Chimerism monitoring using biallelic single nucleotide or insertion/deletion polymorphisms: How many markers to screen?

Vynck, Matthijs; Nollet, Friedel; Sibbens, Lode; Devos, Helena

doi:10.1016/j.cca.2022.05.026

Cited by 7 publications

(4 citation statements)

References 19 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…A limitation is that although use of multiple recipient-specific markers is recommended for chimerism monitoring, one unrelated and 5 related pairs had only one recipient-specific marker by using both KMRtype Core and Extended kits. This may be consistent with a recent study that showed at least 40 markers are required to distinguish a large number of the pairs 26 . There is another issue that some markers frequently showed atypical results which could not determine chimerism.…”

Section: Discussionsupporting

confidence: 93%

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

Minakawa

Ono

Watanabe

et al. 2022

Sci Rep

View full text Add to dashboard Cite

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.

show abstract

Section: Discussionsupporting

confidence: 93%

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

Minakawa

Ono

Watanabe

et al. 2022

Sci Rep

View full text Add to dashboard Cite

show abstract

“…First, the marker panels are variable from 24 to 202 markers, and it is necessary to perform genotyping for all contributors, except for AlloSeq HCT, which proposes an analysis in the absence of a contributor. On the one hand, the high number of markers avoids false-negative results caused by chromosomal deletions in the relapse of some malignancies, but on the other hand, it has been shown that too many markers are unnecessary ( 33 ). Thus, depending on the type of graft, it is necessary to test at least 20 markers if the HSCT is unrelated and at least 40 markers if it is a related HSCT.…”

Section: Discussionmentioning

confidence: 99%

New methods for the quantification of mixed chimerism in transplantation

Picard

Frassati²,

Cherouat³

et al. 2023

Front. Immunol.

View full text Add to dashboard Cite

BackgroundQuantification of chimerism showing the proportion of the donor in a recipient is essential for the follow-up of hematopoietic stem cell transplantation but can also be useful to document an immune tolerance situation after solid organ transplantation. Historically, chimerism has been quantified from genomic DNA, but with technological advances, chimerism from donor-derived cell-free DNA seems particularly relevant in solid organ transplantation.MethodsThe reference method was until recently the short tandem repeat technique, but new innovative techniques as digital PCR (dPCR) and NGS, have revolutionized the quantification of chimerism, such as the so-called microchimerism analysis. After a short review of chimerism methods, a comparison of chimerism quantification data for two new digital PCR systems (QIAcuity™ dPCR (Qiagen®) and QuantStudio Absolute Q (ThermoFisher®) and two NGS-based chimerism quantification methods (AlloSeq HCT™ (CareDx®) and NGStrack™ (GenDX®)) was performed.ResultsThese new methods were correlated and concordant to routinely methods (r²=0.9978 and r²=0.9974 for dPCR methods, r²=0.9978 and r²=0.9988 for NGS methods), and had similar high performance (sensitivity, reproductibility, linearity).ConclusionFinally, the choice of the innovative method of chimerism within the laboratory does not depend on the analytical performances because they are similar but mainly on the amount of activity and the access to instruments and computer services.

show abstract

“…The issues of qPCR are limited informativity, inconsistent quantitative accuracy, false positive results, and technical variations [ 2 , 11 ]. However, the use of 40 or more markers can achieve almost 100% informativity [ 17 , 24 ].…”

Section: Methods Of Chimerism Analysismentioning

confidence: 99%

Prospects and Potential for Chimerism Analysis after Allogeneic Hematopoietic Stem Cell Transplantation

Miura,

Ueda,

Minakawa

et al. 2024

Cells

View full text Add to dashboard Cite

Chimerism analysis after allogeneic hematopoietic stem cell transplantation serves to confirm engraftment, indicate relapse of hematologic malignancy, and attribute graft failure to either immune rejection or poor graft function. Short tandem repeat PCR (STR-PCR) is the prevailing method, followed by quantitative real-time PCR (qPCR), with detection limits of 1–5% and 0.1%, respectively. Chimerism assays using digital PCR or next-generation sequencing, both of which are more sensitive than STR-PCR, are increasingly used. Stable mixed chimerism is usually not associated with poor outcomes in non-malignant diseases, but recipient chimerism may foretell relapse of hematologic malignancies, so higher detection sensitivity may be beneficial in such cases. Thus, the need for and the type of intervention, e.g., immunosuppression regimen, donor lymphocyte infusion, and/or salvage second transplantation, should be guided by donor chimerism in the context of the feature and/or residual malignant cells of the disease to be treated.

show abstract

Chimerism monitoring using biallelic single nucleotide or insertion/deletion polymorphisms: How many markers to screen?

Cited by 7 publications

References 19 publications

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

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

New methods for the quantification of mixed chimerism in transplantation

Prospects and Potential for Chimerism Analysis after Allogeneic Hematopoietic Stem Cell Transplantation

Contact Info

Product

Resources

About