P182 EASY-HLA: A suite of software using haplotypes to handle HLA typing data

Abstract

Aim To develop a user-friendly web application software based on validated and published HLA haplotype frequencies that will deliver a complete suite of HLA elements. Methods Easy-HLA is designed with an algorithm in php language that predicts haplotypes from individual’s genotypes. The input genotypes can be entered with low/mid resolution, such as ambiguous typings and NMDP codes. The predicted haplotypes will then be used as a base to resolve several HLA related features. Results Easy-HLA combines several modules: Easymatch-R (for likelihood computation), HLA-upgrade (statistical resolution of HLA typing ambiguity), HLA-2-haplo (Haplotype inference), HLA-expr (statistical imputation of HLA expression), HLA-AA (Amino Acid equivalence of HLA allele) and HLA-KIRlig (classification of KIR Ligand). Easymatch-R gives the likelihood of finding a specific genotype. It was validated retrospectively in 200 individuals from an unrelated stem cell donor database. HLA-upgrade predicts a complete HLA-A, B, C, DRB1, DQB1 genotype from a limited typing knowledge. It was further validated in 1500 samples with all 5 loci typed at 4 digits. HLA-2-Haplo predicts the pair of haplotypes from a given genotype and their frequencies in different populations. It was validated on 300 family-determined haplotypes (from the parents). HLA-expr gives the HLA-C predicted expression (based on allele specific mean HLA-C expression). HLA-AA gives the amino acids of the HLA alleles as well as their haplotypes. HLA-KIRlig tells in which group belong the HLA alleles of an individual in term of KIR binding: C1/C2 groups, Bw4/Bw6 and KIR2DL2 ligand. Conclusions The major limiting factor of retrospective analysis of large dataset with HLA genotypes is the difficulty in using archived typings recorded in their initial state and used for clinical purposes. However, for research use and population level analysis, assumptions and computations can be made to facilitate large scale study. Easy-HLA is a package built to uncover the full details of the HLA genotypes in an individual (single request) or in a cohort (batch request) and delivers data in the form of database compatible related tables which can be easily used to perform analyses. Easy-HLA is available online: http://hla.univ-nantes.fr .