Published Papers

The paper introducing GFE ('A Gene Feature Enumeration Approach for Describing HLA Allele Polymorphism' Mack SJ. Human Immunology. 2015 76(12):975-981), describes the principles underlying GFE, GFE notation and its applications, and the development of a GFE service.


GFE Example

An example of GFE for the alleles of the classical HLA loci included in IMGT/HLA Database version 3.21.1 was included in Mack SJ (2015) as supplementary data. That supplementary data table (EnumeratedSequenceFeatures_3.21.1.xlsx) is available for download (1.5MB).


GFE Service and Code

An internet-based GFE Service is under development; the goal of this service is to make GFE notations publically accessible for online or offline use, persist GFEs between successive IMGT/HLA Database releases and permit the automated inter-conversion of allele names and GFE notations.

The core element of this GFE service is a feature service that returns an accession number upon the submission of a sequence for a specific gene feature, and that returns the sequence for a given accession number for a given gene feature. A prototype implementation of this service is available at: http://feature.nmdp-bioinformatics.org/

The code for the GFE service is available online at: github.com/nmdp-bioinformatics/service-feature.


Distribution of Gene Features in IMGT/HLA Database Release Version 3.21.1

The extent to which the sequences of gene features at the HLA-A, -B, -C and -DRB1 loci are known for the alleles in IMGT/HLA Database release 3.21.1 are shown in the four figures below.

Each figure describes the percentage of alleles for which the nucleotide sequence of gene features is known (indicated in blue). The % Total value at the bottom of each column represents the percentage of alleles for which nucleotide sequence for each individual GF is known. Each % Total value in the second column represents the percentage of alleles for which nucleotide sequence for the GFs shown in blue in that row are known. The total number of alleles at each locus with available nucleotide sequences is shown at the bottom of the first column.