Overview

GFE is described in more detail on the IGDAWG website.

Paper

In 2015 the paper introducing GFE (“A gene feature enumeration approach for describing HLA allele polymorphism”) was published by Steve Mack in Human Immunology. The paper describes the GFE notation, its applicaitons, and the development of the feature service.

GFE Nomenclature

Note

Currently, the GFE nomenclature returned from the service does not represent partial sequences. In the next release we intend to represent this as an aligned percent for each feature to the reference sequence. This is similar to the aligned value returned for the full sequence.

The GFE allele name is created by joining the feature accesion numbers. Each accession number is generated by making a RESTful call to the feature service with the sequence and it’s corresponding feature. If the sequence has been observed before, the the feature service will return the previously generated accession number, otherwise it will generate a unique accession number for that feature and return it. The GFE allele HLA-Aw1-1-7-20-10-32-7-1-1-1-6-1-5-3-5-1-1 is broken up into the following parts:

Feature	Accession Number
five_prime_UTR	1
Exon 1	1
Intron 1	7
Exon 2	20
Intron 2	10
Exon 3	32
Intron 3	7
Exon 4	1
Intron 4	1
Exon 5	1
Intron 5	6
Exon 6	1
Intron 6	5
Exon 7	3
Intron 7	5
Exon 8	1
three_prime_UTR	1

In the example above all of the features for HLA-A were found in the sequence. If a sequence does not contain a particular feature, then the feature accession number will be zero. The raw sequence is broken up into each of its features using the annotation pipeline.