HLA typing using next generation sequencing: An overview

Human Immunology

Volumn 76, Issue 12, 2015, Pages 887-890

  Erlich, Henry A ^a  

^a CHILDREN S HOSPITAL OAKLAND RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; GENETIC CODE; HIGH THROUGHPUT SEQUENCING; HLA TYPING; HUMAN; NEXT GENERATION SEQUENCING; NOTE; PRIORITY JOURNAL; BIOLOGY; GENETICS; HISTOCOMPATIBILITY TEST; IMMUNOLOGY; OPEN READING FRAME; PROCEDURES; STANDARDS; UNTRANSLATED REGION;

HLA ANTIGEN; UNTRANSLATED REGION;

COMPUTATIONAL BIOLOGY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTOCOMPATIBILITY TESTING; HLA ANTIGENS; HUMANS; OPEN READING FRAMES; UNTRANSLATED REGIONS;

EID: 84959155685     PISSN: 01988859     EISSN: 18791166     Source Type: Journal    
DOI: 10.1016/j.humimm.2015.03.001     Document Type: Note

References (24)

1. Saiki R.K., Gelfand D.H., Stoffel S., Scharf S., Higuchi R.H., Horn G.T., et al. Primer-directed enzymatic amplification of DNA with a thermostable DNA polymerase. Science 1988 Jan, 239(4839):487-491.
2. Saiki R.K., Bugawan T.L., Horn G.T., Mullis K.B., Erlich H.A. Analysis of enzymatically amplified β-globin and HLA-DQα DNA with allele-specific oligonucleotide probes. Nature 1986 Nov, 324(6093):163-166. PMID: 3785382 doi:10.1038/324163a0.
3. Saiki R., Walsh P.S., Levenson C.H., Erlich H.A. Genetic analysis of amplified DNA with immobilized sequence-specific oligonucleotide probes. Proc. Natl. Acad. Sci. U.S.A. 1989 Aug, 86(16):6230-6234. PMCID: PMC297811.
4. Olerup O., Zetterquist J. HLA-DR typing by PCR amplification with sequence-specific primers (PCR-SSP) in 2 h: an alternative to serological DR typing in clinical practice including donor-recipient matching in cadaveric transplantation. Tissue Antigens 1992 May, 39(5):225-235.
5. Santamaria P., Lindstrom A.L., Boyce-Jacino M.T., Myster S.H., Barbosa J.J., Faras A.J., et al. HLA class 1 sequence-based typing. Human Immunol. 1993 May, 37(1):39-50.
6. Bentley G., Higuchi R., Höglund B., Goodridge D., Sayer D., Trachtenberg E.A., et al. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 2009 Nov, 74(5):393-403. PMCID: PMC4205124 doi:10.111/j.1399-0039.2009.01345.x.
7. Holcomb C.L., Höglund B., Anderson M.W., Blake L.A., Böhme I., Egholm M., et al. A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens 2011 Mar, 77(3):206-217. PMCID: PMC4205124. doi:10.1111/j.1399-0039.2010.01606.x.
8. Gabriel C., Danzer M., Hackl C., Kopal G., Hufnagl P., Hofer K., et al. Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol 2009 Nov, 70(11):960-964. Epub 2009 Aug 23. 10.1016/j.humimm.2009.08.009.
9. Moonsamy P.V., Williams T., Bonella P., Holcomb C.L., Höglund B.N., Hillman G., et al. High throughput HLA genotyping using 454 sequencing and the Fluidgm Access Array™ System for simplified amplicon library preparation. Tissue Antigens 2013 Mar, 81(3):141-149. PMID: 23398507. doi:10.1111/tan.12071.
10. Lind C., Ferriola D., Mackiewicz S., Heron S., Rogers M., Slavich L., et al. Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol 2010 Oct, 71(10):1033-1042. Epub 2010 Aug 5. 10.1016/j.humimm.2010.06.016.
11. Shiina T., Suzuki S., Ozaki Y., Taira H., Kikkawa E., Shigenari A., et al. Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers. Tissue Antigens 2012 Oct, 80(4):305-316. 10.1111/j.1399-0039.2012.01941.x.
12. Wang C., Krishnakumar S., Wilhelmy J., Babrzadeh F., Stepanyan L., Su L.F., et al. High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc. Natl. Acad. Sci. U.S.A. 2012 May, 109(22):8676-8681. Published online 2012 May 15. doi:10.1073/pnas.1206614109. PMCID: PMC3365218.
13. Gabriel C., Fürst D., Faé I., Wenda S., Zollikofer C., Mytilineos, et al. HLA typing by next-generation sequencing - getting closer to reality. Tissue Antigens 2014 Feb, 83(2):65-75. 10.1111/tan.12298.
14. Lange V., Böhme I., Hofmann J., Lang K., Sauter J., Schöne B., et al. Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing. BMC Genomics 2014 Jan, 15:63. 10.1186/1471-2164-15-63.
15. Hosomichi K., Jinam T.A., Mitsunaga S., Nakaoka H., Inoue I. Phase-defined complete sequencing of the HLA genes by next-generation sequencing. BMC Genomics 2013 May, 14:355. 10.1186/1471-2164-14-355.
16. Ozaki Y., Suzuki S., Shigenari A., Okudaira Y., Kikkawa E., Oka A., et al. HLA-DRB1, -DRB4 and DRB5 genotyping at a super-high resolution level by long range PCR and high-throughput sequencing. Tissue Antigens 2014 Jan, 83(1):10-16. 10.1111/tan.12258.
17. Mayor N.P., Robinson J., Ranade S., Eng K., Wallis-Jones S., McWhinnie A.J.M., et al. OR57: Generation of 252 HLA class I genomic sequences in a single sequencing reaction using DNA barcodes and single molecule real-time (SMRT) DNA sequencing technology. Hum Immunol 2014 Oct, 75(Suppl.):49. 10.1016/j.humimm.2014.08.060.
18. Major E., Rigó K., Hague T., Bérces A., Juhos S. HLA typing from 1000 genome whole genome and whole exome illumina data. PLoS One 2013 Nov, 8(11):e78410. Published online 2013 November 6.
19. Kidd J.M., Sharpton T.J., Bobos D., Norman P.J., Martin A.R., Carpenter M.L., et al. Exome capture from saliva produces high quality genomic and metagenomic data. BMC Genomics 2014 Apr, 15:262. 10.1186/1471-2164-15-262.
20. Duke J.L., Sasson A., Mackiewicz K., Lind C., Major E., Lind C., et al. 48-OR: deriving HLA typing from whole MHC next-generation sequencing data. Hum Immunol 2013 Nov, 74(Suppl):38. 10.1016/j.humimm.2013.08.059.
21. Zheng X., Shen J., Cox C., Wakefield J.C., Ehm M.G., Nelson M.R., et al. HIBAG-HLA genotype imputation with attribute bagging. Pharmacogenom. J. 2014 Apr, 14(2):192-200. Epub 2013 May 28. 10.1038/tpj.2013.18.
22. Lind C., Ferriola D., Mackiewicz K., Papazoglou A., Sasson A., Monos D. Filling the gaps - the generation of full genomic sequences for 15 common and well-documented HLA class I alleles using next-generation sequencing technology. Hum Immunol 2013 Mar, 74(3):325-329. Epub 2012 Dec 13. 10.1016/j.humimm.2012.12.007.
23. Bergstrom T.F., Josefsson A., Erlich H.A., Gyllensten U. Recent origin of HLA-DRB2 alleles and implications for human evolution. Nat Genet 1998 Mar, 18(3):237-242.
24. Mack S.J., Cano P., Hollenbach J.A., He J., Hurley C.K., Middleton D., et al. Common and well-documented HLA alleles: 2012 update to the CWD catalogue. Tissue Antigens 2013 Apr, 81(4):194-203. 10.1111/tan.12093.