Abstract
After hematopoietic stem cell transplantation, chimerism assay is a useful approach to monitor the success of the transplant and to select the appropriate treatment strategy, such as donor leukocyte infusion or immunosuppressive drug dosage. Short tandem repeat PCR is the method that has been accepted as the gold standard for chimerism. However, it has not yet been sufficient to detect mixed chimerism in patients with minimal residual disease. Simultaneously, recent years have been marked by developing sensitive, high-throughput, and accurate molecular genetic assays. These novel methods have subsequently been adapted for the analysis of post-transplant chimerism. In this review, we discuss the technical features of both novel and conventional gold standard chimerism assays. We also discuss their advantages and disadvantages.
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The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.
References
Anderson D, Billingham R, Lampkin GH, Medawar P (1951) The use of skin grafting to distinguish between monozygotic and dizygotic twins in cattle. Heredity 5:379–397
Ford CE, Hamerton JL, Barnes DW, Loutit JF (1956) Cytological identification of radiation-chimaeras. Nature 177(4506):452–454
Thiede C, Florek M, Bornhäuser M, Ritter M, Mohr B, Brendel C et al (1999) Rapid quantification of mixed chimerism using multiplex amplification of short tandem repeat markers and fluorescence detection. Bone Marrow Transplant 23(10):1055–1060
Fundia AF, De Brasi C, Larripa I (2004) Feasibility of a cost-effective approach to evaluate short tandem repeat markers suitable for chimerism follow-up. Mol Diagn 8(2):87–91
Schichman S, Suess P, Vertino A, Gray PS (2002) Comparison of short tandem repeat and variable number tandem repeat genetic markers for quantitative determination of allogeneic bone marrow transplant engraftment. Bone Marrow Transplant 29:243–248
Martínez-López J, Crooke A, Grande S, Ayala R, Jimenez-Velasco A, Gamarra S et al (2010) Real-time PCR quantification of haematopoietic chimerism after transplantation: a comparison between TaqMan and hybridization probes technologies. Int J Lab Hematol 32:e17–e25
George D, Czech J, John B, Yu M, Jennings LJ (2013) Detection and quantification of chimerism by droplet digital PCR. Chimerism 4(3):102–108
Sharma D, Egidio C, Grskovic M, Fernandez Mina MA, Zhang BM (2020) Chimerism monitoring with highly sensitive and precise next-generation sequencing assay in patients post-allogeneic hematopoietic stem cell transplantation. Biol Blood Marrow Transplant 26(3):s310
Buño I, Nava P, Simón A, González-Rivera M, Jiménez JL, Balsalobre P et al (2005) A comparison of fluorescent in situ hybridization and multiplex short tandem repeat polymerase chain reaction for quantifying chimerism after stem cell transplantation. Haematologica 90(10):1373–1379
Almeida CA, Dreyfuss JL, Azevedo-Shimmoto MM, Figueiredo MS, de Oliveira JS (2013) Evaluation of 16 SNPs allele-specific to quantify post hSCT chimerism by SYBR green-based qRT-PCR. J Clin Pathol 66(3):238–242
Martínez-López J, Crooke A, Grande S, Ayala R, Jiménez-Velasco A, Gamarra S et al (2010) Real-time PCR quantification of haematopoietic chimerism after transplantation: a comparison between TaqMan and hybridization probes technologies. Int J Lab Hematol 32(1 Pt 1):e17-25
Faraci M, Bagnasco F, Leoni M, Giardino S, Terranova P, Subissi L et al (2018) Evaluation of chimerism dynamics after allogeneic hematopoietic stem cell transplantation in children with nonmalignant diseases. Biol Blood Marrow Transplant 24(5):1088–1093
Dumache R, Enache A, Barbarii L, Constantinescu C, Pascalau A, Jinca C et al (2018) Chimerism monitoring by short tandem repeat (STR) markers in allogeneic stem cell transplantation. Clin Lab 64(9):1535–1543
Abatay-Sel F, Savran-Oguz F, Kalayoglu-Besisik S, Mastanzade M, Duvarci-Ogret Y, Yonal-Hindilerden I et al (2019) Short tandem repeat-polymerase chain reaction (STR-PCR) with quantitative real time-polymerase chain reaction (qRT-PCR) method using for chimerism analysis. Clin Lab 65(9):1697–1703
Li SX, Zhu HL, Guo B, Da WM (2011) Application of short-tandem-repeat amplification and fluorescent-multiplex PCR for chimerism analysis. Zhongguo Shi Yan Xue Ye Xue Za Zhi 19(3):749–753
Siddiqui Z, Maldonado J, Grojean J, Ye F, Zhang D, Longtine J et al (2020) Rchimerism: an R package for automated chimerism data analysis. J Mol Diagn 22(1):21–29
Tyler J, Kumer L, Fisher C, Casey H, Shike H (2019) Personalized chimerism test that uses selection of short tandem repeat or quantitative PCR depending on patient’s chimerism status. J Mol Diagn 21(3):483–490
Kruse A, Abdel-Azim N, Kim HN, Ruan Y, Phan V, Ogana H et al (2020) Minimal residual disease detection in acute lymphoblastic leukemia. Int J Mol Sci 21(3):1054
Hagen-Mann K, Mann W (1995) RT-PCR and alternative methods to PCR for in vitro amplification of nucleic acids. Exp Clin Endocrinol Diabetes 103(3):150–155
Sathirapatya T, Worrapitirungsi W, Sukawutthiya P, Rasmeepaisarn K, Vongpaisarnsin K (2020) A SNP panel for early detection of artificial chimerism in HSCT patients using TaqMan technology. Int J Legal Med 134:1553–1561
Alizadeh M, Bernard M, Danic B, Dauriac C, Birebent B, Lapart C et al (2002) Quantitative assessment of hematopoietic chimerism after bone marrow transplantation by real-time quantitative polymerase chain reaction. Blood 99(12):4618–4625
Shabani E, Dowlatshahi S, Abdekhodaie MJ (2021) Laboratory detection methods for the human coronaviruses. Eur J Clin Microbiol Enfect Dis 40(2):225–246
Kireev DE, Farzan VM, Shipulin GA, Korshun VA, Zatsepin TS (2020) RT-qPCR detection of low-copy HIV RNA with Yin-Yang probes. Methods Mol Biol 2063:27–35
Kletzel M, Huang W, Olszewski M, Khan S (2013) Validation of chimerism in pediatric recipients of allogeneic hematopoietic stem cell transplantation (HSCT) a comparison between two methods: real-time PCR (qPCR) vs. variable number tandem repeats PCR (VNTR PCR). Chimerism 4(1):1–8
Oliver DH, Thompson RE, Griffin CA, Eshleman JR (2000) Use of single nucleotide polymorphisms (SNP) and real-time polymerase chain reaction for bone marrow engraftment analysis. J Mol Diagn 2(4):202–208
Jiménez-Velasco A, Barrios M, Román-Gómez J, Navarro G, Buño I, Castillejo JA et al (2005) Reliable quantification of hematopoietic chimerism after allogeneic transplantation for acute leukemia using amplification by real-time PCR of null alleles and insertion/deletion polymorphisms. Leukemia 19(3):336–343
Brookes AJ (1999) The essence of SNPs. Gene 234(2):177–186
Genomes Project Consortium, Auton A, Brooks LD, Durbin RM, Garrison EP, Kang HM et al (2015) A global reference for human genetic variation. Nature 526(7571):68–74
Bader P, Niethammer D, Willasch A, Kreyenberg H, Klingebiel T (2005) How and when should we monitor chimerism after allogeneic stem cell transplantation? Bone Marrow Transplant 35(2):107–119
Jacque N, Nguyen S, Golmard JL, Uzunov M, Garnier A, Leblond V et al (2015) Chimerism analysis in peripheral blood using indel quantitative real-time PCR is a useful tool to predict post-transplant relapse in acute leukemia. Bone Marrow Transplant 50:259–265
Willasch AM, Kreyenberg H, Shayegi N, Rettinger E, Meyer V, Zabel M et al (2014) Monitoring of hematopoietic chimerism after transplantation for pediatric myelodysplastic syndrome: real-time or conventional short tandem repeat PCR in peripheral blood or bone marrow? Biol Blood Marrow Transplant 20(12):1918–1925
Dubois V, Alizadeh M, Bourhis JH, Etancelin P, Farchi O, Ferrand C et al (2017) Étude du chimérisme après allogreffe de cellules hématopoïétiques : recommandations de la Société francophone de greffe de moelle et de thérapie cellulaire (SFGM-TC) [Chimerism analysis after hematopoietic cell transplantation: Guidelines from the Francophone Society of bone marrow transplantation and cellular therapy (SFGM-TC)]. Bull Cancer 104(12S):S59–S64
Haugaard AK, Madsen HO, Marquart HV, Rosthoj S, Masmas TN, Heilman C et al (2019) Highly sensitive chimerism detection in blood is associated with increased risk of relapse after allogeneic hematopoietic cell transplantation in childhood leukemia. Pediatr Transplant 23(7):e13549
Kinsella FAM, Inman CF, Gudger A, Chan YT, Murray DJ, Zuo J et al (2019) Very early lineage-specific chimerism after reduced intensity stem cell transplantation is highly predictive of clinical outcome for patients with myeloid disease. Leuk Res. 83:106173
Lion T (2007) Detection of impending graft rejection and relapse by lineage-specific chimerism analysis. Methods Mol Med 134:197–216
Bach C, Tomova E, Goldmann K, Weisbach V, Roesler W, Mackensen A et al (2015) Monitoring of hematopoietic chimerism by real-time quantitative PCR of micro insertions/deletions in samples with low DNA quantities. Transfus Med Hemother 42(1):38–45
Navarro-Bailón A, Carbonell D, Escudero A, Chicano M, Muniz P, Suarez-Gonzalez J et al (2020) Short Tandem Repeats (STRs) as biomarkers for the quantitative follow-up of chimerism after stem cell transplantation: methodological considerations and clinical application. Genes (Basel). 11(9):993
Andrikovics H, Őrfi Z, Meggyesi N, Bors A, Varga L, Kövy P et al (2019) Current trends in applications of circulatory microchimerism detection in transplantation. Int J Mol Sci 20(18):4450
Santurtún A, Riancho JA, Arozamena J, López-Duarte M, Zarrabeitia MT (2017) Indel analysis by droplet digital PCR: a sensitive method for DNA mixture detection and chimerism analysis. Int J Legal Med. 131(1):67–72
Majumdar N, Banerjee S, Pallas M, Wessel T, Hegerich P (2017) Poisson plus quantification for digital PCR systems. Sci Rep 7:9617
Waterhouse M, Pfeifer D, Follo M, Duyster J, Schafer H, Bertz H et al (2017) Early mixed hematopoietic chimerism detection by digital droplet PCR in patients undergoing gender-mismatched hematopoietic stem cell transplantation. Clin Chem Lab Med 55:1115–1121
Stahl T, Rothe C, Böhme MU, Kohl A, Kröger N, Fehse B (2016) Digital PCR panel for sensitive hematopoietic chimerism quantification after allogeneic stem cell transplantation. Int J Mol Sci 17(9):1515
Mika T, Baraniskin A, Ladigan S, Wulf G, Dierks S, Haase D et al (2019) Digital droplet PCR-based chimerism analysis for monitoring of hematopoietic engraftment after allogeneic stem cell transplantation. Int J Lab Hematol 41(5):615–621
Fortschegger M, Preuner S, Printz D, Poetsch AR, Geyeregger R, Pichler H et al (2020) Detection and monitoring of lineage-specific chimerism by digital droplet PCR-based testing of deletion/ınsertion polymorphisms. Biol Blood Marrow Transplant 26(6):1218–1224
Tozzo P, Delicati A, Zambello R, Caenazzo L (2021) Chimerism monitoring techniques after hematopoietic stem cell transplantation: an overview of the last 15 years of ınnovations. Diagnostics (Basel) 11(4):621
Cruz NM, Mencia-Trinchant N, Hassane DC, Guzman ML (2017) Minimal residual disease in acute myelogenous leukemia. Int J Lab Hematol 39(1):53–60
Waterhouse M, Pfeifer D, Duque-Afonso J, Follo M, Duyster J, Depner M et al (2019) Droplet digital PCR for the simultaneous analysis of minimal residual disease and hematopoietic chimerism after allogeneic cell transplantation. Clin Chem Lab Med 57(5):641–647
Okano T, Tsujita Y, Kanegane H, Mitsui-Sekinaka K, Tanita K, Miyamoto S et al (2018) Droplet Digital PCR based chimerism analysis for primary ımmunodeficiency diseases. J Clin Immunol 38:300–306
Kreuze JF, Perez A, Untiveros M, Quispe D, Fuentes S, Barker I et al (2009) Complete viral genome sequence and discovery of novel viruses by deep sequencing of small RNAs: a genetic method for diagnosis, discovery and sequencing of viruses. Virology 388(1):1–7
Adams IP, Glover RH, Monger WA, Mumford R, Jackeviciene E, Navalinskiene M et al (2009) Next-generation sequencing and metagenomic analysis: a universal diagnostic tool in plant virology. Mol Plant Pathol 10(4):537–545
Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12(6):443–451
Lee EJ, Luo J, Wilson JM, Shi H (2013) Analyzing the cancer methylome through targeted bisulfite sequencing. Cancer Lett 340(2):171–178
Metzker ML (2010) Sequencing technologies — the next generation. Nat Rev Genet 11:31–46
Parkinson NJ, Maslau S, Ferneyhough B, Zhang G, Gregory L, Buck D et al (2012) Preparation of high-quality next-generation sequencing libraries from picogram quantities of target DNA. Genome Res 22(1):125–133
Troll CJ, Kapp J, Rao V, Harkins KM, Cole C, Naughton C et al (2019) A ligation-based single-stranded library preparation method to analyze cell-free DNA and synthetic oligos. BMC Genomics 20:1023
Muzzey D, Evans EA, Lieber C (2015) Understanding the Basics of NGS: From mechanism to variant calling. Curr Genet Med Rep 3(4):158–165
Harkins KM, Schaefer NK, Troll CJ, Rao V, Kapp J, Naughton C et al (2020) A novel NGS library preparation method to characterize native termini of fragmented DNA. Nucleic Acids Res 48(8):e47
Buermans HP, den Dunnen JT (2014) Next generation sequencing technology: advances and applications. Biochim Biophys Acta 1842(10):1932–1941
Aloisio M, Licastro D, Caenazzo L, Torboli V, D’Eustacchio A, Severini GM et al (2016) A technical application of quantitative next generation sequencing for chimerism evaluation. Mol Med Rep 14:2967–2974
Lee JM, Kim YJ, Park SS, Han E, Kim M, Kim Y (2019) Simultaneous monitoring of mutation and chimerism using next-generation sequencing in myelodysplastic Syndrome. J Clin Med 8(12):2077
Minuti B, Lari A, Iozzi S, Palchetti S, Boschi B, Gerundino F et al (2019) Chimerism analysis using next generation sequencing. Forensic Sci Int 7(1):152–153
Behjati S, Tarpey PS (2013) What is next generation sequencing? Arch Dis Child Educ Pract Ed 98(6):236–238
Cao MD, Balasubramanian S, Bodén M (2015) Sequencing technologies and tools for short tandem repeat variation detection. Brief Bioinform 16(2):193–204
Tan B, Zhao Z, Zhang Z, Li S, Li SC (2017) Search for more effective microsatellite markers for forensics with next-generation sequencing. IEEE Trans Nanobioscience 16(5):375–381
Vives J, Casademont-Roca A, Martorell L, Nogues N (2020) Beyond chimerism analysis: methods for tracking a new generation of cell-based medicines. Bone Marrow Transplant 55:1229–1239
Clark JR, Scott SD, Jack AL, Lee H, Mason J, Carter GI et al (2015) Monitoring of chimerism following allogeneic haematopoietic stem cell transplantation (HSCT): technical recommendations for the use of short tandem repeat (STR) based techniques, on behalf of the United Kingdom National External Quality Assessment Service for Leucocyte Immunophenotyping Chimerism Working Group. Br J Haematol 168(1):26–37
Roy DC, Tantravahi R, Murray C, Dear K, Gorgone B, Anderson KC et al (1990) Natural history of mixed chimerism after bone marrow transplantation with CD6-depleted allogeneic marrow: a stable equilibrium. Blood 75(1):296–304
Blouin AG, Askar M (2022) Chimerism analysis for clinicians: a review of the literature and worldwide practices. Bone Marrow Transplant 57(3):347–359
Peci F, Dekker L, Pagliaro A, van Boxtel R, Nierkens S, Belderbos M (2022) The cellular composition and function of the bone marrow niche after allogeneic hematopoietic cell transplantation. Bone Marrow Transplant 57(9):1357–1364
Anasetti C, Logan BR, Lee SJ, Waller EK, Weisdorf DJ, Wingard JR et al (2012) Peripheral-blood stem cells versus bone marrow from unrelated donors. N Engl J Med 367(16):1487–96
Berger M, Barone M, Spadea M, Saglio F, Pessolano R, Fagioli F (2022) HSCT with mismatched unrelated donors: Bone marrow versus peripheral blood stem cells sources in pediatric patients. Pediatr Transplant. 26(4):e14233
Lindahl H, Vonlanthen S, Valentini D, Björklund AT, Sundin M, Mielke S et al (2022) Lineage-specific early complete donor chimerism and risk of relapse after allogeneic hematopoietic stem cell transplantation for acute myeloid leukemia. Bone Marrow Transplant 57(5):753–759
Bendjelloul M, Usureau C, Etancelin P, Saidak Z, Lebon D, Garçon L et al (2022) Utility of assessing CD3+ cell chimerism within the first months after allogeneic hematopoietic stem-cell transplantation for acute myeloid leukemia. HLA 100(1):18–23
Fuchs EJ, O’Donnell PV, Eapen M, Logan B, Antin JH, Dawson P et al (2021) Double unrelated umbilical cord blood vs HLA-haploidentical bone marrow transplantation: the BMT CTN 1101 trial. Blood 137(3):420–428
Kharfan-Dabaja MA, Reljic T, Yassine F, Nishihori T, Kumar A, Tawk MM et al (2022) Efficacy of a second allogeneic hematopoietic cell transplant in relapsed acute myeloid leukemia: results of a systematic review and meta-analysis. Transplant Cell Ther S2666–6367(22):01547
Haugaard AK, Kofoed J, Masmas TN, Madsen HO, Marquart HV, Heilmann C et al (2020) Is microchimerism a sign of imminent disease recurrence after allogeneic hematopoietic stem cell transplantation? A systematic review of the literature. Blood Rev 44:100673
Valero-Garcia J, González-Espinosa MDC, Barrios M, Carmona-Antonanzas G, Garcia-Planells J, Luiz-Lafora C et al (2019) Earlier relapse detection after allogeneic haematopoietic stem cell transplantation by chimerism assays: Digital PCR versus quantitative real-time PCR of insertion/deletion polymorphisms [published correction appears in PLoS One. 2019 Mar 13;14(3):e0213966]. PLoS One 14(2):e0212708
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Sel, F.A., Oğuz, F.S. Can novel methods replace the gold standard chimerism method after allogeneic hematopoietic stem cell transplantation?. Ann Hematol 103, 1035–1047 (2024). https://doi.org/10.1007/s00277-023-05448-3
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DOI: https://doi.org/10.1007/s00277-023-05448-3