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High-throughput, high-fidelity HLA genotyping with deep sequencing
- Source :
- Proceedings of the National Academy of Sciences. 109:8676-8681
- Publication Year :
- 2012
- Publisher :
- Proceedings of the National Academy of Sciences, 2012.
-
Abstract
- 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 multiplexing 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.
- Subjects :
- Genotype
Genotyping Techniques
Molecular Sequence Data
HLA-C Antigens
Human leukocyte antigen
Biology
Polymerase Chain Reaction
Deep sequencing
Cell Line
law.invention
HLA Antigens
law
Sequence Homology, Nucleic Acid
HLA-B Antigens
Humans
Typing
Genotyping
Alleles
Polymerase chain reaction
DNA Primers
Genetics
Polymorphism, Genetic
Multidisciplinary
Base Sequence
HLA-A Antigens
High-Throughput Nucleotide Sequencing
Reproducibility of Results
Biological Sciences
Human genome
HLA-DRB1 Chains
Subjects
Details
- ISSN :
- 10916490 and 00278424
- Volume :
- 109
- Database :
- OpenAIRE
- Journal :
- Proceedings of the National Academy of Sciences
- Accession number :
- edsair.doi.dedup.....6f86050cd9fcef5da95dd6096bc2b456