The clinical application of SNP-based next-generation sequencing (SNP-NGS) for evaluation of chimerism and microchimerism after HLA-mismatched stem cell microtransplantation

Abstract

Genetic diagnostic methods for evaluation of chimerism after HSCT, such as STR-PCR and XY-FISH, have limited sensitivity. When donor chimerism is in the micro range (< 1%), deviations in the accuracy of assessment are the most significant disadvantage of these common methods. We developed a highly sensitive method that applies SNPs based on NGS in order to explore the value of donor cell microchimerism in microtransplantation (MST). This improved SNP-NGS approach has higher sensitivity (0.01–0.05%) and only requires a small amount of DNA (8–200 ng). We retrospectively analyzed the clinical data of 48 patients with AML who received HLA-mismatched stem cell MST at our center to assess the impact of microchimerism on clinical prognosis. Patients whose duration of microchimerism was > 10.5 months (median) had a relapse rate of 26.1%, and had better 5-year LFS and OS (73.4% and 82.6%). In contrast, patients whose duration of microchimerism was < 10.5 months had a higher relapse rate (69.6%), and their 5-year LFS and OS were 30.4% and 43.5%. In conclusion, duration of donor chimerism is highly valuable for assessment of survival and prognosis in patients with AML who have received HLA-mismatched stem cell MST, especially the intermediate-risk group.

Chimerism Testing by Next Generation Sequencing for Detection of Engraftment and Early Disease Relapse in Allogeneic Hematopoietic Cell Transplantation and an Overview of NGS Chimerism Studies

“…They designed a bioinformatics tool for genotyping and quantification of NGS data, which provides clinicians with a novel tool for chimerism testing following allo-HCT. Li et al [22] evaluated chimerism and microchimerism (when donor chimerism is in the micro range <1%) using the SNP-based NGS assay in forty-eight HLA-mismatched stem cell microtransplantations. They developed an improved SNP-NGS method with increased sensitivity (0.01-0.05%) and minimal DNA input (8-200 ng).…”

“…They developed an improved SNP-NGS method with increased sensitivity (0.01-0.05%) and minimal DNA input (8-200 ng). They concluded that SNP-NGS can accurately detect the microchimerism status of donor cells early in patients with acute myeloid leukemia [22]. Vynck et al [20] performed an assessment of the Devyser high-throughput-sequencing-based assay for chimerism monitoring after transplantation in allo-HCT and compared it with the Pow-erPlex 16 HS SRT-PCR assay (Table 1).…”

Haploidentical hematopoietic cell transplantation with or without an unrelated cord blood unit for adult acute myeloid leukemia: a multicenter, randomized, open-label, phase 3 trial

“…Chimerism was monitored by multiparameter fluorescent short tandem repeats analyses and single nucleotide polymorphisms-based NGS (SNP-NGS). 49 Remission status was evaluated based on FCM-based MRD (FCM-MRD), fusion gene and gene mutation in BM (detailed in Supplementary Materials and Methods ). CMV viremia and EBV viremia were detected using qPCR.…”

Some key considerations regarding the design and evaluation of high-throughput sequencing-based biallelic chimerism assays

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With interest I read paper by Li et (2022) [1] on development of a chimerism 12 monitoring assay using next-generation sequencing (NGS) of single nucleotide polymorphisms 13 (SNPs). Such assays have garnered an increasing amount of attention over the last years.

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