Utilization of genome data
Many key components in blood transfusion medicine are determined by genetic factors. The most obvious are blood groups, HLA and thrombocyte alloantigens. In addition, it is plausible that genetic factors play a role in long term effects of regular blood and cell donations.
We are exploiting the genome data produced from blood donors in the Blood Service Biobank. In particular, the FinnGen project returns genome data from over 58000 blood donors to the FRCBS Biobank. These data can be used for the benefits of blood service activities.
For example, we have created bioinformatics tools to predict or impute the key blood cell alloantigens, blood groups, platelet HPA and HLA from the genome data returned to the FRCBS Biobank. These imputation results are now used to screen blood donors with rare blood groups or HLA alleles or combination. Once the imputation results have been verified using clinical grade assays we are able to substantially increase the number of compatible blood donors for patients in need of rare blood groups or for leukaemia patients in need of HLA-typed thrombocytes.
We are also developing a genome-based assay platform to type all relevant genetic variation needed in blood transfusion. The Blood transfusion Genomics Consortium (BGC) is an international initiative lead by Professor Willem Ouwehand, of the University of Cambridge, UK. The aim is a single SNP array integrated with an interpretation software that could be used to type all relevant blood groups and HLA alleles needed in transfusion medicine. In the future other relevant markers can be added into the array. The BGC now collects data for regulatory purposes. BGC Educational sessions can be found on YouTube.
We have developed imputation tools for HLA allele and NK-cell KIR gene content determinations and are now utilizing it in various cohorts:
- Ritari J, Hyvärinen K, Clancy J; FinnGen, Partanen J, Koskela S. Increasing accuracy of HLA imputation by a population-specific reference panel in a FinnGen biobank cohort. NAR Genom Bioinform. 2020;2(2):lqaa030. PMID: 33575586
- Ritari J, Hyvärinen K, Partanen J, Koskela S. KIR gene content imputation from single-nucleotide polymorphisms in the Finnish population. PeerJ. 2022;10:e12692. PMID: 35036093
- Ritari J, Koskela S, Hyvärinen K, FinnGen, Partanen J. HLA-disease association and pleiotropy landscape in over 235,000 Finns. Hum Immunol. 2022;83(5):391-398. PMID: 35221124
FRCBS R&D department publishes the programming code in the GitHub service with open-source licenses.