bioRxivGenomicsPreprint
MHC*IMP - Imputation of Alleles for Genes in the Major Histocompatibility Complex
David SquireiD, Allan MotyeriD, Richard S. AhniD, Joanne NitithamiD, Zhiming HuangiD, Jorge R. OksenbergiD, John FoersteriD, Wilson J. LiaoiD, Stephen LeslieiD
Abstract
We report the development of MHC*IMP, a method for imputing non-classical HLA and other genes in the human Major Histocompatibility Complex (MHC). We created a reference panel for 25 genes in the MHC using allele calls from Whole Genome Sequencing data, combined with SNP data for the same individuals. We used this to construct an allele imputation model, MHC*IMP, for each gene. Cross-validation showed that MHC*IMP performs very well, with allele prediction accuracy 93% or greater for all but two of the genes, and greater than 95% for all but four.
- Citations
- 5
Reproducibility ledger
Nobody has reported trying to reproduce this paper yet. Did you replicate an experiment or run the code? Your report saves the next lab a week.
Sign in to file a reproducibility report.
Related papers
- Accurate multi-population imputation of MICA, MICB, HLA-E, HLA-F and HLA-G alleles from genome SNP data
Silja Tammi, Satu Koskela, … Jarmo Ritari·PLoS Computational BiologyPeer-reviewed·Sep 16, 2024
- Practical Use of Methods for Imputation of HLA Alleles from SNP Genotype Data
Allan Motyer, Damjan Vukcevic, … Stephen Leslie·bioRxiv·Dec 9, 2016
- A statistical genetics guide to identifying HLA alleles driving complex disease
Saori Sakaue, Saisriram Gurajala, … Soumya Raychaudhuri·bioRxiv·Aug 24, 2022
- Optimal HLA imputation of admixed population with dimension reduction
Venceslas Douillard, Nayane dos Santos Brito Silva, … Nicolas Vince·bioRxiv·Apr 12, 2023
- HLA Allele Imputation with Multitask Deep Convolutional Neural Network
Calvin Chi·bioRxiv·Jun 3, 2021
- Complete sequences of six Major Histocompatibility Complex haplotypes, including all the major MHC class II structures
Torsten Houwaart, Stephan Scholz, … Alexander Dilthey·HLAPeer-reviewed·Mar 18, 2023