Development and validation of a sample sparing strategy for HLA typing utilizing next generation sequencing

Human Immunology

Volumn 76, Issue 12, 2015, Pages 917-922

  McKinney, Denise M ^a   Fu, Zheng ^a   Le, Lucas ^a   Greenbaum, Jason A ^a   Peters, Bjoern ^a   Sette, Alessandro ^a  

^a LA JOLLA INSTITUTE FOR ALLERGY AND IMMUNOLOGY   (United States)

Author keywords

HLA typing; Next generation sequencing; Pipeline; Sample sparing

Indexed keywords

DNA; HLA DRB1 ANTIGEN; HLA ANTIGEN;

ALPHA CHAIN; AMPLICON; ANTIGEN PRESENTATION; ARTICLE; BETA CHAIN; COMPARATIVE STUDY; EXON; GENE AMPLIFICATION; GENE LOCUS; HETEROZYGOTE; HLA TYPING; HOMOZYGOSITY; HUMAN; HUMAN CELL; INTRON; NEXT GENERATION SEQUENCING; PERIPHERAL BLOOD MONONUCLEAR CELL; POLYMERASE CHAIN REACTION; PRIORITY JOURNAL; VALIDATION STUDY; ALLELE; BIOLOGY; CELL LINE; DNA SEQUENCE; GENE LIBRARY; GENETICS; HIGH THROUGHPUT SEQUENCING; HISTOCOMPATIBILITY TEST; METABOLISM; MONONUCLEAR CELL; PROCEDURES; REPRODUCIBILITY; STANDARDS; WORKFLOW;

ALLELES; CELL LINE; COMPUTATIONAL BIOLOGY; GENE LIBRARY; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HISTOCOMPATIBILITY TESTING; HLA ANTIGENS; HUMANS; LEUKOCYTES, MONONUCLEAR; POLYMERASE CHAIN REACTION; REPRODUCIBILITY OF RESULTS; SEQUENCE ANALYSIS, DNA; WORKFLOW;

EID: 84959106510     PISSN: 01988859     EISSN: 18791166     Source Type: Journal    
DOI: 10.1016/j.humimm.2015.04.007     Document Type: Article

References (36)

1. Trowsdale J., Knight J.C. Major histocompatibility complex genomics and human disease. Annu. Rev. Genomics Hum. Genet. 2013, 14:301.
2. De Santis D., Dinauer D., Duke J., Erlich H.A., Holcomb C.L., Lind C., et al. 16(th) IHIW: review of HLA typing by NGS. Int. J. Immunogenet. 2013, 40:72.
3. Erlich H. HLA DNA typing: past, present, and future. Tissue Antigens 2012, 80:1.
4. Robinson J., Halliwell J.A., McWilliam H., Lopez R., Parham P., Marsh S.G. The IMGT/HLA database. Nucleic Acids Res. 2013, 41:D1222.
5. Dunn P.P. Human leucocyte antigen typing: techniques and technology, a critical appraisal. Int. J. Immunogenet. 2011, 38:463.
6. Grumbt B., Eck S.H., Hinrichsen T., Hirv K. Diagnostic applications of next generation sequencing in immunogenetics and molecular oncology. Transfus. Med. Hemother. 2013, 40:196.
7. Warren R.L., Choe G., Freeman D.J., Castellarin M., Munro S., Moore R., et al. Derivation of HLA types from shotgun sequence datasets. Genome Med. 2012, 4:95.
8. Liu C., Yang X., Duffy B., Mohanakumar T., Mitra R.D., Zody M.C., et al. ATHLATES: accurate typing of human leukocyte antigen through exome sequencing. Nucleic Acids Res. 2013, 41:e142.
9. Kim H.J., Pourmand N. HLA haplotyping from RNA-seq data using hierarchical read weighting. PLoS ONE 2013, 8:e67885.
10. Erlich R.L., 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.
11. 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.
12. 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:e78410.
13. Szolek A., Schubert B., Mohr C., Sturm M., Feldhahn M., Kohlbacher O. OptiType: precision HLA typing from next-generation sequencing data. Bioinformatics 2014.
14. de Bourcy C.F., De Vlaminck I., Kanbar J.N., Wang J., Gawad C., Quake S.R. A quantitative comparison of single-cell whole genome amplification methods. PLoS ONE 2014, 9:e105585.
15. Han T., Chang C.W., Kwekel J.C., Chen Y., Ge Y., Martinez-Murillo F., et al. Characterization of whole genome amplified (WGA) DNA for use in genotyping assay development. BMC Genomics 2012, 13:217.
16. Koressaar T., Remm M. Enhancements and modifications of primer design program Primer3. Bioinformatics 2007, 23:1289.
17. Untergasser A., Cutcutache I., Koressaar T., Ye J., Faircloth B.C., Remm M., et al. Primer3-new capabilities and interfaces. Nucleic Acids Res. 2012, 40:e115.
18. Langmead B., Salzberg S.L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 2012, 9:357.
19. Gonzalez-Galarza F.F., Christmas S., Middleton D., Jones A.R. Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations. Nucleic Acids Res. 2011, 39:D913.
20. Rykalina V.N., Shadrin A.A., Amstislavskiy V.S., Rogaev E.I., Lehrach H., Borodina T.A. Exome sequencing from nanogram amounts of starting DNA: comparing three approaches. PLoS ONE 2014, 9:e101154.
21. Treff N.R., Su J., Tao X., Northrop L.E., Scott R.T. Single-cell whole-genome amplification technique impacts the accuracy of SNP microarray-based genotyping and copy number analyses. Mol. Hum. Reprod. 2011, 17:335.
22. Creary L.E., Girdlestone J., Zamora J., Brown J., Navarrete C.V. Molecular typing of HLA genes using whole genome amplified DNA. Transfusion 2009, 49:57.
23. Khan F., Liacini A., Arora E., Wang S., Assad M., Doulla J., et al. Assessment of fidelity and utility of the whole-genome amplification for the clinical tests offered in a histocompatibility and immunogenetics laboratory. Tissue Antigens 2012, 79:372.
24. Ndlovu B.G., Danaviah S., Moodley E., Ghebremichael M., Bland R., Viljoen J., et al. Use of dried blood spots for the determination of genetic variation of interleukin-10, killer immunoglobulin-like receptor and HLA class I genes. Tissue Antigens 2012, 79:114.
25. 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.
26. Sette A., Rappuoli R. Reverse vaccinology: developing vaccines in the era of genomics. Immunity 2010, 33:530.
27. McKinney D.M., Southwood S., Hinz D., Oseroff C., Arlehamn C.S., Schulten V., et al. A strategy to determine HLA class II restriction broadly covering the DR, DP, and DQ allelic variants most commonly expressed in the general population. Immunogenetics 2013, 65:357.
28. Nepom G.T. MHC class II tetramers. J. Immunol. 2012, 188:2477.
29. Newell E.W., Sigal N., Nair N., Kidd B.A., Greenberg H.B., Davis M.M. Combinatorial tetramer staining and mass cytometry analysis facilitate T-cell epitope mapping and characterization. Nat. Biotechnol. 2013, 31:623.
30. Newell E.W., Klein L.O., Yu W., Davis M.M. Simultaneous detection of many T-cell specificities using combinatorial tetramer staining. Nat. Methods 2009, 6:497.
31. Apps R., Qi Y., Carlson J.M., Chen H., Gao X., Thomas R., et al. Influence of HLA-C expression level on HIV control. Science 2013, 340:87.
32. Weiskopf D., Angelo M.A., de Azeredo E.L., Sidney J., Greenbaum J.A., Fernando A.N., et al. Comprehensive analysis of dengue virus-specific responses supports an HLA-linked protective role for CD8+ T cells. Proc. Natl. Acad. Sci. U.S.A. 2013, 110:E2046.
33. Tsai S., Santamaria P. MHC class II polymorphisms, autoreactive T-Cells, and autoimmunity. Front. Immunol. 2013, 4:321.
34. Marks C. Immunobiological determinants in organ transplantation. Ann. R. Coll. Surg. Engl. 1983, 65:139.
35. Holcomb C.L., Rastrou M., Williams T.C., Goodridge D., Lazaro A.M., Tilanus M., 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.
36. Danzer M., Niklas N., Stabentheiner S., Hofer K., Proll J., Stuckler C., et al. Rapid, scalable and highly automated HLA genotyping using next-generation sequencing: a transition from research to diagnostics. BMC Genomics 2013, 14:221.