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High-Throughput Sequencing of the Major Histocompatibility Complex following Targeted Sequence Capture

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Haplotyping

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1551))

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Abstract

The Human Major Histocompatibility Complex (MHC) is a highly polymorphic region full of immunoregulatory genes. The MHC codes for the human leukocyte antigens (HLA), proteins that present on the cellular surface and that are involved in self-non-self recognition. For matching donors and recipients for organ and stem-cell transplants it is important to know an individual’s HLA haplotype determinable in this region. Now, as next-generation sequencing (NGS) platforms mature and become more and more accepted as a standard method, NGS applications have spread from research laboratories to the clinic, where they provide valid genetic insights. Here, we describe a cost-effective microarray-based sequence capture, enrichment, and NGS sequencing approach to characterize MHC haplotypes. Using this approach, ~4 MB of MHC sequence for four DNA samples (donor, recipient and the parents of the recipient) were sequenced in parallel in one NGS instrument run. We complemented this approach using microarray-based genome-wide SNP analysis. Taken together, the use of recently developed tools and protocols for sequence capture and massively parallel sequencing allows for detailed MHC analysis and donor-recipient matching.

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Acknowledgment

This project was supported by the Austrian Research Promotion Agency (FFG grant: Nr. 815468 B1) and Roche Austria.

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Authors and Affiliations

  1. Red Cross Transfusion Service of Upper Austria, Krankenhausstr. 7, 4020, Linz, Austria

    Johannes Pröll, Carina Fischer, Martin Danzer & Norbert Niklas

  2. Center for Medical Research, Graz, Austria

    Gabriele Michelitsch

Authors
  1. Johannes Pröll
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  2. Carina Fischer
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  3. Gabriele Michelitsch
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  4. Martin Danzer
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  5. Norbert Niklas
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Corresponding author

Correspondence to Johannes Pröll .

Editor information

Editors and Affiliations

  1. Johannes Kepler University Institute of Biophysics, Linz, Austria

    Irene Tiemann-Boege

  2. Vetmeduni Vienna InstitutPopulationsgenetik, Wien, Austria

    Andrea Betancourt

1 Electronic Supplementary Material

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HG18_Austrian_Red_Cross_CG (XLSX 228 kb)

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Pröll, J., Fischer, C., Michelitsch, G., Danzer, M., Niklas, N. (2017). High-Throughput Sequencing of the Major Histocompatibility Complex following Targeted Sequence Capture. In: Tiemann-Boege, I., Betancourt, A. (eds) Haplotyping. Methods in Molecular Biology, vol 1551. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6750-6_5

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  • DOI: https://doi.org/10.1007/978-1-4939-6750-6_5

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-6748-3

  • Online ISBN: 978-1-4939-6750-6

  • eBook Packages: Springer Protocols

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