Feasibility to detect genomic loss of HLA alleles by One Lambda LABType products combined with novel data analysis algorithm

Loss of heterozygosity in human leukocyte antigens (HLA) is a phenomenon frequently observed in relapses of myeloid leukemia treated by allogeneic hematopoietic stem cell transplantation. Loss of HLA was also described in multiple studies of solid tumors (Montesion et al. 2021, Zhang et al. 2022) where loss of HLA may be particularly important for patients treated by HLA restrictive immunotherapy. Identifying loss of heterozygosity (LOH) during relapses may provide information critical for treatment selection in affected patients. One Lambda LABType products utilize reverse-sequence-specific oligonucleotide (rSSO) typing method with the LABScan 100 or LABScan3D instruments, to provide HLA typing in up to 11 HLA loci. Though this product is used for HLA genotyping in transplant diagnostic practices, we explored potential feasibility to use LABType kits to detect complete or partial loss of HLA alleles in human genome. We used homozygous DNA samples well characterized for all 11 HLA loci and tested different ratios of DNAs in each mixture to mimic LOH characteristics and analyzed all samples with One Lambda LABType products for several loci. Our new loss of HLA analysis algorithm was able to clearly distinguish between homozygous DNA and DNA mix containing only 10% of minor allele. Assay allowed clearly distinguish 1:1 DNA mix from 30, 20 and 10% of minor allele and comparing different SSO products showed that LABType CWD kits were quantifying residual allele with higher level of confidence. To challenge our algorithm further, we tested mixture of 3 DNAs imitating haplo-matched stem cell transplant, when donor is sharing one set of HLA alleles with the patient while other donor's allele is different. We mimicked different levels of chimerism and different levels of HLA loss by mixing these 3 DNAs representing heterozygous donor and two patients alleles in different ratios. Experiment demonstrated ability of LABType CWD test to detect as little as 1% of minor allele present in 20 ng of total DNA per reaction. Further evaluation of new data analysis approach using LABType technology for complete or partial loss of HLA may be beneficial for both transplant medicine related research and oncology fields. New algorithm is intended for research use only and is not commercially available at this time.