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Evaluation of a quantitative PCR-based method for chimerism analysis of Japanese donor/recipient pairs.

ABSTRACT: Chimerism analysis is a surrogate indicator of graft rejection or relapse after allogeneic hematopoietic stem cell transplantation (HSCT). Although short tandem repeat PCR (STR-PCR) is the usual method, limited sensitivity and technical variability are matters of concern. Quantitative PCR-based methods to detect single nucleotide polymorphisms (SNP-qPCR) are more sensitive, but their informativity and quantitative accuracy are highly variable. For accurate and sensitive chimerism analysis, a set of KMR kits (GenDx, Utrecht, Netherlands), based on detection of insertions/deletions (indels) by qPCR, have been developed. Here, we investigated informativity and validated the accuracy of KMR kits in Japanese donor/recipient pairs and virtual samples of DNA mixtures representative of Japanese genetic diversity. We found that at least one recipient-specific marker among 39 KMR-kit markers was informative in all of 65 Japanese donor/recipient pairs. Moreover, the percentage of recipient chimerism estimated by KMRtrack correlated well with ratios of mixed DNA in virtual samples and with the percentage of chimerism in HSCT recipients estimated by STR-PCR/in-house SNP-qPCR. Moreover, KMRtrack showed better sensitivity with high specificity when compared to STR-PCR to detect recipient chimerism. Chimerism analysis with KMR kits can be a standardized, sensitive, and highly informative method to evaluate the graft status of HSCT recipients.

SUBMITTER: Minakawa K

PROVIDER: S-EPMC9734659 | biostudies-literature | 2022 Dec

REPOSITORIES: biostudies-literature

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Evaluation of a quantitative PCR-based method for chimerism analysis of Japanese donor/recipient pairs.

Minakawa Keiji K Ono Satoshi S Watanabe Mao M Sato Yuka Y Suzuki Saki S Odawara Shou S Kawabata Kinuyo K Ueda Koki K Nollet Kenneth E KE Sano Hideki H Ikezoe Takayuki T Kikuta Atsushi A Ikeda Kazuhiko K

Scientific reports 20221209 1

Chimerism analysis is a surrogate indicator of graft rejection or relapse after allogeneic hematopoietic stem cell transplantation (HSCT). Although short tandem repeat PCR (STR-PCR) is the usual method, limited sensitivity and technical variability are matters of concern. Quantitative PCR-based methods to detect single nucleotide polymorphisms (SNP-qPCR) are more sensitive, but their informativity and quantitative accuracy are highly variable. For accurate and sensitive chimerism analysis, a set ...[more]

PMID: 36494422

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Project description:Immune reconstitution kinetics and subsequent clinical outcomes in HLA-matched recipients of allogeneic stem cell transplantation (SCT) are variable and difficult to predict. Considering SCT as a dynamical system may allow sequence differences across the exomes of the transplant donors and recipients to be used to simulate an alloreactive T cell response, which may allow better clinical outcome prediction. To accomplish this, whole exome sequencing was performed on 34 HLA-matched SCT donor-recipient pairs (DRPs) and the nucleotide sequence differences translated to peptides. The binding affinity of the peptides to the relevant HLA in each DRP was determined. The resulting array of peptide-HLA binding affinity values in each patient was considered as an operator modifying a hypothetical T cell repertoire vector, in which each T cell clone proliferates in accordance with the logistic equation of growth. Using an iterating system of matrices, each simulated T cell clone's growth was calculated with the steady-state population being proportional to the magnitude of the binding affinity of the driving HLA-peptide complex. Incorporating competition between T cell clones responding to different HLA-peptide complexes reproduces a number of features of clinically observed T cell clonal repertoire in the simulated repertoire, including sigmoidal growth kinetics of individual T cell clones and overall repertoire, Power Law clonal frequency distribution, increase in repertoire complexity over time with increasing clonal diversity, and alteration of clonal dominance when a different antigen array is encountered, such as in SCT. The simulated, alloreactive T cell repertoire was markedly different in HLA-matched DRPs. The patterns were differentiated by rate of growth and steady-state magnitude of the simulated T cell repertoire and demonstrate a possible correlation with survival. In conclusion, exome wide sequence differences in DRPs may allow simulation of donor alloreactive T cell response to recipient antigens and may provide a quantitative basis for refining donor selection and titration of immunosuppression after SCT.

Project description:BackgroundCompatible pair participation in kidney paired donation (KPD) may increase the likelihood of finding suitable matches for all registered pairs. Retrospective studies have shown variable enthusiasm for participating in KPD in compatible pairs.ObjectiveThe study objective was to gather potential living donor (PLD) and transplant candidate (TC) perspectives on compatible pair participation in KPD.DesignSurveys and qualitative interviews.SettingThree transplant programs in Canada: Centre hospitalier de l'Université de Montréal in Montreal (Québec), Vancouver General Hospital, and St. Paul's Hospital in Vancouver (British Columbia).PatientsBoth PLDs and TCs undergoing evaluation for donation/transplantation between 2016 and 2018 at 3 transplant programs in Canada.MethodsDescriptive statistical analysis was performed for the results of the survey and thematic and content analysis method was used for the content of the qualitative interviews.ResultsA total of 116 PLDs and 111 TCs completed surveys and an additional 18 PLDs and 17 TCs underwent semi-directed interviews. Of those surveyed, 61.2% of PLDs and 76.6% of TCs reported a willingness to participate in KPD as a compatible pair. The possibility of a more optimally matched kidney for the TC and policies ensuring prioritization of the TC for repeat transplantation in the event of early graft failure increased willingness to participate in KPD. Major concerns expressed during the interviews included the desire to retain the emotional bond of directed donation, the fear of chain breaks or donor reneging, delays in transplantation, and additional travel associated with participation in KPD.LimitationThe limitations of this study are that it was conducted in only 3 Canadian transplant programs and that the interviews and surveys were in French and in English. As a consequence, the results may not be reflective of the views of individuals not living in these 2 provinces and from ethnic minority populations.ConclusionMost of the compatible PLDs and TCs surveyed were willing to participate in KPD. Ensuring timely transplantation and a more optimal match for TCs and offering a policy of reciprocity to ensure timely repeat transplantation for compatible recipients if their allograft fails post KPD transplant may further increase compatible pair participation in KPD.

Dataset Information

Evaluation of a quantitative PCR-based method for chimerism analysis of Japanese donor/recipient pairs.

Publications

Evaluation of a quantitative PCR-based method for chimerism analysis of Japanese donor/recipient pairs.

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