Next-generation sequencing for HLA typing of class I loci

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• 作者：Rachel L Erlich (1)
  Xiaoming Jia (1) (2)
  Scott Anderson (1)
  Eric Banks (1)
  Xiaojiang Gao (3) (4)
  Mary Carrington (3) (4)
  Namrata Gupta (1)
  Mark A DePristo (1)
  Matthew R Henn (1)
  Niall J Lennon (1)
  Paul IW de Bakker (1) (5) (6) (7)
  
• 刊名：BMC Genomics
• 出版年：2011
• 出版时间：December 2011
• 年：2011
• 卷：12
• 期：1
• 全文大小：6225KB
• 参考文献：1. Consortium: Complete sequence and gene map of a human major histocompatibility complex. The MHC sequencing consortium. / Nature 1999, 401: 921鈥?23. CrossRef
  2. de Bakker PI, McVean G, Sabeti PC, Miretti MM, Green T, Marchini J, Ke X, Monsuur AJ, Whittaker P, Delgado M, / et al.: A high-resolution HLA and SNP haplotype map for disease association studies in the extended human MHC. / Nature genetics 2006, 38: 1166鈥?172. CrossRef
  3. Horton R, Gibson R, Coggill P, Miretti M, Allcock RJ, Almeida J, Forbes S, Gilbert JG, Halls K, Harrow JL, / et al.: Variation analysis and gene annotation of eight MHC haplotypes: the MHC Haplotype Project. / Immunogenetics 2008, 60: 1鈥?8. CrossRef
  4. Horton R, Wilming L, Rand V, Lovering RC, Bruford EA, Khodiyar VK, Lush MJ, Povey S, Talbot CC Jr, Wright MW, / et al.: Gene map of the extended human MHC. / Nat Rev Genet 2004, 5: 889鈥?99. CrossRef
  5. Carrington M, O'Brien SJ: The influence of HLA genotype on AIDS. / Annu Rev Med 2003, 54: 535鈥?51. CrossRef
  6. Fernando MM, Stevens CR, Walsh EC, De Jager PL, Goyette P, Plenge RM, Vyse TJ, Rioux JD: Defining the role of the MHC in autoimmunity: a review and pooled analysis. / PLoS Genet 2008, 4: e1000024. CrossRef
  7. Rioux JD, Goyette P, Vyse TJ, Hammarstrom L, Fernando MM, Green T, De Jager PL, Foisy S, Wang J, de Bakker PI, / et al.: Mapping of multiple susceptibility variants within the MHC region for 7 immune-mediated diseases. / Proc Natl Acad Sci USA 2009, 106: 18680鈥?8685. CrossRef
  8. Ryder LP, Svejgaard A, Dausset J: Genetics of HLA disease association. / Annu Rev Genet 1981, 15: 169鈥?87. CrossRef
  9. Morishima Y, Sasazuki T, Inoko H, Juji T, Akaza T, Yamamoto K, Ishikawa Y, Kato S, Sao H, Sakamaki H, / 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鈥?206. CrossRef
  10. Robinson J, Waller MJ, Fail SC, McWilliam H, Lopez R, Parham P, Marsh SG: The IMGT/HLA database. / Nucleic acids research 2009, 37: D1013鈥?017. CrossRef
  11. Hansen JA, (Ed): Immunobiology of the Human MHC. / Proceedings of the 13th International Histocompatibility Workshop and Conference 2002.
  12. Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, Marth G, Abecasis G, Durbin R: The Sequence Alignment/Map format and SAMtools. In / Bioinformatics. / Volume 25. Oxford, England; 2009:2078鈥?079.
  13. McKenna AH, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, Depristo M: The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. / Genome research 2010, 20: 1297鈥?303. CrossRef
  14. Marsh SG: Nomenclature for factors of the HLA system, update May 2006. / Tissue antigens 2006, 68: 273鈥?75. CrossRef
  15. Marsh SG: Nomenclature for factors of the HLA system, update March 2005. / Hum Immunol 2005, 66: 1017鈥?018. CrossRef
  16. 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鈥?03. CrossRef
  17. 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鈥?017. CrossRef
  18. Gabriel C, Danzer M, Hackl C, Kopal G, Hufnagl P, Hofer K, Polin H, Stabentheiner S, Proll J: Rapid high-throughput human leukocyte antigen typing by massively parallel pyrosequencing for high-resolution allele identification. / Hum Immunol 2009, 70: 960鈥?64. CrossRef
  19. Middleton D, Menchaca L, Rood H, Komerofsky R: New allele frequency database. [http://www.allelefrequencies.net] / Tissue antigens 2003, 61: 403鈥?07. CrossRef
  20. Robinson J, Waller MJ, Parham P, de Groot N, Bontrop R, Kennedy LJ, Stoehr P, Marsh SG: IMGT/HLA and IMGT/MHC: sequence databases for the study of the major histocompatibility complex. / Nucleic acids research 2003, 31: 311鈥?14. CrossRef
  21. Edgar RC: MUSCLE: multiple sequence alignment with high accuracy and high throughput. / Nucleic acids research 2004, 32: 1792鈥?797. CrossRef
  22. Kent WJ, Sugnet CW, Furey TS, Roskin KM, Pringle TH, Zahler AM, Haussler D: The human genome browser at UCSC. / Genome research 2002, 12: 996鈥?006.
  23. Rozen S, Skaletsky H: Primer3 on the WWW for general users and for biologist programmers. / Methods in molecular biology (Clifton, NJ 2000, 132: 365鈥?86.
  24. Waterhouse AM, Procter JB, Martin DM, Clamp M, Barton GJ: Jalview Version 2--a multiple sequence alignment editor and analysis workbench. In / Bioinformatics. / Volume 25. Oxford, England; 2009:1189鈥?191.
  25. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, / et al.: Genome sequencing in microfabricated high-density picolitre reactors. / Nature 2005, 437: 376鈥?80.
  26. Lennon NJ, Lintner RE, Anderson S, Alvarez P, Barry A, Brockman W, Daza R, Erlich RL, Giannoukos G, Green L, / et al.: A scalable, fully automated process for construction of sequence-ready barcoded libraries for 454. / Genome biology 2010, 11: R15. CrossRef
  27. Marsh SG, Albert ED, Bodmer WF, Bontrop RE, Dupont B, Erlich HA, Fernandez-Vina M, Geraghty DE, Holdsworth R, Hurley CK, / et al.: Nomenclature for factors of the HLA system, 2010. / Tissue antigens 2010, 75: 291鈥?55. CrossRef
  28. Marsh SG: Nomenclature for factors of the HLA system, update February 2010. / Tissue antigens 2010, 76: 165鈥?70.
  
• 作者单位：Rachel L Erlich (1)
  Xiaoming Jia (1) (2)
  Scott Anderson (1)
  Eric Banks (1)
  Xiaojiang Gao (3) (4)
  Mary Carrington (3) (4)
  Namrata Gupta (1)
  Mark A DePristo (1)
  Matthew R Henn (1)
  Niall J Lennon (1)
  Paul IW de Bakker (1) (5) (6) (7)
  
  1. Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
  2. Harvard-MIT Division of Health Sciences and Technology, Boston, Massachusetts, USA
  3. Cancer and Inflammation Program, Laboratory of Experimental Immunology, SAIC-Frederick Inc., National Cancer Institute, 21702, Frederick, Maryland, USA
  4. Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, 02114, Boston, Massachusetts, USA
  5. Division of Genetics, Department of Medicine, Brigham and Women鈥檚 Hospital, Harvard Medical School, Boston, Massachusetts, USA
  6. Department of Medical Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
  7. Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
  

文摘

Background Comprehensive sequence characterization across the MHC is important for successful organ transplantation and genetic association studies. To this end, we have developed an automated sample preparation, molecular barcoding and multiplexing protocol for the amplification and sequence-determination of class I HLA loci. We have coupled this process to a novel HLA calling algorithm to determine the most likely pair of alleles at each locus. Results We have benchmarked our protocol with 270 HapMap individuals from four worldwide populations with 96.4% accuracy at 4-digit resolution. A variation of this initial protocol, more suitable for large sample sizes, in which molecular barcodes are added during PCR rather than library construction, was tested on 95 HapMap individuals with 98.6% accuracy at 4-digit resolution. Conclusions Next-generation sequencing on the 454 FLX Titanium platform is a reliable, efficient, and scalable technology for HLA typing.