HLA Informatics Group

This on-going study of over 2,500 patient and donor paired samples, coordinated by Anthony Nolan, aims to identify how genetically similar, or different, patients and their unrelated donors are and correlate this with the transplant outcome. These studies include looking at which HLA genes we should be matching for and to what resolution, as well as what other genetic factors should be included during the matching process to improve the transplant outcome for all patients.

To date, we have demonstrated the importance of the following:

• Using 12/12 ultra-high resolution HLA matched donors where possible.
• Including the HLA-DPB1 gene into our matching algorithms.
• The beneficial impact of younger donor age on patient outcome.
• Combining CMV status matching with HLA matching to improve transplant outcomes.
• Identifying which HLA mismatches to avoid.
• How KIR genes affect transplant outcome for patients with AML.

We are currently typing our project cohort for their full-length HLA-DRB1, -DQB1 and -DPB1 genes, aiming to show for the first time, the impact of matching at this resolution on patient outcome. We are also expanding our panel of HLA gene typing to include, among others, HLA-E.

This is a national, collaborative study with all UK centres that perform unrelated-donor transplantation being part of the project. The results of the Patient/Donor Project studies are translated into practice at Anthony Nolan and influences clinical practice worldwide.

Key publications:

Presence of donor-encoded centromeric KIR B content increases the risk of infectious mortality in recipients of myeloablative, T-cell deplete, HLA-matched HCT to treat AML. 
Bultitude WP, Schellekens J, Szydlo RM, Anthias C, Cooley SA, Miller JS, Weisdorf DJ, Shaw BE, Roberts CH, Garcia-Sepulveda CA, Lee J, Pearce RM, Wilson MC, Potter M, Byrne JL, Russell NH, MacKinnon S, Bloor AJ, Patel A, McQuaker IG, … Marsh, SGE 
Bone Marrow Transplantation (2020) 55(10), 1975–1984. 

Recipients Receiving Better HLA Matched Haematopoietic Cell Grafts, Uncovered By A Novel HLA Typing Methodology, Have Superior Survival: A Retrospective Study 
Mayor NP, Hayhurst JD, Turner TR, Szydlo RM, Shaw BE, Bultitude WP, Sayno JR, Tavarozzi F, Latham K, Anthias C, Robinson J, Braund H, Danby R, Perry J, Wilson MC, Bloor AJ, McQuaker IG, MacKinnon S, Marks DI, Pagliuca A, Potter MN, Potter VT, Russell NH, Thomson KJ, Madrigal JA, Marsh SGE 
Biol Blood Marrow Transplant. 2019 Mar;25(3):443-450 

Recipient/donor HLA and CMV matching in recipients of T-cell-depleted unrelated donor haematopoietic cell transplants. 
Shaw BE, Mayor NP, Szydlo RM, Bultitude WP, Anthias C, Kirkland K, Perry J, Clark A, Mackinnon S, Marks DI, Pagliuca A, Potter MN, Russell NH, Thomson K, Madrigal JA, Marsh SGE. 
Bone Marrow Transplantation (2017) May;52(5):717-725 

The Feasibility Project builds on the work of the Patient/Donor Project by using the data from the retrospective studies to determine the probability of finding the best matched donor, and how to improve our chances of finding this donor. Following on from our most recent clinical publication, we are currently working on determining the probabilities of finding a donor when we consider HLA-DPB1 matching and allow for permissive mismatching, as well as CMV status matching. This project will help determine the best approach for how we select our donors for each patient, based on their immunogenetic profile. 

The Bioinformatics group maintain a number of internationally recognised databases of gene specific variation. These databases provide extensive information on the variation of the key genes involved in transplantation. They are published in collaboration with the EMBL-European Bioinformatics Institute, and internationally recognised as the gold-standard for providing data on the genes of interest: 

The IPD-IMGT/HLA Database provides sequences of the human major histocompatibility complex (MHC) and includes all official sequences for the World Health Organisation Nomenclature Committee for Factors of the HLA System. The IPD-IMGT/HLA Database currently contains over 28,000 allele sequences. In addition to the DNA sequences, it holds detailed information about the material the sequence was derived from and how the data was validated.  

The IPD-KIR Databases provides a centralised repository for sequences of Killer cell Immunoglobulin-like Receptors (KIRs). KIRs are members of the immunoglobulin superfamily (IgSF), formerly called Killer Cell Inhibitory Receptors. They are composed of two or three Ig-domains, a transmembrane region and cytoplasmic tail, which can in turn be short (activatory) or long (inhibitory). The Leukocyte Receptor Complex (LRC) which encodes KIR genes has been shown to be polymorphic, polygenic and complex like the MHC. 

The Bioinformatics group also work with other groups interested in providing similar databases for other polymorphic gene systems. 

Key publications 

IPD-IMGT/HLA Database. 
Barker DJ, Maccari G, Georgiou X, Cooper MA, Flicek P, Robinson J, Marsh, SGE 
Nucleic Acids Research (2023), 51(D1), D1053–D1060. 

Distinguishing functional polymorphism from random variation in the sequences of >10,000 HLA-A, -B and -C alleles. 
Robinson J, Guethlein LA, Cereb N, Yang SY, Norman PJ, Marsh SGE, Parham P 
PLoS Genetics (2017) 13(6), e1006862. 

Anthony Nolan maintains a large register of potential donors, each of whom have had their HLA genes sequenced. This data is an ideal source of information for studying HLA diversity in different UK populations, including those of minority ethnic backgrounds.

We are undertaking several projects to characterise the HLA genetic diversity of the UK and other populations around the world. This will identify regions with higher diversity within the UK and allow us to improve and refine our recruitment strategies. It will give us a better understanding of the needs of our patients and contribute to creating a more diverse register that will increase the chances of every patient finding a suitable donor.

This work requires the team to develop novel software to complete the complex mathematical and statistical analysis needed to compare the HLA tissue types of nearly one million individuals. This has also meant looking at new computing methods and hardware to provide a suitable platform for analysing these large data sets.

Key publications:

The HLA diversity of the Anthony Nolan register.
Leen G, Stein JE, Robinson J, Maldonado Torres H, Marsh SGE 
HLA (2021) 97(1), 15–29. 

To study complex immunogenetic markers, we need to use DNA sequencing techniques that allow us to sequence more of the gene than has ever been possible previously, and to generate highly accurate data.  

With support from The Wolfson Foundation, Anthony Nolan has been able to invest in a new third-generation sequencing platform, the Pacific Biosciences Sequel System, that will allow us to generate sequences of a quality that has not been achieved previously. The Immunogenetics Group are working to develop our typing assays on this new platform, to increase the efficiency that is now possible and to expand the portfolio of genetic markers that we can type for.  

As our sequencing technologies improve, so does our need to store, analyse and report more complex data. The Bioinformatics Group are working alongside the Immunogenetics Group to develop bespoke automated workflows, and software for the processing of this data, generated by different sequencing platforms. 

The implementation of this work enabled Anthony Nolan to be one of the first registries in the world to provide clinical HLA typing using the Pacific Biosciences RS II sequencing technology. Work is also currently underway to implement workflows for the Pacific Biosciences Sequel system using Google Cloud to provide the computing infrastructure.  

Key publications 

Single molecule real-time DNA sequencing of the full HLA-E gene for 212 reference cell lines. 
Lucas JAM, Hayhurst JD, Turner TR, Gymer AW, Leen G, Robinson J, Marsh SGE, Mayor NP 
HLA (2020) Jun;95(6):561-572 

Single molecule real-time DNA sequencing of HLA genes at ultra-high resolution from 126 International HLA and Immunogenetics Workshop cell lines. 
Turner TR, Hayhurst JD, Hayward DR, Bultitude WP, Barker DJ, Robinson J, Madrigal JA, Mayor NP, Marsh SGE 
HLA (2018) 91(2), 88–101. 

HLA Typing for the Next Generation. 
Mayor NP, Robinson J, McWhinnie AJ, Ranade S, Eng K, Midwinter W, Bultitude WP, Chin CS, Bowman B, Marks P, Braund H, Madrigal JA, Latham K, Marsh SGE 
PloS One (2015) 10(5), e0127153.