Open Access Highly Accessed Methodology article

Next-generation sequencing for HLA typing of class I loci

Rachel L Erlich1, Xiaoming Jia12, Scott Anderson1, Eric Banks1, Xiaojiang Gao34, Mary Carrington34, Namrata Gupta1, Mark A DePristo1, Matthew R Henn1, Niall J Lennon1 and Paul IW de Bakker1567*

Author Affiliations

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, Frederick, Maryland 21702, USA

4 Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Boston, Massachusetts 02114, USA

5 Division of Genetics, Department of Medicine, Brigham and Women's 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

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BMC Genomics 2011, 12:42  doi:10.1186/1471-2164-12-42

Published: 18 January 2011



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.


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.


Next-generation sequencing on the 454 FLX Titanium platform is a reliable, efficient, and scalable technology for HLA typing.