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Volumn 83, Issue 2, 2014, Pages 65-75

HLA typing by next-generation sequencing - getting closer to reality

Author keywords

454 Roche; Ambiguities; Human leukocyte antigen typing; Illumina; Ion Torrent; Next generation sequencing; Sequencing platforms

Indexed keywords

COMPLEMENTARY DNA;

EID: 84892976830     PISSN: 00012815     EISSN: 13990039     Source Type: Journal    
DOI: 10.1111/tan.12298     Document Type: Article
Times cited : (83)

References (44)
  • 1
    • 80855144587 scopus 로고    scopus 로고
    • Human leucocyte antigen typing: techniques and technology, a critical appraisal
    • Dunn PP. Human leucocyte antigen typing: techniques and technology, a critical appraisal. Int J Immunogenet 2011: 38: 463-73.
    • (2011) Int J Immunogenet , vol.38 , pp. 463-473
    • Dunn, P.P.1
  • 3
    • 0023047540 scopus 로고
    • Fluorescence detection in automated DNA sequence analysis
    • Smith LM, Sanders JZ, Kaiser RJ et al. Fluorescence detection in automated DNA sequence analysis. Nature 1986: 321: 674-9.
    • (1986) Nature , vol.321 , pp. 674-679
    • Smith, L.M.1    Sanders, J.Z.2    Kaiser, R.J.3
  • 5
    • 79956314887 scopus 로고    scopus 로고
    • Genotype and SNP calling from next-generation sequencing data
    • Nielsen R, Paul JS, Albrechtsen A, Song YS. Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 2011: 12: 443-51.
    • (2011) Nat Rev Genet , vol.12 , pp. 443-451
    • Nielsen, R.1    Paul, J.S.2    Albrechtsen, A.3    Song, Y.S.4
  • 7
  • 8
    • 84861660542 scopus 로고    scopus 로고
    • HLA DNA typing: past, present, and future
    • Erlich H. HLA DNA typing: past, present, and future. Tissue Antigens 2012: 80: 1-11.
    • (2012) Tissue Antigens , vol.80 , pp. 1-11
    • Erlich, H.1
  • 9
    • 84864920004 scopus 로고    scopus 로고
    • Comparison of nest-generation sequencing systems
    • Liu L, Li Y, Li S et al. Comparison of nest-generation sequencing systems. J Biomed Biotechnol 2012: 2012: 251364.
    • (2012) J Biomed Biotechnol , vol.2012 , pp. 251364
    • Liu, L.1    Li, Y.2    Li, S.3
  • 10
    • 61849172898 scopus 로고    scopus 로고
    • Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes
    • Simen BB, Simons JF, Hullsiek KH et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009: 199: 693-701.
    • (2009) J Infect Dis , vol.199 , pp. 693-701
    • Simen, B.B.1    Simons, J.F.2    Hullsiek, K.H.3
  • 11
    • 77955199812 scopus 로고    scopus 로고
    • Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study
    • Lataillade M, Chiarella J, Yang R et al. Prevalence and clinical significance of HIV drug resistance mutations by ultra-deep sequencing in antiretroviral-naïve subjects in the CASTLE study. PLoS One 2010: 5: e10952.
    • (2010) PLoS One , vol.5
    • Lataillade, M.1    Chiarella, J.2    Yang, R.3
  • 12
    • 77956237515 scopus 로고    scopus 로고
    • Next-generation sequencing technology reveals a characteristic pattern of molecular mutations in 72.8% of chronic myelomonocytic leukemia by detecting frequent alterations in TET2, CBL, RAS, and RUNX1
    • Kohlmann A, Grossmann V, Klein HU et al. Next-generation sequencing technology reveals a characteristic pattern of molecular mutations in 72.8% of chronic myelomonocytic leukemia by detecting frequent alterations in TET2, CBL, RAS, and RUNX1. J Clin Oncol 2010: 28: 3858-65.
    • (2010) J Clin Oncol , vol.28 , pp. 3858-3865
    • Kohlmann, A.1    Grossmann, V.2    Klein, H.U.3
  • 13
    • 70350043898 scopus 로고    scopus 로고
    • High-resolution, high-throughput HLA genotyping by next-generation sequencing
    • Bentley G, Higuchi R, Hoglund B et al. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 2009: 74: 393-403.
    • (2009) Tissue Antigens , vol.74 , pp. 393-403
    • Bentley, G.1    Higuchi, R.2    Hoglund, B.3
  • 14
    • 70349954786 scopus 로고    scopus 로고
    • Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification
    • Gabriel C, Danzer M, Hackl C et al. Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol 2009: 70: 960-4.
    • (2009) Hum Immunol , vol.70 , pp. 960-964
    • Gabriel, C.1    Danzer, M.2    Hackl, C.3
  • 15
    • 84875689644 scopus 로고    scopus 로고
    • Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics
    • Danzer M, Niklas N, Stabentheiner S et al. Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics. BMC Genomics 2013: 14: 221.
    • (2013) BMC Genomics , vol.14 , pp. 221
    • Danzer, M.1    Niklas, N.2    Stabentheiner, S.3
  • 16
    • 84864497082 scopus 로고    scopus 로고
    • Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing
    • Lank SM, Golbach BA, Creager HM et al. Ultra-high resolution HLA genotyping and allele discovery by highly multiplexed cDNA amplicon pyrosequencing. BMC Genomics 2012: 13: 378.
    • (2012) BMC Genomics , vol.13 , pp. 378
    • Lank, S.M.1    Golbach, B.A.2    Creager, H.M.3
  • 17
    • 77956618377 scopus 로고    scopus 로고
    • A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping
    • Lank SM, Wiseman RW, Dudley DM, O'Connor DH. A novel single cDNA amplicon pyrosequencing method for high-throughput, cost-effective sequence-based HLA class I genotyping. Hum Immunol 2010: 71: 1011-7.
    • (2010) Hum Immunol , vol.71 , pp. 1011-1017
    • Lank, S.M.1    Wiseman, R.W.2    Dudley, D.M.3    O'Connor, D.H.4
  • 18
    • 80053503104 scopus 로고    scopus 로고
    • What next? The next transit from biology to diagnostics: next generation sequencing for immunogenetics
    • Gabriel C, Stabentheiner S, Danzer M, Pröll J. What next? The next transit from biology to diagnostics: next generation sequencing for immunogenetics. Transfus Med Hemother 2011: 38: 308-17.
    • (2011) Transfus Med Hemother , vol.38 , pp. 308-317
    • Gabriel, C.1    Stabentheiner, S.2    Danzer, M.3    Pröll, J.4
  • 19
    • 77956618378 scopus 로고    scopus 로고
    • Next-generation sequencing: the solution for high-resolution, unambiguous HLA typing
    • Lind C, Ferriola D, Mackiewicz K et al. Next-generation sequencing: the solution for high-resolution, unambiguous HLA typing. Hum Immunol 2010: 71: 1033-42.
    • (2010) Hum Immunol , vol.71 , pp. 1033-1042
    • Lind, C.1    Ferriola, D.2    Mackiewicz, K.3
  • 20
    • 84879551555 scopus 로고    scopus 로고
    • Next generation sequencing reveals the association of DRB3*02:02 with type 1 diabetes
    • Erlich HA, Valdes AM, McDevitt SL et al. Next generation sequencing reveals the association of DRB3*02:02 with type 1 diabetes. Diabetes 2013: 62: 2618-22.
    • (2013) Diabetes , vol.62 , pp. 2618-2622
    • Erlich, H.A.1    Valdes, A.M.2    McDevitt, S.L.3
  • 21
    • 84861192497 scopus 로고    scopus 로고
    • Next-generation DNA re-sequencing identifies common variants of TYR and HLA-A that modulate the risk of generalized vitiligo via antigen presentation
    • Jin Y, Ferrara T, Gowan K et al. Next-generation DNA re-sequencing identifies common variants of TYR and HLA-A that modulate the risk of generalized vitiligo via antigen presentation. J Invest Dermatol 2012: 132: 1730-3.
    • (2012) J Invest Dermatol , vol.132 , pp. 1730-1733
    • Jin, Y.1    Ferrara, T.2    Gowan, K.3
  • 22
    • 84862796365 scopus 로고    scopus 로고
    • Multi-locus HLA class I and II allele and haplotype associations with follicular lymphoma
    • Skibola CF, Akers NK, Conde L et al. Multi-locus HLA class I and II allele and haplotype associations with follicular lymphoma. Tissue Antigens 2012: 79: 279-86.
    • (2012) Tissue Antigens , vol.79 , pp. 279-286
    • Skibola, C.F.1    Akers, N.K.2    Conde, L.3
  • 23
    • 84873708504 scopus 로고    scopus 로고
    • Filling the gaps - the generation of full genomic sequences for 15 common and well-documented HLA class I alleles using next-generation sequencing technology
    • 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: 74: 325-9.
    • (2013) Hum Immunol , vol.74 , pp. 325-329
    • Lind, C.1    Ferriola, D.2    Mackiewicz, K.3    Papazoglou, A.4    Sasson, A.5    Monos, D.6
  • 24
    • 79551676183 scopus 로고    scopus 로고
    • A multi-site study using high-resolution HLA genotyping by next generation sequencing
    • Holcomb CL, Höglund B, Anderson MW et al. A multi-site study using high-resolution HLA genotyping by next generation sequencing. Tissue Antigens 2011: 77: 206-17.
    • (2011) Tissue Antigens , vol.77 , pp. 206-217
    • Holcomb, C.L.1    Höglund, B.2    Anderson, M.W.3
  • 26
    • 36148937913 scopus 로고    scopus 로고
    • A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing
    • Parameswaran P, Jalili R, Tao L et al. A pyrosequencing-tailored nucleotide barcode design unveils opportunities for large-scale sample multiplexing. Nucleic Acids Res 2007: 35: e130.
    • (2007) Nucleic Acids Res , vol.35
    • Parameswaran, P.1    Jalili, R.2    Tao, L.3
  • 27
    • 84873578476 scopus 로고    scopus 로고
    • High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ System for simplified amplicon library preparation
    • Moonsamy PV, Williams T, Bonella P et al. High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ System for simplified amplicon library preparation. Tissue Antigens 2013: 81: 141-9.
    • (2013) Tissue Antigens , vol.81 , pp. 141-149
    • Moonsamy, P.V.1    Williams, T.2    Bonella, P.3
  • 29
    • 84892956991 scopus 로고    scopus 로고
    • Drug giant Roche to lay off more workers
    • Turmelle L. Drug giant Roche to lay off more workers. http://www.nhregister.com/business/20131003/drug-giant-roche-to-lay-off-more-workers.
    • Turmelle, L.1
  • 30
    • 55549089660 scopus 로고    scopus 로고
    • Accurate whole human genome sequencing using reversible terminator chemistry
    • Bentley DR, Balasubramanian S, Swerdlow HP et al. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008: 456: 53-9.
    • (2008) Nature , vol.456 , pp. 53-59
    • Bentley, D.R.1    Balasubramanian, S.2    Swerdlow, H.P.3
  • 31
    • 84893015394 scopus 로고    scopus 로고
    • Illumina Sequencing Technology
    • Illumina Sequencing Technology. http://res.illumina.com/documents/products/techspotlights/techspotlight_sequencing.pdf.
  • 32
    • 84884251320 scopus 로고    scopus 로고
    • Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform
    • Kozich JJ, Westcott SL, Baxter NT, Highlander SK, Schloss PD. Development of a dual-index sequencing strategy and curation pipeline for analyzing amplicon sequence data on the MiSeq Illumina sequencing platform. Appl Environ Microbiol 2013: 79: 5112-20.
    • (2013) Appl Environ Microbiol , vol.79 , pp. 5112-5120
    • Kozich, J.J.1    Westcott, S.L.2    Baxter, N.T.3    Highlander, S.K.4    Schloss, P.D.5
  • 33
    • 77649224709 scopus 로고    scopus 로고
    • Rapid quantification of DNA libraries for next-generation sequencing
    • Buehler B, Hogrefe HH, Scott G et al. Rapid quantification of DNA libraries for next-generation sequencing. Methods 2010: 50: S15-8.
    • (2010) Methods , vol.50
    • Buehler, B.1    Hogrefe, H.H.2    Scott, G.3
  • 34
    • 68549104404 scopus 로고    scopus 로고
    • The sequence alignment/map format and SAMtools
    • Li H, Handsaker B, Wysoker A et al. The sequence alignment/map format and SAMtools. Bioinformatics 2009: 25: 2078-9.
    • (2009) Bioinformatics , vol.25 , pp. 2078-2079
    • Li, H.1    Handsaker, B.2    Wysoker, A.3
  • 35
    • 65649092976 scopus 로고    scopus 로고
    • Biopython: freely available Python tools for computational molecular biology and bioinformatics
    • Cock PJ, Antao T, Chang JT et al. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics 2009: 25: 1422-3.
    • (2009) Bioinformatics , vol.25 , pp. 1422-1423
    • Cock, P.J.1    Antao, T.2    Chang, J.T.3
  • 36
    • 28744458859 scopus 로고    scopus 로고
    • Bioconductor: open software development for computational biology and bioinformatics
    • Gentleman RC, Carey VJ, Bates DM et al. Bioconductor: open software development for computational biology and bioinformatics. Genome Biol 2004: 5: R80.
    • (2004) Genome Biol , vol.5
    • Gentleman, R.C.1    Carey, V.J.2    Bates, D.M.3
  • 37
    • 0026865024 scopus 로고
    • Preferential PCR amplification of alleles: mechanisms and solutions
    • Walsh PS, Erlich HA, Higuchi R. Preferential PCR amplification of alleles: mechanisms and solutions. PCR Methods Appl 1992: 1: 241-50.
    • (1992) PCR Methods Appl , vol.1 , pp. 241-250
    • Walsh, P.S.1    Erlich, H.A.2    Higuchi, R.3
  • 38
    • 79960597679 scopus 로고    scopus 로고
    • An integrated semiconductor device enabling non-optical genome sequencing
    • Rothberg JM, Hinz W, Rearick TM et al. An integrated semiconductor device enabling non-optical genome sequencing. Nature 2011: 475: 348-52.
    • (2011) Nature , vol.475 , pp. 348-352
    • Rothberg, J.M.1    Hinz, W.2    Rearick, T.M.3
  • 39
    • 84866632618 scopus 로고    scopus 로고
    • Super high resolution for single molecule-sequence-based typing of classical HLA loci at the 8-digit level using next generation sequencers
    • Shiina T, Suzuki S, Ozaki Y 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: 80: 305-16.
    • (2012) Tissue Antigens , vol.80 , pp. 305-316
    • Shiina, T.1    Suzuki, S.2    Ozaki, Y.3
  • 40
    • 77951226627 scopus 로고    scopus 로고
    • The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
    • Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM. The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants. Nucleic Acids Res 2010: 8: 1767-71.
    • (2010) Nucleic Acids Res , vol.8 , pp. 1767-1771
    • Cock, P.J.1    Fields, C.J.2    Goto, N.3    Heuer, M.L.4    Rice, P.M.5
  • 41
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998: 8: 186-94.
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 42
    • 84861865679 scopus 로고    scopus 로고
    • High-throughput, high-fidelity HLA genotyping with deep sequencing
    • Wang C, Krishnakumar S, Wilhelmy J et al. High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci U S A 2012: 109: 8676-81.
    • (2012) Proc Natl Acad Sci U S A , vol.109 , pp. 8676-8681
    • Wang, C.1    Krishnakumar, S.2    Wilhelmy, J.3
  • 43
    • 84890731574 scopus 로고    scopus 로고
    • Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database
    • Holcomb CL, Rastrou M, Williams TC et al. Next-generation sequencing can reveal in vitro-generated PCR crossover products: some artifactual sequences correspond to HLA alleles in the IMGT/HLA database. Tissue Antigens 2014: 83: 32-40.
    • (2014) Tissue Antigens , vol.83 , pp. 32-40
    • Holcomb, C.L.1    Rastrou, M.2    Williams, T.C.3
  • 44
    • 84878234942 scopus 로고    scopus 로고
    • Characterizing and measuring bias in sequence data
    • Ross MG, Russ C, Costello M et al. Characterizing and measuring bias in sequence data. Genome Biol 2013: 14: R51.
    • (2013) Genome Biol , vol.14
    • Ross, M.G.1    Russ, C.2    Costello, M.3


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