Accurate HLA Typing at High-Digit Resolution from NGS Data
Human leukocyte antigen (HLA) typing from next generation sequencing (NGS) data has the potential for applications in clinical laboratories and population genetic studies. Here we introduce a novel technique for HLA typing from NGS data based on read-mapping using a comprehensive reference panel containing all known HLA alleles and de novo assembly of the gene-specific short reads. An accurate HLA typing at high-digit resolution was achieved when it was tested on publicly available NGS data, outperforming other newly-developed tools such as HLAminer and PHLAT.
Digital Object Identifier (DOI): doi.org/10.5281/zenodo.1338172Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1966
 de Bakker PI, McVean G, Sabeti PC, et al., “A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC,” Nat Genet, vol. 38, 2006, pp. 1166–1172.
 de Bakker PI, Raychaudhuri S., “Interrogating the major histocompatibility complex with high-throughput genomics,” Hum Mol Genet, vol. 21, 2012, pp. 29–36.
 IMGT/HLA (International immunogenetics project/Human major histocompatibility complex). London: Royal Free Hospital, Anthony Nolan Research Institute, HLA Informatics Group, 1998. http://www.ebi.ac.uk/ipd/imgt/hla/.
 Bentley G, Higuchi R, Hoglund B, et al. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens, vol. 74, 2009, pp. 393–403.
 Lind C, Ferriola D, Mackiewicz K, et al., “Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing,” Hum Immunol, vol. 10, 2010, pp. 1033–1042.
 Noble JA, Martin A, Valdes AM, et al., “Type 1 diabetes risk for HLA-DR3 haplotypes depends on genotypic context: Association of DPB1 and HLA class I loci among DR3 and DR4 matched Italian patients and controls,” Hum Immunol, vol. 69, 2008, pp. 291–300.
 Solberg OD, Mack SJ, Lancastera AK, et al, “Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies,” Hum Immunol, vol. 69, 2008, pp. 443–464.
 Boegel S, Lower M, Schafer M, et al, “HLA typing from RNA-Seq sequence reads,” Genome Med, vol. 4, 2012, pp. 102–113.
 Warren RL, Choe G, Freeman D, et al, “Derivation of HLA types from shotgun sequence datasets,” Genome Med, vol. 4, 2012, pp. 95–102.
 Gonzalez-Galarza FF, Christmas S, Middleton D, et al., “Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations,” Nucleic Acids Res, vol. 39, 2011, pp. 913-919.
 Li H, Durbin R, “Fast and accurate long-read alignment with Burrows-Wheeler Transform,” Bioinformatics, vol. 26, 2010, pp. 589–595.
 Inflammgen (The laboratory in genetics and genomic medicine of inflammation). http://www.inflammgen.org/.
 Erlich RL, Jia X, Anderson S, et al., “Next-generation sequencing for HLA typing of class I loci,” BMC Genomics, vol. 12, 2011, pp. 42-54.
 Bai Y, Ni M, Cooper B, et al., “Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads,” BMC Genomics, vol. 15, 2014, pp. 325-340.
 Stephens M, Smith NJ, Donnelly P, “A new statistical method for haplotype reconstruction from population data,” Am J Hum Genet, vol. 68, 2001, pp. 978–989.
 Major E, Rigo K, Hague T, et al., “HLA typing from 1000 genomes whole genome and whole exome illumina data,” PLoS ONE, vol. 8, 2013, pp. 11–19.
 RefSeq (NCBI reference sequence database). Bethesda: National Library of Medicine, National Center for Biotechnology Information, 2002. http://www.ncbi.nlm.nih.gov/refseq/.