Helix PGx Database

Frequency tables for pharmacogenomics alleles and genotypes as called by the Helix® PGx pipeline.

This data is being made available via the Creative Commons Attribution Non-Commercial Share Alike license

📚 Datasets

Star allele frequency table [star_allele_frequencies.tsv]

Column	Description
gene	The HGNC gene symbol.
allele	Star allele designation.
PV id	PharmVar identifier. Can be resolved by appending the numeric id to the end of the URL: https://www.pharmvar.org/haplotype/
function	Annotated allele function sourced from PharmVar API.
SV	Whether this allele is a structural variant, e.g. a hybrid allele or whole gene deletion/duplication.
overall freq	Population frequency of the star allele in this study.
non EUR freq	Frequency of star allele within the set of individuals who were not predominant EUR ancestry. Non EUR determined by <=80% EUR Admixture value.
AFR freq	Frequency of star allele within the set of individuals assigned to the Africa (AFR) population in this study. AFR determined by >80% Admixture value.
AMR freq	Frequency of star allele within the set of individuals assigned to the Americas (AMR) population in this study. AMR determined by >80% Admixture value.
EAS freq	Frequency of star allele within the set of individuals assigned to the East Asia (EAS) population in this study. EAS determined by >80% Admixture value.
EUR freq	Frequency of star allele within the set of individuals assigned to the Europe (EUR) population in this study. EUR determined by >80% Admixture value.
SAS freq	Frequency of star allele within the set of individuals assigned to the South Asia (SAS) population in this study. SAS determined by >80% Admixture value.
OTHER freq	Frequency of star allele within the set of individuals that could not be readily assigned a specific population in this study.

Genotype-to-phenotype frequency table [genotype_phenotype_frequencies.tsv]

Column	Description
gene	The HGNC gene symbol.
alleles	Comma delimited list of all star alleles comprising the genotype. Novel pLoF alleles are listed at the end with the format chr#:POS, where POS is the position in hg38. "Incomplete Match" is appended when the reported allele combination does not completely explain the variants supported by the underlying data.
alleles amp	Reformatted list of alleles, using the amplification syntax. For example, (*1, *1, *1) would be rewritten as (*1, *1x2).
activity scores	Comma delimited list of activity scores for each allele in column 2. Novel pLoF variants and incomplete matches default to "null".
metabolizer status	Metabolic status for the gene derived from the activity score. Defaults to "Unknown" if genotype contains an incomplete match or includes an allele of Unknown fuction.
risk	CPIC assignment of PGx risk dependent on metabolizer status using EHR Priority Result Notation. Defaults to "Unknown" if genotype is an incomplete match. (A priority result is defined as a genetic test result that results in a change in drug, drug dose, or drug monitoring.)
overall gt freq	Population frequency of the genotype in this study.
non EUR gt freq	Frequency of genotype within the set of individuals who were not predominant EUR ancestry. Non EUR determined by <=80% EUR Admixture value.
AFR gt freq	Frequency of genotype within the set of individuals assigned to the Africa (AFR) population in this study. AFR determined by >80% Admixture value.
AMR gt freq	Frequency of genotype within the set of individuals assigned to the Americas (AMR) population in this study. AMR determined by >80% Admixture value.
EAS gt freq	Frequency of genotype within the set of individuals assigned to the East Asia (EAS) population in this study. EAS determined by >80% Admixture value.
EUR gt freq	Frequency of genotype within the set of individuals assigned to the Europe (EUR) population in this study. EUR determined by >80% Admixture value.
SAS gt freq	Frequency of genotype within the set of individuals assigned to the South Asia (SAS) population in this study. SAS determined by >80% Admixture value.
OTHER gt freq	Frequency of genotype within the set of individuals that could not be readily assigned a specific population in this study.