Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing

BMC Genomics

Volumn 15, Issue 1, 2014, Pages

  Lange, Vinzenz ^a   Böhme, Irina ^a   Hofmann, Jan ^b   Lang, Kathrin ^a   Sauter, Jürgen ^b   Schöne, Bianca ^a   Paul, Patrick ^a   Albrecht, Viviane ^a   Andreas, Johanna M ^a   Baier, Daniel M ^b   Nething, Jochen ^c   Ehninger, Ulf ^b,c   Schwarzelt, Carmen ^a   Pingel, Julia ^b   Ehninger, Gerhard ^d   Schmidt, Alexander H ^a,b  

^a DKMS Life Science Lab   (Germany)

^b DKMS German Bone Marrow Donor Center   (Germany)

^c Molpe Software Entwicklungs GmbH   (Germany)

^d UNIVERSITY HOSPITAL CARL GUSTAV CARUS   (Germany)

Author keywords

4 primer approach; Amplicon based sequencing; Dual indexing; Fluidigm Access Array; HLA typing; Human leukocyte antigen; Illumina MiSeq; NGS

Indexed keywords

ALLELES; DNA; DNA PRIMERS; EXONS; HISTOCOMPATIBILITY TESTING; HLA ANTIGENS; HUMANS; MICROFLUIDIC ANALYTICAL TECHNIQUES; POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA;

EID: 84892693336     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-15-63     Document Type: Article

References (21)

1. Petersdorf EW, Anasetti C, Martin PJ, Gooley T, Radich J, Malkki M, Woolfrey A, Smith A, Mickelson E, Hansen JA. Limits of HLA mismatching in unrelated hematopoietic cell transplantation. Blood 2004, 104:2976-2980. 10.1182/blood-2004-04-1674, 15251989.
2. Tu B, Cha N, Yang R, Ng J, Hurley CK. A one-step DNA sequencing strategy to HLA type hematopoietic stem cell donors at recruitment - rethinking typing strategies. Tissue Antigens 2013, 81:150-160. 10.1111/tan.12072, 23398508.
3. Wang C, Krishnakumar S, Wilhelmy J, Babrzadeh F, Stepanyan L, Su LF, Levinson D, Fernandez-Viña MA, Davis RW, Davis MM, Mindrinos M. High-throughput, high-fidelity HLA genotyping with deep sequencing. Proc Natl Acad Sci USA 2012, 109:8676-8681. 10.1073/pnas.1206614109, 3365218, 22589303.
4. Shiina T, Suzuki S, Ozaki Y, Taira H, Kikkawa E, Shigenari A, Oka A, Umemura T, Joshita S, Takahashi O, Hayashi Y, Paumen M, Katsuyama Y, Mitsunaga S, Ota M, Kulski JK, Inoko H. 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, 80:305-316. 10.1111/j.1399-0039.2012.01941.x, 22861646.
5. Lind C, Ferriola D, Mackiewicz K, Heron S, Rogers M, Slavich L, Walker R, Hsiao T, McLaughlin L, D'Arcy M, Gai X, Goodridge D, Sayer D, Monos D. Next-generation sequencing: the solution for high-resolution, unambiguous human leukocyte antigen typing. Hum Immunol 2010, 71:1033-1042. 10.1016/j.humimm.2010.06.016, 20603174.
6. Bentley G, Higuchi R, Hoglund B, Goodridge D, Sayer D, Trachtenberg EA, Erlich HA. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 2009, 74:393-403. 10.1111/j.1399-0039.2009.01345.x, 19845894.
7. Gabriel C, Danzer M, Hackl C, Kopal G, Hufnagl P, Hofer K, Polin H, Stabentheiner S, Pröll J. Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. Hum Immunol 2009, 70:960-964. 10.1016/j.humimm.2009.08.009, 19706315.
8. Moonsamy PV, Williams T, Bonella P, Holcomb CL, Höglund BN, Hillman G, Goodridge D, Turenchalk GS, Blake LA, Daigle DA, Simen BB, Hamilton A, May AP, Erlich HA. High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ system for simplified amplicon library preparation. Tissue Antigens 2013, 81:141-149. 10.1111/tan.12071, 23398507.
9. Kircher M, Sawyer S, Meyer M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res 2012, 40:e3. 10.1093/nar/gkr771, 3245947, 22021376.
10. Bochtler W, Maiers M, Bakker JNA, Oudshoorn M, Marsh SGE, Baier D, Hurley CK, Müller CR. World Marrow Donor Association framework for the implementation of HLA matching programs in hematopoietic stem cell donor registries and cord blood banks. Bone Marrow Transplant 2011, 46:338-343. 10.1038/bmt.2010.132, 20531286.
11. Hurley CK, Oudshoorn M, Setterholm M. Donor registries and search strategies. Methods Mol Biol 2012, 882:531-547. 10.1007/978-1-61779-842-9_30, 3612349, 22665254.
12. Xiao Y, Lazaro AM, Masaberg C, Haagenson M, Vierra-Green C, Spellman S, Dakshanamurthy S, Ng J, Hurley CK. Evaluating the potential impact of mismatches outside the antigen recognition site in unrelated hematopoietic stem cell transplantation: HLA-DRB1*1454 and DRB1*140101. Tissue Antigens 2009, 73:595-598. 10.1111/j.1399-0039.2009.01245.x, 3224974, 19392807.
13. Davidson CJ, Zeringer E, Champion KJ, Gauthier M-P, Wang F, Boonyaratanakornkit J, Jones JR, Schreiber E. Improving the limit of detection for Sanger sequencing: a comparison of methodologies for KRAS variant detection. Biotechniques 2012, 53:182-188.
14. Danzer M, Niklas N, Stabentheiner S, Hofer K, Pröll J, Stückler C, Raml E, Polin H, Gabriel C. Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics. BMC Genomics 2013, 14:221. 10.1186/1471-2164-14-221, 3639865, 23557197.
15. Erlich H. HLA DNA typing: past, present, and future. Tissue Antigens 2012, 80:1-11. 10.1111/j.1399-0039.2012.01881.x, 22651253.
16. Rastrou MV, Holcomb CL, Williams TC, Goodridge D, Lazaro AM, Tilanus M, Erlich HA. 12-OR: In vitro generated PCR crossover products identified by next generation sequencing correspond to some alleles in the IMGT database. Hum Immunol 2012, 73:10.
17. Haas BJ, Gevers D, Earl AM, Feldgarden M, Ward DV, Giannoukos G, Ciulla D, Tabbaa D, Highlander SK, Sodergren E, Methé B, DeSantis TZ, Petrosino JF, Knight R, Birren BW. Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons. Genome Res 2011, 21:494-504. 10.1101/gr.112730.110, 3044863, 21212162.
18. Judo MSB, Wedel AB, Wilson C. Stimulation and suppression of PCR-mediated recombination. Nucleic Acids Res 1998, 26:1819-1825. 10.1093/nar/26.7.1819, 147471, 9512558.
19. Schmidt AH, Baier D, Solloch UV, Stahr A, Cereb N, Wassmuth R, Ehninger G, Rutt C. Estimation of high-resolution HLA-A, -B, -C, -DRB1 allele and haplotype frequencies based on 8862 German stem cell donors and implications for strategic donor registry planning. Hum Immunol 2009, 70:895-902. 10.1016/j.humimm.2009.08.006, 19683023.
20. Robinson J, Halliwell JA, McWilliam H, Lopez R, Parham P, Marsh SGE. The IMGT/HLA database. Nucleic Acids Res 2013, 41(Database issue):D1222-D1227. 3531221, 23080122.
21. Marsh SGE, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernández-Viña M, Geraghty DE, Holdsworth R, Hurley CK, Lau M, Lee KW, Mach B, Maiers M, Mayr WR, Müller CR, Parham P, Petersdorf EW, Sasazuki T, Strominger JL, Svejgaard A, Terasaki PI, Tiercy JM, Trowsdale J. Nomenclature for factors of the HLA system, 2010. Tissue Antigens 2010, 75:291-455. 10.1111/j.1399-0039.2010.01466.x, 2848993, 20356336.