Next generation sequencing to determine HLA class II genotypes in a cohort of hematopoietic cell transplant patients and donors

Human Immunology

Volumn 75, Issue 10, 2014, Pages 1040-1046

  Smith, Anajane G ^a   Pyo, Chul Woo ^a   Nelson, Wyatt ^a   Gow, Edward ^a   Wang, Ruihan ^a   Shen, Shu ^a   Sprague, Maggie ^b   Pereira, Shalini E ^a,b   Geraghty, Daniel E ^a   Hansen, John A ^a,b  

^a Fred Hutchinson Cancer Research Center   (United States)

^b SEATTLE CANCER CARE ALLIANCE   (United States)

Author keywords

Genotyping; High resolution; HLA class II; Multiplex reaction PCR; Next generation sequencing

Indexed keywords

GENOMIC DNA; HLA ANTIGEN CLASS 2; HLA DPA1 ANTIGEN; HLA DPB1 ANTIGEN; HLA DQA1 ANTIGEN; HLA DQB1 ANTIGEN; HLA DRB1 ANTIGEN; HLA DRB3 ANTIGEN; HLA DRB4 ANTIGEN; HLA DRB5 ANTIGEN; UNCLASSIFIED DRUG; HLA DP ANTIGEN; HLA DQ ANTIGEN; HLA DR ANTIGEN; HLA-DPA1 ANTIGEN; HLA-DPB1 ANTIGEN; HLA-DQA1 ANTIGEN; HLA-DQB1 ANTIGEN;

ACCURACY; ALLELE; AMPLICON; ARTICLE; COHORT ANALYSIS; COMPUTER PROGRAM; DNA DETERMINATION; DONOR; EXON; GENOTYPE; GRAFT RECIPIENT; HEMATOPOIETIC STEM CELL TRANSPLANTATION; HLA TYPING; HUMAN; MAJOR CLINICAL STUDY; NEXT GENERATION SEQUENCING; RELIABILITY; SEQUENCE ANALYSIS; CHEMISTRY; EVALUATION STUDY; GENETICS; HIGH THROUGHPUT SEQUENCING; HISTOCOMPATIBILITY TEST; LIVING DONOR; PROCEDURES; REPRODUCIBILITY;

COHORT STUDIES; EXONS; GENOTYPE; HEMATOPOIETIC STEM CELL TRANSPLANTATION; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTOCOMPATIBILITY ANTIGENS CLASS II; HISTOCOMPATIBILITY TESTING; HLA-DP ALPHA-CHAINS; HLA-DP BETA-CHAINS; HLA-DQ ALPHA-CHAINS; HLA-DQ BETA-CHAINS; HLA-DR ANTIGENS; HUMANS; LIVING DONORS; REPRODUCIBILITY OF RESULTS; SOFTWARE;

EID: 84908011842     PISSN: 01988859     EISSN: 18791166     Source Type: Journal    
DOI: 10.1016/j.humimm.2014.08.206     Document Type: Article

References (32)

1. Morishima Y., Sasazuki T., Inoko H., Juji T., Akaza T., Yamamoto K., et al. The clinical significance of human leukocyte antigen (HLA) allele compatibility in patients receiving a marrow transplant from serologically HLA-A, HLA-B, and HLA-DR matched unrelated donors. Blood 2002, 99:4200-4206.
2. Lee S.J., Klein J., Haagenson M., Baxter-Lowe L.A., Confer D.L., Eapen M., et al. High-resolution donor-recipient HLA matching contributes to the success of unrelated donor marrow transplantation. Blood 2007, 110:4576-4583.
3. Woolfrey A., Klein J.P., Haagenson M., Spellman S., Petersdorf E., Oudshoorn M., et al. HLA-C antigen mismatch is associated with worse outcome in unrelated donor peripheral blood stem cell transplantation. Biol Blood Marrow Transplant 2011, 17:885-892.
4. Spellman S.R., Eapen M., Logan B.R., Mueller C., Rubinstein P., Setterholm M.I., et al. A perspective on the selection of unrelated donors and cord blood units for transplantation. Blood 2012, 120:259-265.
5. Furst D., Muller C., Vucinic V., Bunjes D., Herr W., Gramatzki M., et al. High-resolution HLA matching in hematopoietic stem cell transplantation: a retrospective collaborative analysis. Blood 2013, 122:3220-3229.
6. Horn P.A., Albis-Camps M., Verboom M., Bunce M., Yousaf K., Williams S., et al. The nature of diversity of HLA-DRB1 exon 3. Tissue Antigens 2007, 70:335-337.
7. 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, 71:1033-1042.
8. Erlich H. HLA DNA typing: past, present, and future (Review). Tissue Antigens 2012, 80:1-11.
9. Chien J.W., Zhang X.C., Fan W., Wang H., Zhao L.P., Martin P.J., et al. Evaluation of published single nucleotide polymorphisms associated with acute graft versus host disease. Blood 2012, 119:5311-5319.
10. Adey A., Morrison H.G., Asan, Xun X., Kitzman J.O., Turner E.H., et al. Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition. Genome Biol 2010, 11:R119.
11. Marsh S.G., Albert E.D., Bodmer W.F., Bontrop R.E., Dupont B., Erlich H.A., et al. Nomenclature for factors of the HLA system, 2010 (Review). Tissue Antigens 2010, 75:291-455.
12. Petersdorf E.W., Smith A.G., Haase A.M., Martin P.J., Hansen J.A. Polymorphism of HLA-DRw52-associated DRB1 genes as defined by sequence-specific oligonucleotide probe hybridization and sequencing. Tissue Antigens 1991, 38:169-177.
13. Mickelson E., Smith A., McKinney S., Anderson G., Hansen J.A. A comparative study of HLA-DRB1 typing by standard serology and hybridization of non-radioactive sequence-specific oligonucleotide probes to PCR-amplified DNA. Tissue Antigens 1993, 41:86-93.
14. Smith A.G., Nelson J.L., Regen L., Guthrie L.A., Donadi E., Mickelson E.M., et al. Six new DR52-associated DRB1 alleles, three of DR8, two of DR11, and one of DR6, reflect a variety of mechanisms which generate polymorphism in the MHC. Tissue Antigens 1996, 48:118-126.
15. Bentley G., Higuchi R., Hoglund B., Goodridge D., Sayer D., Trachtenberg E.A., et al. High-resolution, high-throughput HLA genotyping by next-generation sequencing. Tissue Antigens 2009, 74:393-403.
16. Moonsamy P.V., Williams T., Bonella P., Holcomb C.L., Hoglund B.N., Hillman G., et al. High throughput HLA genotyping using 454 sequencing and the Fluidigm Access Array™ System for simplified amplicon library preparation. Tissue Antigens 2013, 81:141-149.
17. 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, 109:8676-8681.
18. 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, 80:305-316.
19. Lange V., Bohme I., Hofmann J., Lang K., Sauter J., Schone B., et al. Cost-efficient high-throughput HLA typing by MiSeq amplicon sequencing. BMC Genomics 2014, 15:63.
20. Bodmer J.G., Marsh S.G., Albert E.D., Bodmer W.F., Dupont B., Erlich H.A., et al. Nomenclature for factors of the HLA system, 1994. Tissue Antigens 1994, 44:1-18.
21. *1102. Tissue Antigens 2007, 70:73-75.
22. *1454 in South German Caucasians. Tissue Antigens 2010, 76:57-59.
23. *14 allelic frequencies in Koreans. Hum Immunol 2009, 70:464-467.
24. *140101. Tissue Antigens 2009, 73:595-598.
25. Begovich A.B., McClure G.R., Suraj V.C., Helmuth R.C., Fildes N., Bugawan T.L., et al. Polymorphism, recombination, and linkage disequilibrium within the HLA class II region. J Immunol 1992, 148:249-258.
26. Maiers M., Gragert L., Klitz W. High-resolution HLA alleles and haplotypes in the United States population. Hum Immunol 2007, 68:779-788.
27. Shaw B.E., Gooley T.A., Malkki M., Madrigal J.A., Begovich A.B., Horowitz M.M., et al. The importance of HLA-DPB1 in unrelated donor haematopoietic cell transplantation. Blood 2007, 110:4560-4566.
28. Fleischhauer K., Shaw B.E., Gooley T., Malkki M., Bardy P., Bignon J.D., et al. Effect of T-cell-epitope matching at HLA-DPB1 in recipients of unrelated-donor haemopoietic-cell transplantation: a retrospective study. Lancet Oncol 2012, 13:366-374. [Erratum appears in Lancet Oncol. 2012 Apr, 13(4), pp. e134-5].
29. Fernandez-Vina M.A., Klein J.P., Haagenson M., Spellman S.R., Anasetti C., Noreen H., et al. Multiple mismatches at the low expression HLA loci DP, DQ, and DRB3/4/5 associate with adverse outcomes in hematopoietic stem cell transplantation. Blood 2013, 121:4603-4610.
30. Pidala J., Wang T., Haagenson M., Spellman S.R., Askar M., Battiwalla M., et al. Amino acid substitution at peptide-binding pockets of HLA class I molecules increases risk of severe acute GVHD and mortality. Blood 2013, 122:3651-3658.
31. Kamani N., Spellman S., Hurley C.K., Barker J.N., Smith F.O., Oudshoorn M., et al. State of the art review: HLA matching and outcome of unrelated donor umbilical cord blood transplants (Review). Biol Blood Marrow Transplant 2008, 14:1-6.
32. Eapen M., Klein J.P., Ruggeri A., Spellman S., Lee S.J., Anasetti C., et al. Impact of allele-level HLA matching on outcomes after myeloablative single unit umbilical cord blood transplantation for hematologic malignancy. Blood 2013, [Epub ahead of print; PMID 24141369].