Practical informativeness of short tandem repeat loci for chimerism analysis in hematopoietic stem cell transplantation

Han, Eunhee; Kim, Myungshin; Kim, Yonggoo; Han, Kyungja; Lim, Jihyang; Kang, Dain; Lee, Gun Dong; Kim, Jung Rok; Lee, Jae‐Wook; Chung, Nack‐Gyun; Cho, Bin; Eom, Ki‐Seong; Kim, Yoo-Jin; Kim, Hee-Je; Lee, Seok; Cho, Seok-Goo; Min, Chang‐Ki; Kim, Dong-Wook; Lee, JongWook; Min, Woo-Sung

doi:10.1016/j.cca.2017.02.004

Cited by 8 publications

(9 citation statements)

References 15 publications

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“…We did not detect any donor carrying a clonal hematopoiesis-related mutation [20]. The number of informative SNPs was variable (median 25.5, range 9-41) and higher than that of STR (median 10.5, range [5][6][7][8][9][10][11][12][13][14]. Donor chimerism from NGS analysis highly correlated with results from STR analysis, with r 2 = 0.994 (p < 0.0001) by least-squares analysis (Figure 2a), and all data points were within 3 SDs of the mean % difference on Blant-Altman plot (Figure 2b).…”

Section: Analytical Performance Of Ngs Donor Chimerismmentioning

confidence: 82%

“…STR analysis was performed using AmpFlSTR Identifier PCR Amplification (Applied Biosystems, Warrington, UK) as previously reported [11]. Briefly, 16 STR markers were amplified; D8S1179 at chromosome 8, D21S11 at 21q11.2-q21, D7S820 at 7q11.2-22, CSF1PO at 5q33.3-34, D3S1358 at 3p, TH01 at 11p15.5, D13S317 at 13q22-31, D16S539 at 16q24-qter, D2S1338 at 2q35-37.1, D19S433 at 19q12-13.1, vWA at 12p12-pter, TPOX at 2p23-2per, D18S51 at 18q21.3, D5S818 at 5q21-31, and FGA at 4q28, the amelogenin locus at X (p22.1-22.3) and Y (p11.2) chromosomes.…”

Section: Str Analysismentioning

confidence: 99%

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Simultaneous Monitoring of Mutation and Chimerism Using Next-Generation Sequencing in Myelodysplastic Syndrome

Lee

Kim

Han

et al. 2019

JCM

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Monitoring minimal residual disease (MRD) provides important information during treatment of hematologic malignancies. Chimerism analysis also provides key information after allogeneic hematopoietic stem cell transplantation (allo-HSCT). Recent advances in next-generation sequencing (NGS) have enabled identification of various mutations and quantification of mutant allele burden. In this study, we developed a new analytic algorithm to monitor chimerism applicable to NGS multi-gene panel in use to identify mutations of myelodysplastic syndrome (MDS). We enrolled patients who were diagnosed with MDS and received allo-HSCT and their corresponding donors. Monitoring MRD by NGS assay was performed using 53 DNA samples by calculating mutant allele burden after treatment. For monitoring chimerism by NGS, we selected 121 single nucleotide polymorphisms (SNPs) after careful stepwise evaluation and calculated average donor allele burden. Data obtained from NGS were compared with bone marrow findings, chromosome analysis and short tandem repeat (STR)-based chimerism. SNP-based NGS chimerism analysis was accurate and even superior to conventional STR method by overcoming the various technical limitations of STR. In addition, simultaneous monitoring of mutation and chimerism using NGS could implement comprehensive pre- and post-HSCT monitoring of various clinical conditions such as complete donor chimerism, persistent mixed chimerism, early relapse, and even donor cell-derived diseases.

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Section: Analytical Performance Of Ngs Donor Chimerismmentioning

confidence: 82%

Section: Str Analysismentioning

confidence: 99%

Simultaneous Monitoring of Mutation and Chimerism Using Next-Generation Sequencing in Myelodysplastic Syndrome

Lee

Kim

Han

et al. 2019

JCM

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“…However, some authors have suggested that undertaking a careful process of STR-marker selection is crucial in all the cases of chimerism monitoring in order to guarantee an accurate and reliable result. This selection should be performed to choose the most suitable STR for the chimerism monitoring considering all the variables (both instrumental and biological) that can affect the analysis [ 18 , 35 , 52 ]. For instance, many scholars agree that STR markers should be excluded from the chimerism calculation when the recipient’s stutter peak coincides with one of the donor’s peaks or vice versa in order to avoid interference in chimerism quantification.…”

Section: Resultsmentioning

confidence: 99%

“…For instance, many scholars agree that STR markers should be excluded from the chimerism calculation when the recipient’s stutter peak coincides with one of the donor’s peaks or vice versa in order to avoid interference in chimerism quantification. This is also true for markers which are shared between the donor and the recipient, given the impossibility of identifying the origin of the STR alleles [ 18 , 35 , 36 , 37 , 41 ]. As claimed by Kristt et al [ 28 ] and Navarro-Bailón et al [ 34 ], this latter circumstance is more common in the case of transplantation occurring between related donor–recipient pairs than in the case of transplantation between unrelated pairs.…”

Section: Resultsmentioning

confidence: 99%

“…The main reason STRs are more suitable for chimerism analysis compared with other polymorphisms is their higher informativity rate [ 31 , 32 , 33 , 34 ]. Nevertheless, a careful selection of STR alleles is required to select the most suitable STR for chimerism monitoring considering all the variables which can affect the analysis [ 18 , 35 , 36 ].…”

Section: Introductionmentioning

confidence: 99%

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Chimerism Monitoring Techniques after Hematopoietic Stem Cell Transplantation: An Overview of the Last 15 Years of Innovations

et al. 2021

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Chimerism analysis is a well-established method for monitoring the state of hematopoietic stem cell transplantation (HSCT) over time by analyzing peripheral blood or bone marrow samples of the recipient in several malignant and non-malignant hematologic diseases. From a clinical point of view, a continuous monitoring is fundamental for an effective early therapeutic intervention. This paper provides a comparative overview of the main molecular biology techniques which can be used to study chimerism after bone marrow transplantation, focusing on their advantages and disadvantages. According to the examined literature, short tandem repeats (STR) analysis through simple PCR coupled with capillary electrophoresis (STR-PCR) is the most powerful method which guarantees a high power of differentiation between different individuals. However, other methods such as real-time quantitative PCR (qPCR), digital PCR (dPCR), and next-generation sequencing (NGS) technology were developed to overcome the technical limits of STR-PCR. In particular, these other techniques guarantee a higher sensitivity, which allows for the detection of chimerism at an earlier stage, hence expanding the window for therapeutic intervention. After a comparative evaluation of the various techniques, it seems clear that STR-PCR still remains the gold standard option for chimerism study, even if it is likely that both dPCR and NGS could supplement or even replace the common methods of STR analysis.

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Multiplex STR panel for assessment of chimerism following hematopoietic stem cell transplantation (HSCT)

et al. 2019

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Practical informativeness of short tandem repeat loci for chimerism analysis in hematopoietic stem cell transplantation

Cited by 8 publications

References 15 publications

Simultaneous Monitoring of Mutation and Chimerism Using Next-Generation Sequencing in Myelodysplastic Syndrome

Simultaneous Monitoring of Mutation and Chimerism Using Next-Generation Sequencing in Myelodysplastic Syndrome

Chimerism Monitoring Techniques after Hematopoietic Stem Cell Transplantation: An Overview of the Last 15 Years of Innovations

Multiplex STR panel for assessment of chimerism following hematopoietic stem cell transplantation (HSCT)

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