.1002/pros.24058
#license=Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0). © 2020 Ambry Genetics.
rsIDchr_namechr_positioneffect_alleleother_alleleeffect_weight...

PGS Scoring Files — Columns

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. This column also contains HLA alleles in the standard notation (e.g. HLA-DQA1*0102) that aren’t always provided with chromosomal positions.
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
other_allele	Other allele(s)	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. Additional information on how the effect_weight was derived is in the weight_type field of the header, and score development method in the metadata downloads.	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
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_dominant	FLAG: Dominant Inheritance Model	This is a TRUE/FALSE variable that flags whether the weight should be added to the PGS sum if there is at least 1 copy of the effect allele (e.g. it is a dominant allele).	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

Example of PGS Scoring Files data

Scoring Files header
rsID        chr_name  chr_position  effect_allele  other_allele  effect_weight
rs2843152   1         2245570       G              C             -2.76009e-02
rs35465346  1         22132518      G              A             2.39340e-02
rs28470722  1         38386727      G              A             -1.74935e-02
rs11206510  1         55496039      T              C             2.93005e-02
rs9970807   1         56965664      C              T             4.70027e-02
rs61772626  1         57015668      A              G             -2.71202e-02
rs7528419   1         109817192     A              G             2.91912e-02
rs1277930   1         109822143     A              G             2.60105e-02
rs11102000  1         110298166     G              C             2.45969e-02
rs11810571  1         151762308     G              C             2.09215e-02
rs6689306   1         154395946     G              A             -1.97906e-02
rs72702224  1         154911689     G              A             -2.81310e-02
rs3738591   1         155764808     C              G             4.23731e-02
...

PGS Scoring Files — Format changes

Version 2.0
- Header (metadata)
  - The metadata labels will change from the previous text-based titles to new field labels that match the outputs of the REST API Score and Publication endpoints. We will also adopt new formatting by removing spaces (e.g. 'PGS ID' is changed to 'pgs_id').
    This should make the data easier to parse and more consistent across methods of data access.
  - Addition of the #format_version field.
    New versioning to keep track of the format changes.
  - Addition of the new metadata fields #trait_mapped and #trait_efo.
    These fields should make it easier to group scores based on structured trait terms.
  - Addition of the #weight_type field.
    This information was previously included as a column in the scoring file. This lets users know how the effect_weight column was derived (if known), otherwise it is labeled as NR (Not Reported).
- Scoring File Schema (Column data)
  - Move redundant information of the column weight_type into the header.
    In all cases the weight_type was identical across all variants in a score. To remove redundant columns with identical data we moved this information into a metadata field that is now presented on the website and API as well as in the scoring file header.
  - Rename the column reference_allele to other_allele.
    We are renaming this column other_allele to remove the use of the word "reference". "Reference allele" may have been confused with the allele included in the reference genome assembly. The other/non-effect allele may or may not be the reference genome allele. Initially we had named it reference_allele to refer to the allele that when homozygous has zero (reference) dosage. We now rename it other_allele to reflect that it is the non-effect allele. This terminology is consistent with the GWAS summary statistics standard format used by the GWAS Catalog.
Format version 2.0
###PGS CATALOG SCORING FILE - see ... #format_version=Version of the scoring file format, e.g. '2.0' ##POLYGENIC SCORE (PGS) INFORMATION #pgs_id=PGS identifier, e.g. 'PGS000001' #pgs_name=PGS name, e.g. 'PRS77_BC' - optional #trait_reported=trait, e.g. 'Breast Cancer' #trait_mapped=Ontology trait name, e.g. 'breast carcinoma' #trait_efo=Ontology trait ID (EFO), e.g. 'EFO_0000305' #genome_build=Genome build/assembly, e.g. 'GRCh38' #variants_number=Number of variants listed in the PGS #weight_type=Variant weight type, e.g. 'beta', 'OR/HR' (default 'NR') ##SOURCE INFORMATION #pgp_id=PGS publication identifier, e.g. 'PGP000001' #citation=Information about the publication #license=License and terms of PGS use/distribution ... rsIDchr_namechr_positioneffect_alleleother_allele...
Schema version 1.0
### PGS CATALOG SCORING FILE - see ... ## POLYGENIC SCORE (PGS) INFORMATION # PGS ID = PGS identifier, 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 identifier, e.g. 'PGP000001' # Citation = Information about the publication # LICENSE = License and terms of PGS use/distribution ... rsIDchr_namechr_positioneffect_allelereference_allele...
- New header information
- Column name change

PGS Scoring Files — Previous formats

Version 1.0 (up to December 14, 2021)

Header