Abstract
BackgroundHighly polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases. Additionally, it is routinely performed for identifying matched donors in transplantation medicine. Although many HLA typing approaches have been developed, the complexity, low-efficiency and high-cost of current HLA-typing assays limit their application in population-based high-throughput HLA typing for donors, which is required for creating large-scale databases for transplantation and precision medicine.ResultsHere, we present a cost-efficient Saturated Tiling Capture Sequencing (STC-Seq) approach to capturing 14 HLA class I and II genes. The highly efficient capture (an approximately 23,000-fold enrichment) of these genes allows for simplified allele calling. Tests on five genes (HLA-A/B/C/DRB1/DQB1) from 31 human samples and 351 datasets using STC-Seq showed results that were 98% consistent with the known two sets of digitals (field1 and field2) genotypes. Additionally, STC can capture genomic DNA fragments longer than 3 kb from HLA loci, making the library compatible with the third-generation sequencing.ConclusionsSTC-Seq is a highly accurate and cost-efficient method for HLA typing which can be used to facilitate the establishment of population-based HLA databases for the precision and transplantation medicine.
Highlights
Polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system
The human leukocyte antigen (HLA) complex is located on chromosome 6p21 which encodes major histocompatibility complex (MHC) proteins involved in immune functions [1, 2]
To perform targeted sequencing of the coding regions of 14 HLA genes, we selected the HLA alleles with the longest coding regions from the IMGT/ HLA reference database which were used as the bait panel: HLA-A*01:01:01, B*08:01:01, C*16:01:01, DPA1*02:01:01, DPB1*01:01:01, DQA1*0 1:03:01, DQB1*03:02:01, DRA*01:01:01, DRB1*13:03:0 1, DRB3*01:01:02, DRB4*01:03:01, DRB5*01:01:01, E *01:01:01 and G*01:01:02
Summary
Polymorphic human leukocyte antigen (HLA) genes are responsible for fine-tuning the adaptive immune system. High-resolution HLA typing is important for the treatment of autoimmune and infectious diseases It is routinely performed for identifying matched donors in transplantation medicine. The highly polymorphic HLA class I (A, B and C) and II (DRB1 and DQB1) genes are crucial in immune rejection of transplantations, immune response to infections, pathogenesis of autoimmune diseases, adverse reactions to medications and cancer development [3,4,5]. For high-resolution typing (the first and second field), these methods involve iterative procedures that start with low-resolution typing followed by additional characterizations. These methods are both time and labor intensive prohibiting them for highthroughput processing. There are shortcomings with Sanger sequencing-based approaches because
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