HLA Genotyping

Generated on 2026-05-07

HLA Genotyping

DRAGEN includes a dedicated genotyper for genotyping the Human Leukocyte Antigen (HLA) genes. This typer is capable of matching to established HLA alleles from the IMGT Database as well as calling novel alleles. For WGS data or panels covering the entire HLA genes, DRAGEN can output HLA types at full resolution. For more information, refer to DRAGEN manual.

Assessment based on 47 samples with long read truth calls. 3- and 4-field resolution for HLA Class I accuracy is not supported in DRAGEN 4.4.

HLA Class I Accuracy Table

2-field comparison

Gene	Field resolution	DRAGEN version	Accuracy	2-field improvement (4.5.4 - 4.4)
A	2-field	4.4	98.94%
B	2-field	4.4	96.81%
C	2-field	4.4	98.94%
All	2-field	4.4	98.23%
A	2-field	4.5.4	98.94%	+0.00 pp
B	2-field	4.5.4	98.94%	+2.13 pp
C	2-field	4.5.4	100.00%	+1.06 pp
All	2-field	4.5.4	99.29%	+1.06 pp

Other field resolutions

Gene	Field resolution	DRAGEN version	Accuracy
A	3-field	4.5.4	98.94%
B	3-field	4.5.4	96.81%
C	3-field	4.5.4	100.00%
All	3-field	4.5.4	98.58%
A	4-field	4.5.4	94.68%
B	4-field	4.5.4	92.55%
C	4-field	4.5.4	93.62%
All	4-field	4.5.4	93.62%

HLA Class I Accuracy

HLA Class II Accuracy Table

Gene	Field resolution	DRAGEN version	Accuracy
DPA1	2-field	4.5.4	94.05%
DPB1	2-field	4.5.4	98.81%
DQA1	2-field	4.5.4	99.40%
DQB1	2-field	4.5.4	100.00%
DRB1	2-field	4.5.4	93.45%
All	2-field	4.5.4	97.14%
DPA1	3-field	4.5.4	91.67%
DPB1	3-field	4.5.4	98.21%
DQA1	3-field	4.5.4	98.81%
DQB1	3-field	4.5.4	92.26%
DRB1	3-field	4.5.4	93.45%
All	3-field	4.5.4	94.88%
DPA1	4-field	4.5.4	87.50%
DPB1	4-field	4.5.4	93.45%
DQA1	4-field	4.5.4	89.29%
DQB1	4-field	4.5.4	83.33%
DRB1	4-field	4.5.4	75.00%
All	4-field	4.5.4	85.71%

HLA Class II Accuracy