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Next-generation sequencing for HLA typing of class I loci

  1. Author:
    Erlich, R. L.
    Jia, X. M.
    Anderson, S.
    Banks, E.
    Gao, X. J.
    Carrington, M.
    Gupta, N.
    DePristo, M. A.
    Henn, M. R.
    Lennon, N. J.
    de Bakker, P. I. W.

  2. Author Address

    [Erlich, Rachel L.; Jia, Xiaoming; Anderson, Scott; Banks, Eric; Gupta, Namrata; DePristo, Mark A.; Henn, Matthew R.; Lennon, Niall J.; de Bakker, Paul I. W.] MIT & Harvard, Broad Inst, Cambridge, MA 02142 USA. [Jia, Xiaoming] Harvard MIT Div Hlth Sci & Technol, Boston, MA USA. [Gao, Xiaojiang; Carrington, Mary] NCI, Canc & Inflammat Program, Expt Immunol Lab, SAIC Frederick Inc, Frederick, MD 21702 USA. [Gao, Xiaojiang; Carrington, Mary] Massachusetts Gen Hosp, Ragon Inst, MIT, Boston, MA 02114 USA. [de Bakker, Paul I. W.] Harvard Univ, Div Genet, Dept Med, Brigham & Womens Hosp,Med Sch, Boston, MA 02114 USA. [de Bakker, Paul I. W.] Univ Med Ctr Utrecht, Dept Med Genet, Utrecht, Netherlands. [de Bakker, Paul I. W.] Univ Med Ctr Utrecht, Julius Ctr Hlth Sci & Primary Care, Utrecht, Netherlands.;de Bakker, PIW, MIT & Harvard, Broad Inst, Cambridge, MA 02142 USA.;pdebakker@rics.bwh.harvard.edu
    1. Year: 2011
    2. Date: Jan
  2. Journal: Bmc Genomics
    1. 12
    2. Pages: 13
  4. Type of Article: Article
  5. Article Number: 42
  6. ISSN: 1471-2164
  1. Abstract:

    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.

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External Sources

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  2. DOI: 10.1186/1471-2164-12-42
  3. View record in Web of Science®
  4. WOS: 000287083500003

Library Notes

  1. Fiscal Year: FY2010-2011
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