Projects
The analysis of HLA class I non-coding regions
Linda Smith
Rationale:
Sequencing of HLA non-coding regions has been vastly overlooked. This is mainly due to the assumption that there is minimal functional significance (except at splice sites), the enormous effort directed towards sequencing coding regions of HLA and the technical challenges of analysing non-coding regions. In a recent unpublished study we revealed several novel alleles within non-coding regions of HLA class I (characterised by polymorphisms in non-coding regions). We identified three differences (when compared to the reference sequence) in the non-coding regions of HLA-B*18:01:01 located in intron 3, 5, and the 3ยด UTR. The intron 3 region was sequenced in 48 samples with B*18:01:01 and the results demonstrated the novel polymorphism was present on B*18:01:01 of the 18.1 ancestral haplotype (A*25, B*18, DRB1*15:01). The alternative polymorphism was found on the 18.2 ancestral haplotype (A*30, B*18, C*05, DRB1*03:01). This study was presented at the 2010 European Federation for Immunogenetics (EFI) and will also be presented at the 2010 American Society of Histocompatibility and Immunogenetics (ASHI).
Whilst some polymorphisms may not have a direct functional significance, the novel polymorphisms identified may be markers for specific ancestral haplotypes. These may be utilised in donor selection for unrelated bone marrow transplantation. At the very least we will be able to determine the level of heterogeneity in population samples.
Proposal:
In this workshop component we propose to identify novel HLA class I non-coding variations in different populations. Laboratories could;
- Survey of the level of heterogeneity of non-coding sequence.
- Identify rare versus common non-coding polymorphisms.
- Determine the frequency of currently defined alleles characterised by polymorphisms in coding sequences
- Examine common polymorphisms to determine if they are associated with or split conserved haplotypes.
- Determine if unrelated stem transplants include class I non-coding sequence differences.
- Add novel alleles to the IMGT/HLA Database
Outline of plan:
- Participants are to analyse SBT results for non-coding polymorphisms. If labs are unable to analyse data DCI-Perth will do the analysis.
- To maintain a register of numbers of loci, alleles and non-coding sequences analysed.
- We will catalogue the number of novel alleles including the HLA types at other loci for haplotype characterisation.
- Submit data for collation.
- >Present data at the 16th IHIW.
Lab requirements:
- Ability to perform SBT and/or access to HLA class I sequence data.
- Software capable of complete gene analysis.
(Conexio Genomics will provide software to participants who do not have software that enables complete HLA gene sequencing based genotyping).
Contacts:
Please let us know if you would like to participate in the workshop. We will provide you with further information as the project proceeds.
Linda Smith
Department of Clinical Immunology
Royal Perth Hospital, PathWest
Level 2, North Block,
Wellington St, Perth 6000
Western Australia
E-mail: linda [dot] k [dot] smith [at] health [dot] wa [dot] gov [dot] au
Ph: 61-8-92242899
Fax: 61-8-9224 2920
Download a PDF of the ASHI 2011 Presentation - download PDF file.
