Abstract
The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. Here, we describe the TARGT pipeline for targeted analysis of polymorphic loci from low-coverage shotgun sequence data. The pipeline was successfully applied to medieval aDNA samples and validated using both simulated aDNA and modern empirical sequence data from the 1000 Genomes Project. Thus the TARGT pipeline enables accurate analysis of HLA polymorphisms in historical (and modern) human populations.
Highlights
The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases
After pre-processing and quality control, sequence reads from genomic shotgun sequencing are aligned against a comprehensive reference file containing the exon sequences coding for the peptide-binding groove of all known classical HLA gene variants: class I (HLA-A, HLA-B, HLA-C) and class II loci (HLA-DRB1, HLA-DRB3/4/5, HLA-DQA1, HLA-DQB1, HLA-DPA, HLA-DPB1)
One of the main purposes of this work was the accurate genotyping of HLA genes in ancient DNA (aDNA) samples
Summary
The highly polymorphic human leukocyte antigen (HLA) plays a crucial role in adaptive immunity and is associated with various complex diseases. Accurate analysis of HLA genes using ancient DNA (aDNA) data is crucial for understanding their role in human adaptation to pathogens. The classical human leukocyte antigen (HLA) genes play a central role in adaptive immunity They encode for glycoproteins that present antigenic peptides on the cell surface for recognition by immune effector cells, enabling the immune system to distinguish between ‘self ’ and ‘non-self ’, eventually stimulating a specific immune response[1]. The TARGT pipeline is highly versatile; this step could be adapted and used to target any gene or polymorphic region in the genome by providing a corresponding reference sequence for read selection. Using a sequence alignment software, the FASTA files can be manually analyzed to genotype individual samples
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