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.
[1] 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.
[2] de Bakker PI, Raychaudhuri S., “Interrogating the major
histocompatibility complex with high-throughput genomics,” Hum Mol
Genet, vol. 21, 2012, pp. 29–36.
[3] 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/.
[4] 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.
[5] 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.
[6] 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.
[7] 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.
[8] Boegel S, Lower M, Schafer M, et al, “HLA typing from RNA-Seq
sequence reads,” Genome Med, vol. 4, 2012, pp. 102–113.
[9] Warren RL, Choe G, Freeman D, et al, “Derivation of HLA types from
shotgun sequence datasets,” Genome Med, vol. 4, 2012, pp. 95–102.
[10] 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.
[11] Li H, Durbin R, “Fast and accurate long-read alignment with
Burrows-Wheeler Transform,” Bioinformatics, vol. 26, 2010, pp.
589–595.
[12] Inflammgen (The laboratory in genetics and genomic medicine of
inflammation). http://www.inflammgen.org/.
[13] 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.
[14] 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.
[15] 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.
[16] 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.
[17] RefSeq (NCBI reference sequence database). Bethesda: National Library
of Medicine, National Center for Biotechnology Information, 2002.
http://www.ncbi.nlm.nih.gov/refseq/.
[1] 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.
[2] de Bakker PI, Raychaudhuri S., “Interrogating the major
histocompatibility complex with high-throughput genomics,” Hum Mol
Genet, vol. 21, 2012, pp. 29–36.
[3] 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/.
[4] 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.
[5] 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.
[6] 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.
[7] 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.
[8] Boegel S, Lower M, Schafer M, et al, “HLA typing from RNA-Seq
sequence reads,” Genome Med, vol. 4, 2012, pp. 102–113.
[9] Warren RL, Choe G, Freeman D, et al, “Derivation of HLA types from
shotgun sequence datasets,” Genome Med, vol. 4, 2012, pp. 95–102.
[10] 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.
[11] Li H, Durbin R, “Fast and accurate long-read alignment with
Burrows-Wheeler Transform,” Bioinformatics, vol. 26, 2010, pp.
589–595.
[12] Inflammgen (The laboratory in genetics and genomic medicine of
inflammation). http://www.inflammgen.org/.
[13] 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.
[14] 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.
[15] 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.
[16] 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.
[17] RefSeq (NCBI reference sequence database). Bethesda: National Library
of Medicine, National Center for Biotechnology Information, 2002.
http://www.ncbi.nlm.nih.gov/refseq/.
@article{"International Journal of Medical, Medicine and Health Sciences:69322", author = "Yazhi Huang and Jing Yang and Dingge Ying and Yan Zhang and Vorasuk Shotelersuk and Nattiya Hirankarn and Pak Chung Sham and Yu Lung Lau and Wanling Yang", title = "Accurate HLA Typing at High-Digit Resolution from NGS Data", abstract = "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.
", keywords = "Human leukocyte antigens, next generation
sequencing, whole exome sequencing, HLA typing.", volume = "9", number = "3", pages = "263-9", }
