Allele Frequencies in World Populations

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New Gold Population Standards


We have defined new classifications of data (gold, silver and bronze) to assist users in identifying the most suitable populations for their tasks.

Three important criteria (allele frequency sums to 1, sample size>50, and four digit resolution) define the gold standard dataset (see Table 1 below).
Silver standard is derived from a less stringent level that users might wish to consult if the region of the world they are interested in is not well covered by gold standard data.
Bronze standard includes populations that do not meet these criteria, but remain in AFND as a record of published data sets which are likely to require some care when interpreting. The bronze standard set includes all data at two digit resolution for which very large sets exist, for example from some Bone Marrow Donor Registries.


Table 1. Features and criteria for defining gold, silver and bronze standard datasets.

Criteria Gold standard Silver standard Bronze standard
Allele frequency Allele frequencies Sum to 1 (± 0.015; or ± 0.05 if estimated from phenotype frequencies) Sums to 1 (± 0.015; or ± 0.05 if estimated from phenotype frequencies) Any that do not match to gold and silver criteria
Sample size ≥50 individuals Any Any
Resolution

Frequency of all alleles given in at least four digits. Higher resolution adjusted to four digits Frequency of all alleles given in mixed two/four or more digits. Any that do not match to gold and silver criteria

 

   

Allele frequency net 2015 update: new features for HLA epitopes, KIR and disease and HLA adverse drug reaction associations.
Gonzalez-Galarza FF, Takeshita LY, Santos EJ, Kempson F, Maia MH, Silva AL, Silva AL, Ghattaoraya GS, Alfirevic A, Jones AR and Middleton D Nucleic Acid Research 2015, 39, 28, D784-8.
Liverpool, U.K.

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