Chimerism Assay Using Single Nucleotide Polymorphisms Adjacent and in Linkage-Disequilibrium Enables Sensitive Disease Relapse Monitoring after Hematopoietic Stem-Cell Transplantation. (14th February 2021)

• Record Type: Journal Article
• Authors: Kim, JinJu; Yun, Woobin; Park, Yu Jin; Seo, Jieun; Lee, Richard Dong Wook; Shin, Saeam; Lee, Hyun-Ji; Kim, In Suk; Choi, Jong Rak; Lee, Seung-Tae
• Is Part Of: Clinical chemistry. Volume 67:Number 5(2021)
• Page Start: 781
• Page End: 787
• Publication Date: 2021-02-14
• Subjects: chimerism -- transplantation monitoring -- next-generation sequencing -- SNP -- STR -- hematopoietic stem-cell transplantation; Clinical chemistry -- Periodicals; Pharmaceutical chemistry -- Periodicals; Biochemistry -- Periodicals; Biochimie -- Périodiques; Diagnostics biologiques -- Périodiques; Biochemistry; Clinical chemistry; Pharmaceutical chemistry; Biochemistry; Laboratory Techniques and Procedures; Klinische chemie; Periodicals; 616.075605
• DOI: 10.1093/clinchem/hvab010
• Languages: English
• ISSNs: 0009-9147

Abstract

Abstract: Background: Short tandem repeat (STR)-based chimerism analysis has been widely used for chimerism monitoring after hematopoietic stem-cell transplantation (HSCT), but technical artifacts can be problematic. We designed a chimerism assay using single nucleotide polymorphisms (SNPs) adjacent and in linkage-disequilibrium (CASAL), which doubly checked for SNP pairs, and thus could reduce background errors and increase analytical sensitivity. Methods: CASAL targeted 84 SNP pairs within 10 bp distance and in perfect linkage-disequilibrium. Using undiluted and serially diluted samples, baseline error rates, and linearity was calculated. Clinical performance of CASAL was evaluated in comparison with a conventional STR assay, using 191 posttransplant samples from 42 patients with HSCT. Results: CASAL had ∼10 times lower baseline error rates compared to that of ordinary next-generation sequencing. Limit of detection and quantification of CASAL were estimated to be 0.09 and 0.39%, respectively, with a linear range of 0.1–100%. CASAL correlated well with STR assay ( r 2 = 0.99) and the higher sensitivity enabled detection of low-level recipient chimerism and earlier prediction of relapse. Conclusions: CASAL is a simple, analytically sensitive and accurate assay that can be used in clinical samples after HSCT with a higher performance compared to that of traditional assays. It should also be useful in other forensic and archeological testing.