NGS of Full-length HLA genes

NGS of Full-length HLA genes

NGS of Full-length HLA genes

The HLA genes are the most polymorphic loci in the human genome; over 12,000 genetic variants (alleles) have been identified at 19 HLA genes, with some individual genes displaying several thousand alleles. The allelic and structural variation that characterizes these genes pose extreme challenges for routine genotyping of these genetic loci; this variation cannot be characterized by a few SNPs, and the high level of polymorphism confounds de novo sequence assembly efforts. Until recently, HLA genotyping has been accomplished using a variety of PCR-based approaches involving sequence-specific oligonucleotide probe (SSOP) hybridization and/or Sanger sequencing of 400-600 base pair amplicons. These… Read More

Component: NGS of full length HLA genes: Preliminary results of the Pilot Study

Lisa E Creary1, Steven J Mack2 and Marcelo Fernandez-Vina1
1Department of Pathology, Stanford Blood Center
2Children’s Hospital Oakland Research Institute


The ultimate goal of the 17th International HLA and Immunogenetics Workshop (IHIW) is to advance the fields of Histocompatibility and Immunogenetics (H & I) research through the application of Next-Generation Sequencing (NGS) technologies for HLA and KIR genotyping, and to advance the development of NGS technologies tailored to meet the needs of the H & I community.

In 2014, we initiated an international multi-center pilot study in order to assess the performance of various NGS protocols, platforms,… Read More

T Cell Receptor (TCR)-HLA Interaction

The T cell receptor is the natural receptor of the HLA-peptide complex and interacts directly with MHC molecules, notably their CDR regions.  The goal of this project will be to combine analysis of TCR and HLA in the context of disease, vaccination/immune alterations and populations.  We would expect samples to be CD4 or CD8 T cells and to have full HLA class I and class II typing by NGS.

Required NGS HLA loci: HLA-A, B, C, DRB1, DRB3/4/5, DQB, HLA-DQA, DPA, DPB
Optional NGS HLA Loci: MICA, MICB

Subprojects for this component will include:
  • Disease study:  This will involve… Read More
  • Extension of HLA allele sequences by full-length HLA allele-specific hemizygous Sanger sequencing (SSBT)

    The Human Leucocyte Antigen (HLA) is one of the most polymorphic gene systems present in the human genome and due to this high polymorphism, the golden standard for typing at the allele level has been and still is sequence based typing. Since sequencing strategies have mainly focused on identification of the peptide binding groove, therefore the majority of HLA alleles lack full length sequence information.

    The goal of this project is to extend the sequences of as many incompletely covered HLA alleles as possible by full length unambiguous Sanger Sequencing. Although NGS approaches are currently implemented in several laboratories, many… Read More

    Pharmacogenetics and HLA

    Serious adverse reactions to some drugs are associated with certain HLA alleles in some ethnic groups, but have not been investigated in other populations. The project will include a retrospective study of HLA alleles in patients of different ethnic groups who had adverse reactions to carbamazepine. Additional associations may be established for other drugs with increasing awareness of possible immunogenetic predisposition.

    Project Leaders:

    Clara Gorodezky Ph.D. (
    Maria Bettinotti Ph.D. (

    Immunogenetics of Aging

    The aging process is very complex and longevity is a multifactorial trait, which is determined by genetic and environmental factors.  The aim of the component “Immunogenetics of Aging” is to identify new biomarkers for successful aging and an increased capacity to reach the extreme limits of lifespan by analysis of immune response genes.

    Project Leaders

    Elissaveta Naumova, Ph.D. (
    Milena Ivanova, Ph.D.  (

    Download Project Requirements

    Immunogenetics of Aging (PDF)


    Disease Association

    The application of NGS-HLA typing to screen susceptibility to certain diseases could be useful to further refine and pinpoint the causative HLA polymorphism. One of the goals of the 17th IHIWS disease component is to collect NGS HLA-disease association data conducted worldwide on autoimmune diseases, infectious diseases, cancers, and identify additional genetic determinants predisposing to disease. Investigators may submit both family and population based NGS HLA data or samples only.

    Study of Unrelated Subjects by NGS HLA

    Anthropological studies by NGS of full-length HLA genes to confirm and further characterize alleles and haplotypes identified in unrelated subjects from populations of interest. Subjects should be previously HLA typed at any level (serology, DNA). Investigators may submit samples only or samples and NGS data.

    Project leader: Harriet Noreen (
    Project Leader: Steven J Mack (

    Study of Haplotypes in Families by NGS HLA

    Anthropological study of families by NGS of full-length HLA genes to determine haplotype segregation in multiple populations. Samples from family quartets consisting of two parents and at least two non-HLA identical children or family trios consisting of one parent and at least two non-HLA identical children are required. The families should be previously HLA typed at any level (serology, DNA). Investigators may submit samples only or samples and NGS data.

    Project Leader: Medhat Askar (
    Kazutoyo Osoegawa, PhD (


    Characteristics and Distribution of Unusual Haplotypes by NGS HLA

    NGS of full-length HLA genes typing to confirm and further characterize alleles identified as unusual haplotypes and compare the frequency of these to haplotypes identified from the family studies project in multiple populations. The subjects and families should be previously HLA typed at any level (serology, DNA).

    Project leader: Harriet Noreen (