HLAreporter: A tool for HLA typing from next generation sequencing data

Genome Medicine

Volumn 7, Issue 1, 2015, Pages

  Huang, Yazhi ^a   Yang, Jing ^a   Ying, Dingge ^a   Zhang, Yan ^a   Shotelersuk, Vorasuk ^b   Hirankarn, Nattiya ^b   Sham, Pak Chung ^a   Lau, Yu Lung ^a   Yang, Wanling ^a  

^a UNIVERSITY OF HONG KONG   (Hong Kong)

^b CHULALONGKORN UNIVERSITY   (Thailand)

Author keywords

[No Author keywords available]

Indexed keywords

HLA ANTIGEN;

ALLELE; ARTICLE; CONTROLLED STUDY; GENE EXPRESSION; GENE FREQUENCY; GENE LOCUS; GENE MAPPING; GENETIC DATABASE; GENETIC SCREENING; GENETIC VARIABILITY; HAPLOTYPE MAP; HLA TYPING; HLAREPORTER; HUMAN; HUMAN EXPERIMENT; NEXT GENERATION SEQUENCING; POPULATION GENETICS; PRIORITY JOURNAL;

EID: 84928227021     PISSN: None     EISSN: 1756994X     Source Type: Journal    
DOI: 10.1186/s13073-015-0145-3     Document Type: Article

References (22)

1. de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J, et al. A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. Nat Genet. 2006;38:1166-72.
2. de Bakker PI, Raychaudhuri S. Interrogating the major histocompatibility complex with high-throughput genomics. Hum Mol Genet. 2012;21:29-36.
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, Goodridge D, Sayer D, Trachtenberg EA, et al. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens. 2009;74:393-403.
5. Lind C, Ferriola D, Mackiewicz K, Heron S, Rogers M, Slavich L, et al. Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol. 2010;10:1033-42.
6. Noble JA, Martin A, Valdes AM, Lane JA, Galgani A, Petrone A, 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. 2008;69:291-300.
7. Solberg OD, Mack SJ, Lancastera AK, Single RM, Tsai Y, Sanchez-Mazas A, et al. Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum Immunol. 2008;69:443-64.
8. Boegel S, Lower M, Schafer M, Bukur T, de Graaf J, Boisguérin V, et al. HLA typing from RNA-Seq sequence reads. Genome Med. 2012;4:102-13.
9. Warren RL, Choe G, Freeman DJ, Castellarin M, Munro S, Moore R, et al. Derivation of HLA types from shotgun sequence datasets. Genome Med. 2012;4:95-102.
10. Gonzalez-Galarza FF, Christmas S, Middleton D, Jones AR. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res. 2011;39:D913-9.
11. Li H, Durbin R. Fast and accurate long-read alignment with Burrows-Wheeler Transform. Bioinformatics. 2010;26:589-95.
12. HLA Nomenclature. http://hla.alleles.org/alleles/g_groups.html.
13. Inflammgen (The laboratory in genetics and genomic medicine of inflammation). http://www.inflammgen.org/.
14. Erlich RL, Jia X, Anderson S, Banks E, Gao X, Carrington M, et al. Next-generation sequencing for HLA typing of class I loci. BMC Genomics. 2011;12:42-54.
15. Bai Y, Ni M, Cooper B, Wei Y, Fury W. Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads. BMC Genomics. 2014;15:325-40.
16. Paedlab (Department of Paediatrics and Adolescent Medicine) Hong Kong: The University of Hong Kong, Li Ka Shing Faculty of Medicine. http://paed.hku.hk/genome/.
17. The 1000 Genomes Project. ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/data/.
18. The International HapMap Project. http://hapmap.ncbi.nlm.nih.gov/.
19. Stephens M, Smith NJ, Donnelly P. A new statistical method for haplotype reconstruction from population data. Am J Hum Genet. 2001;68:978-89.
20. The Allele Frequency Net Database. http://www.allelefrequencies.net/.
21. Major E, Rigo K, Hague T, Berces A, Juhos S. HLA typing from 1000 genomes whole genome and whole exome illumina data. PLoS One. 2013;8:11.
22. RefSeq (NCBI reference sequence database). Bethesda: National Library of Medicine, National Center for Biotechnology Information, 2002. http://www.ncbi.nlm.nih.gov/refseq/.