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High-throughput, high-fidelity HLA genotyping with deep sequencing
Stanford Univ, Stanford Genome Technol Ctr, Palo Alto, CA. (Nyrén)
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2012 (English)In: Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, E-ISSN 1091-6490, Vol. 109, no 22, 8676-8681 p.Article in journal (Refereed) Published
Abstract [en]

Human leukocyte antigen (HLA) genes are the most polymorphic in the human genome. They play a pivotal role in the immune response and have been implicated in numerous human pathologies, especially autoimmunity and infectious diseases. Despite their importance, however, they are rarely characterized comprehensively because of the prohibitive cost of standard technologies and the technical challenges of accurately discriminating between these highly related genes and their many allelles. Here we demonstrate a high-resolution, and cost-effective methodology to type HLA genes by sequencing, which combines the advantage of long-range amplification, the power of high-throughput sequencing platforms, and a unique genotyping algorithm. We calibrated our method for HLA-A, -B, -C, and -DRB1 genes with both reference cell lines and clinical samples and identified several previously undescribed alleles with mismatches, insertions, and deletions. We have further demonstrated the utility of this method in a clinical setting by typing five clinical samples in an Illumina MiSeq instrument with a 5-d turnaround. Overall, this technology has the capacity to deliver low-cost, high-throughput, and accurate HLA typing by multi-plexing thousands of samples in a single sequencing run, which will enable comprehensive disease-association studies with large cohorts. Furthermore, this approach can also be extended to include other polymorphic genes.

Place, publisher, year, edition, pages
2012. Vol. 109, no 22, 8676-8681 p.
Keyword [en]
hematopoietic stem cell transplantation, sequence-based typing
National Category
Medical and Health Sciences
URN: urn:nbn:se:kth:diva-137232DOI: 10.1073/pnas.1206614109ISI: 000304881700065ScopusID: 2-s2.0-84861865679OAI: diva2:678483

QC 20131218

Available from: 2013-12-12 Created: 2013-12-12 Last updated: 2013-12-18Bibliographically approved

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Babrzadeh, Farbod
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