Project: HLA-DP haplotypes

DPA1-promotor-DPB1 haplotypes

Project leaders: Dianne De Santis, Effie Petersdorf, Marcel Tilanus

HLA-DPA1 and HLA-DPB1 orientation is unique in the way that they share a promoter region. In contrast to other HLA class II genes, HLA-DPA1 and HLA-DPB1 genes are oriented head to head overlapping 2.4 kb in the promoter region. It has been described that there is extensive degree of polymorphism of HLA-DPB1 and HLA-DPA1, and they are nearly always in linkage disequilibrium at 2-field resolution1. It has also been shown that the promoter region is polymorphic albeit only part of the promoter has been sequenced2, 3.

Currently, 1,449 HLA-DPB1 alleles, 132 HLA-DPA1 alleles and 9 promoters have been identified mainly based on partial sequence2-4. Of all the described alleles, only 423 HLA-DPB1 and 71 HLA-DPA1 full length sequences are defined and there is no full length promoter sequence for this region. In addition, Petersdorf et al had identified SNP outside the gene that has impacted the expression level5. Truong et al developed a dual sequencing strategy to cover the entire haplotype region from HLA-DPA1 to HLA-DPB1 including the rs9277534 SNP. Full-length sequencing of the entire 22kb HLA-DP region gave rise to 12 promoter haplotypes which are in strong linkage disequilibrium with HLA-DPA1. Interestingly, the promoter haplotype that was found predominately from Chinese descendent had a SNP density of 3.2 SNP/100 bases compared to 0.7 SNP/100 bases in other promoter haplotypes. The cohort that was used for this study comprised of many different HLA-DPA1 and HLA-DPB1 alleles.

The goal of this project is to uncover the polymorphism of the 22kb HLA-DPA1 ~ promoter ~ HLA-DPB1 region of samples with HLA-DPA1 and HLA-DPB1 alleles from a variety of different populations.

Milestones in years:

2019: Identify alleles of interest and collect samples submitted by the participants and defined by project leaders; organise a consistent source of primer for the amplification of the 22kb DP region (project leaders)

2020: amplification and sequencing; full phasing labs may provide sequencing service at a small cost; 2 progress evaluation meetings at EFI and ASHI

2021: data analysis, preparation of manuscript and presentation at the workshop, EFI abstract.

Patient/Sample description:

Samples with HLA-DPA1 and HLA-DPB1 alleles from a variety of different populations, preferably samples which were not included in Truong et al publication. Samples can be sequenced in the participant’s laboratory by Next-Generation Sequencing (NGS) and/or Third-Generation Sequencing (TGS – MinION/PacBio). Detailed protocols will be made available. Sample must be available for confirmatory typing for further evaluation.

Alternatively, high quality DNA samples can be sent to the Perth laboratory with a small service cost. If phasing difficulties are encountered by NGS, samples can be sent to laboratories with TGS technology.

Data required:

The raw read data and the corresponding interpretation of the haplotypes should be made available to the project leaders.

The following information should also be provided by participants:

  • Lab name / IHWS number
  • Number of samples and a list of HLA-DPA1/-DPB1 alleles
  • Sequences obtained by own laboratory or a reference laboratory
  • Protocols used to obtained full-length sequence
  • DNA available (Yes/No)
  • Is the submitted allele included in the Table 1?

References:

  1. Hollenbach JA, Madbouly A, Gragert L, Vierra-Green C, Flesch S, Spellman S, et al. A combined DPA1~DPB1 amino acid epitope is the primary unit of selection on the HLA-DP heterodimer. Immunogenetics. 2012;64:559-69.
  2. Liu X, Xu Y, Shen Y, Zhang H, Fu Y, Liu Z, et al. HLA-DPA1 promoter haplotypes are differently distributed in southern Chinese ethnic groups. Tissue antigens. 2005;65:172-7.
  3. Varney MD, Gavrilidis A, Tait BD. Polymorphism in the regulatory regions of the HLA-DPB1 gene. Hum Immunol. 1999;60:955-61.
  4. Robinson J, Halliwell JA, Hayhurst JD, Flicek P, Parham P, Marsh SGE. The IPD and IMGT/HLA database: allele variant databases. Nucleic acids research. 2015;43:D423-D31.
  5. Petersdorf EW, Malkki M, O’HUigin C, Carrington M, Gooley T, Haagenson MD, et al. High HLA-DP Expression and Graft-versus-Host Disease. The New England journal of medicine. 2015;373:599-609.

http://

Promoter SNP HaplotypeDPA1*DPB1*CountPromoter SNP HaplotypeDPA1*DPB1*Count
ProDP 11:03:012:01:021ProDP 21:03:012:01:0215
ProDP 11:03:013:01:0113ProDP 21:03:012:02:011
ProDP 11:03:014:01:0131ProDP 21:03:014:01:011
ProDP 11:03:014:02:0110ProDP 21:03:0116:01:012
ProDP 11:03:015:01:011ProDP 21:03:0147:01:011
ProDP 11:03:016:01:014ProDP 21:03:0181:01:011
ProDP 11:03:0111:01:011ProDP 21:03:01416:01:011
ProDP 11:03:0115:01:011ProDP 21:03:01652:01:001
ProDP 11:03:0118:01:012ProDP 32:01:0111:01:015
ProDP 11:03:0120:01:011ProDP 32:01:0117:01:013
ProDP 11:03:0121:01:003ProDP 32:01:0127:01:002
ProDP 11:03:0123:01:011ProDP 32:01:0186:01:001
ProDP 11:03:0133:01:011ProDP 32:01:021:01:013
ProDP 11:03:0136:01:001ProDP 32:01:0413:01:012
ProDP 11:03:0180:01:001ProDP 32:01:081:01:013
ProDP 11:03:01124:01:011ProDP 42:01:019:01:013
ProDP 11:03:01126:01:011ProDP 42:01:0110:01:018
ProDP 11:03:01128:01:001ProDP 42:01:0114:01:017
ProDP 11:03:01130:01:001ProDP 42:01:0135:01:012
ProDP 11:03:01138:01:003ProDP 42:01:0145:01:001
ProDP 11:03:01104:01:016ProDP 448:00:0010:01:011
ProDP 11:04:0115:01:012ProDP 52:01:015:01:011
ProDP 13:01:0118:01:011ProDP 52:02:021:01:015
ProDP 13:01:01105:01:013ProDP 52:02:022:02:011
ProDP 13:01:02105:01:012ProDP 52:02:025:01:019
ProDP 52:02:0214:01:011
ProDP 52:02:0222:01:001
ProDP 52:02:005:01:011
ProDP 62:07:0119:01:014
ProDP 62:12:0085:01:011
ProDP 71:03:014:02:014
ProDP 81:03:012:01:021
ProDP 91:03:012:01:023
ProDP 101:03:014:01:011
ProDP 114:01:00107:01:005
ProDP 122:02:02135:01:002


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