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Pedini P, Cherouat N, Basire A, Simon S, Budon L, Pourtein M, Grondin S, Moskovtchenko P, Chiaroni J, Michel G, Frassati C, Picard C. Evaluation of Next-Generation Sequencing and Crystal Digital PCR for Chimerism Monitoring of Post-Allogeneic Hematopoietic Stem Cell Transplantation. Transplant Cell Ther 2020; 27:89.e1-89.e10. [PMID: 32980546 DOI: 10.1016/j.bbmt.2020.09.023] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2020] [Revised: 09/15/2020] [Accepted: 09/16/2020] [Indexed: 10/23/2022]
Abstract
Hematopoietic stem cell transplantation (HSCT) is a curative treatment for most hematologic diseases. To evaluate the level of donor engraftment, chimerism must be carefully monitored after HSCT. Short tandem repeats, quantitative PCR (qPCR), and, more recently, digital PCR (dPCR) are widely used to determine the proportions of donor and recipient cells after HSCT. The screening and quantification of chimerism have been evaluated by 2 new methods: a ready-to-use next-generation sequencing (NGS)-based method using the Devyser ChimerismNGS kit and an original combination of the Stilla crystal digital PCR (cdPCR) platform with 3-color multiplexing capacity using GenDX KMRtrack reagents. The genotyping of 4 HSCT pairs by cdPCR using 11 triplex mixes of the GenDX KMRtype kit was consistent at 98.8% with qPCR. Informative samples (n = 20) from 6 donor-recipient pairs and 1 external proficiency test demonstrated the reliability of the results (0.1% to 50%) for the 2 methods. The methods are also highly sensitive (0.1%) and accurate. The chimerism values of the 2 methods are correlated and concordant with those of the reference methods. In addition, the ADVYSER software (Devyser) is user-friendly and well adapted to chimerism monitoring. In conclusion, these 2 innovative methods are easy to perform and user-friendly in all molecular, hematology, and immunogenetic laboratories and allow the genotyping and monitoring of chimerism with high performance and sensitivity.
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Affiliation(s)
- Pascal Pedini
- Immunogenetic Laboratory, Etablissement Français du Sang Provence-Alpes-Côte d'Azur-Corse, Marseille, France; Aix-Marseille University, CNRS, Etablissement Français du Sang, Anthropologie bio-culturelle-Droit-Ethique-Santé, Marseille, France.
| | - Nicem Cherouat
- Immunogenetic Laboratory, Etablissement Français du Sang Provence-Alpes-Côte d'Azur-Corse, Marseille, France
| | - Agnes Basire
- Immunogenetic Laboratory, Etablissement Français du Sang Provence-Alpes-Côte d'Azur-Corse, Marseille, France
| | - Sophie Simon
- Immunogenetic Laboratory, Etablissement Français du Sang Provence-Alpes-Côte d'Azur-Corse, Marseille, France
| | - Laurène Budon
- Immunogenetic Laboratory, Etablissement Français du Sang Provence-Alpes-Côte d'Azur-Corse, Marseille, France
| | | | - Sandra Grondin
- Immunogenetic Laboratory, Etablissement Français du Sang Auvergne-Rhône-Alpes, Lyon, France
| | - Philippe Moskovtchenko
- Immunogenetic Laboratory, Etablissement Français du Sang Auvergne-Rhône-Alpes, Lyon, France
| | - Jacques Chiaroni
- Aix-Marseille University, CNRS, Etablissement Français du Sang, Anthropologie bio-culturelle-Droit-Ethique-Santé, Marseille, France
| | - Gérard Michel
- Department of Pediatric Hematology-Oncology, Hôpital Enfants la Timone, Marseille, France
| | - Coralie Frassati
- Immunogenetic Laboratory, Etablissement Français du Sang Provence-Alpes-Côte d'Azur-Corse, Marseille, France; Aix-Marseille University, CNRS, Etablissement Français du Sang, Anthropologie bio-culturelle-Droit-Ethique-Santé, Marseille, France
| | - Christophe Picard
- Immunogenetic Laboratory, Etablissement Français du Sang Provence-Alpes-Côte d'Azur-Corse, Marseille, France; Aix-Marseille University, CNRS, Etablissement Français du Sang, Anthropologie bio-culturelle-Droit-Ethique-Santé, Marseille, France
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Han E, Kim M, Kim Y, Han K, Lim J, Kang D, Lee GD, Kim JR, Lee JW, Chung NG, Cho B, Eom KS, Kim YJ, Kim HJ, Lee S, Cho SG, Min CK, Kim DW, Lee J, Min WS. Practical informativeness of short tandem repeat loci for chimerism analysis in hematopoietic stem cell transplantation. Clin Chim Acta 2017; 468:51-59. [PMID: 28192074 DOI: 10.1016/j.cca.2017.02.004] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2016] [Revised: 01/31/2017] [Accepted: 02/03/2017] [Indexed: 11/19/2022]
Abstract
OBJECTIVE Short tandem repeat (STR) loci are most frequently used for chimerism analysis after hematopoietic stem cell transplantation (HSCT). The aim of this study was to evaluate the practical informativeness of STR chimerism by integrating theoretical and analytical points. METHODS Theoretical and practical informativess of 16 STR loci were evaluated from 1249 pairs of recipients and donors who were prepared for HSCT. RESULTS Theoretical informativeness was influenced by genetic diversity including allele frequency and heterozygosity, and was higher in the unrelated HSCT group (90.5±5.3%) compared to the related HSCT group (66.2±4.4%). Practical informativeness was lower than theoretical (6.1±1.7%) because several STR loci were excluded due to stutter peaks and less reliable results, especially in type II-2 donor-recipient match pattern with no recipient-specific allele. We simulated an efficient STR combination for reliable chimerism analysis. Eight informative STR loci were required to analyze chimerism with at least one practically informative locus in the related HSCT group (D18S51, FGA, D2S1338, D13S317, D8S1179, D21S11, D16S539 and D7S820) while only three loci were needed in the unrelated group (D2S1338, FGA and D18S51). A minimum set of 2, 4 or 7 STR loci were required to provide at least 1, 3 or 5 practically informative loci in 95% of the unrelated HSCT group while 3, 8 or 12 loci were required in the related HSCT group. CONCLUSION We deducted the practical informativeness of STR chimerism, identified the major influencing factors on the practical informativeness of each STR locus, and successfully simulated the efficient STR combination for reliable chimerism analysis.
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Affiliation(s)
- Eunhee Han
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Myungshin Kim
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Yonggoo Kim
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea; Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea.
| | - Kyungja Han
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jihyang Lim
- Department of Laboratory Medicine, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dain Kang
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Gun Dong Lee
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jung Rok Kim
- Catholic Genetic Laboratory Center, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Jae-Wook Lee
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Nack-Gyun Chung
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Bin Cho
- Department of Pediatrics, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Ki-Seong Eom
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Yoo-Jin Kim
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Hee-Je Kim
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seok Lee
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Seok-Goo Cho
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Chang-Ki Min
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Dong-Wook Kim
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - JongWook Lee
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
| | - Woo-Sung Min
- Division of Hematology, Department of Internal Medicine, Catholic Blood and Marrow Transplantation Center, Leukemia Research Institute, Seoul St. Mary's Hospital, College of Medicine, The Catholic University of Korea, Seoul, Republic of Korea
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Aloisio M, Licastro D, Caenazzo L, Torboli V, D'Eustacchio A, Severini GM, Athanasakis E. A technical application of quantitative next generation sequencing for chimerism evaluation. Mol Med Rep 2016; 14:2967-74. [PMID: 27499173 PMCID: PMC5042788 DOI: 10.3892/mmr.2016.5593] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2016] [Accepted: 07/12/2016] [Indexed: 11/24/2022] Open
Abstract
At present, the most common genetic diagnostic method for chimerism evaluation following hematopoietic stem cell transplantation is microsatellite analysis by capillary electrophoresis. The main objective was to establish, through repeated analysis over time, if a complete chimerism was present, or if the mixed chimerism was stable, increasing or decreasing over time. Considering the recent introduction of next generation sequencing (NGS) in clinical diagnostics, a detailed study evaluating an NGS protocol was conducted, coupled with a custom bioinformatics pipeline, for chimerism quantification. Based on the technology of Ion AmpliSeq, a 44-amplicon custom chimerism panel was designed, and a custom bioinformatics pipeline dedicated to the genotyping and quantification of NGS data was coded. The custom chimerism panel allowed identification of an average of 16 informative recipient alleles. The limit of detection of the protocol was fixed at 1% due to the NGS background (<1%). The protocol followed the standard Ion AmpliSeq library preparation and Ion Torrent Personal Genome Machine guidelines. Overall, the present study added to the scientific literature, identifying novel technical details for a possible future application of NGS for chimerism quantification.
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Affiliation(s)
| | - Danilo Licastro
- Cluster in Biomedicine, CBM S.c.r.l., Bioinformatic Services, Area Science Park, I‑34149 Basovizza, Italy
| | - Luciana Caenazzo
- Department of Molecular Medicine, University of Padova, I‑35121 Padova, Italy
| | - Valentina Torboli
- Department of Life Sciences, University of Trieste, I‑34127 Trieste, Italy
| | - Angela D'Eustacchio
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I‑34137 Trieste, Italy
| | - Giovanni Maria Severini
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I‑34137 Trieste, Italy
| | - Emmanouil Athanasakis
- Department of Advanced Diagnostic and Clinical Trials, Institute for Maternal and Child Health, IRCCS 'Burlo Garofolo', I‑34137 Trieste, Italy
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Chen DP, Tseng CP, Wang WT, Wang MC, Tsai SH, Sun CF. Real-time biallelic polymorphism-polymerase chain reaction for chimerism monitoring of hematopoietic stem cell transplantation relapsed patients. Clin Chim Acta 2010; 412:625-30. [PMID: 21185273 DOI: 10.1016/j.cca.2010.12.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2010] [Revised: 10/15/2010] [Accepted: 12/15/2010] [Indexed: 11/27/2022]
Abstract
BACKGROUND An accurate analysis of chimerism kinetics permits early detection of hematopoietic stem cell transplantation (HSCT) in patients with high risks of graft-versus-host disease or those liable to relapse. Although short tandem repeats-PCR (STR-PCR) is the golden standard for quantitative chimerism analysis in most of the clinical laboratories, it has a relatively low sensitivity of 5% and the detection of low percentage in mixed chimerism is usually delayed. In this study, we developed a real-time PCR for chimerism analysis based on the informative biallelic polymorphisms (BP). METHODS The allele frequencies of 19 selective biallelic polymorphic markers were analyzed using the genomic DNA from 100 healthy Taiwanese volunteers. The informative biallelic polymorphic markers with high discrimination power in the Taiwanese population were identified. The TaqMan probe-based real-time BP-PCR for amplification of the informative loci was designed and the detection sensitivity was determined. Clinical application of real-time BP-PCR in chimerism monitoring was evaluated and was compared with the conventional STR-PCR by analyzing the DNA samples obtained at different time points post-HSCT from 4 relapsed and 10 non-relapsed patients. RESULTS Allele distribution analysis revealed that the loci of S01a, S03, S04a, S05b, S06, S07b, S08b, S09b, S10b and S11a had a relatively high discrimination power and were the informative BP for chimerism monitoring in the Taiwanese population. Real-time BP-PCRs for these 10 BP loci were set up with the detection sensitivity equivalent to 0.003-0.006%. Real-time BP-PCR of the 4 HSCT patients revealed the presence of recipient-specific DNA at early time point than STR-PCR for 3 of the patients, whereas real-time BP-PCR was as effective as STR-PCR in uncovering the sign of relapse for one of the patients. In addition, the baseline value for the patients with no sign of relapse was 0.127 ± 0.193% of recipient DNA. CONCLUSION We conclude that real-time BP-PCR is a sensitive and reliable method for chimerism monitoring and is superior to the STR-PCR in identifying patients who are at high risk for relapse after transplantation.
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Affiliation(s)
- Ding-Ping Chen
- Department of Laboratory Medicine, Chang-Gung Memorial Hospital, Taoyuan County, Taiwan
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Gineikiene E, Stoskus M, Griskevicius L. Recent advances in quantitative chimerism analysis. Expert Rev Mol Diagn 2010; 9:817-32. [PMID: 19895227 DOI: 10.1586/erm.09.66] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Quantitative chimerism analysis is a diagnostic tool used to monitor engraftment kinetics after allogeneic stem cell transplantation. It reflects the proportion of recipient and donor genotypes and is based on the identification of genetic markers characteristic to a given transplant pair. Currently, PCR amplification of short tandem repeats and single-nucleotide polymorphism-specific quantitative real-time PCR are the most widely used techniques for this purpose. In this review, we will address advances as well as technology-specific imperfections, of both techniques that have emerged over the recent years. We will discuss new principles that may simplify assay design, and improve its robustness and reliability. A better chimerism assay could then guide clinical interventions and may, eventually, improve the outcome of allogeneic stem cell transplantation.
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Affiliation(s)
- Egle Gineikiene
- Department of Molecular and Regenerative Medicine, Hematology, Oncology and Transfusion Medicine Center, Vilnius University Hospital Santariskiu Clinics, Santariskiu 2, LT-08661, Vilnius, Lithuania.
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