title: High-throughput, high-fidelity HLA genotyping with deep sequencing.
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.
authors.affiliation: Stanford Genome Technology Center, Stanford University, Palo Alto, CA 94003, USA.
authors.forename: Chunlin
authors.initials: C
authors.lastname: Wang
authors.forename: Sujatha
authors.initials: S
authors.lastname: Krishnakumar
authors.forename: Julie
authors.initials: J
authors.lastname: Wilhelmy
authors.forename: Farbod
authors.initials: F
authors.lastname: Babrzadeh
authors.forename: Lilit
authors.initials: L
authors.lastname: Stepanyan
authors.forename: Laura F
authors.initials: LF
authors.lastname: Su
authors.forename: Douglas
authors.initials: D
authors.lastname: Levinson
authors.forename: Marcelo A
authors.initials: MA
authors.lastname: Fernandez-Viña
authors.forename: Ronald W
authors.initials: RW
authors.lastname: Davis
authors.forename: Mark M
authors.initials: MM
authors.lastname: Davis
authors.forename: Michael
authors.initials: M
authors.lastname: Mindrinos
mesh_terms: D000483:Alleles; D001483:Base Sequence; D002460:Cell Line; D017931:DNA Primers / Q000235:genetics; D005838:Genotype; D060005:Genotyping Techniques / Q000379:methods*; D006680:HLA Antigens / Q000235:genetics*; D015234:HLA-A Antigens / Q000235:genetics; D015235:HLA-B Antigens / Q000235:genetics; D015236:HLA-C Antigens / Q000235:genetics; D059811:HLA-DRB1 Chains / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods; D011110:Polymorphism, Genetic; D015203:Reproducibility of Results; D012689:Sequence Homology, Nucleic Acid
chemical_list: D017931:DNA Primers; D006680:HLA Antigens; D015234:HLA-A Antigens; D015235:HLA-B Antigens; D015236:HLA-C Antigens; D059811:HLA-DRB1 Chains