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Efficient HLA imputation from sequential SNPs data by transformer

Authors :
Tanaka, Kaho
Kato, Kosuke
Nonaka, Naoki
Seita, Jun
Source :
Journal of Human Genetics; October 2024, Vol. 69 Issue: 10 p533-540, 8p
Publication Year :
2024

Abstract

Human leukocyte antigen (HLA) genes are associated with a variety of diseases, yet the direct typing of HLA alleles is both time-consuming and costly. Consequently, various imputation methods leveraging sequential single nucleotide polymorphisms (SNPs) data have been proposed, employing either statistical or deep learning models, such as the convolutional neural network (CNN)-based model, DEEP*HLA. However, these methods exhibit limited imputation efficiency for infrequent alleles and necessitate a large size of reference dataset. In this context, we have developed a Transformer-based model to HLA allele imputation, named “HLA Reliable IMpuatioN by Transformer (HLARIMNT)” designed to exploit the sequential nature of SNPs data. We evaluated HLARIMNT’s performance using two distinct reference panels; Pan-Asian reference panel (n= 530) and Type 1 Diabetes genetics Consortium (T1DGC) reference panel (n= 5225), alongside a combined panel (n= 1060). HLARIMNT demonstrated superior accuracy to DEEP*HLA across several indices, particularly for infrequent alleles. Furthermore, we explored the impact of varying training data sizes on imputation accuracy, finding that HLARIMNT consistently outperformed across all data size. These findings suggest that Transformer-based models can efficiently impute not only HLA types but potentially other gene types from sequential SNPs data.

Details

Language :
English
ISSN :
14345161 and 1435232X
Volume :
69
Issue :
10
Database :
Supplemental Index
Journal :
Journal of Human Genetics
Publication Type :
Periodical
Accession number :
ejs67070033
Full Text :
https://doi.org/10.1038/s10038-024-01278-x