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Kakodkar P, Zhao Y, Pan H, Wu F, Pearce T, Webster D, Elemary M, Sabry W, Kwan L, Pelzer L, Bosch M, Sherwood KR, Lan J, Tran J, Liwski R, Keown P, Mostafa A. Validation of next-generation sequencing-based chimerism testing for accurate detection and monitoring of engraftment in hematopoietic stem cell transplantation. Front Genet 2023; 14:1282947. [PMID: 37937195 PMCID: PMC10626454 DOI: 10.3389/fgene.2023.1282947] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 10/09/2023] [Indexed: 11/09/2023] Open
Abstract
Allogenic hematopoietic stem cell transplantation (allo-HSCT) is a life-saving treatment for various hematological disorders. The success of allo-HSCT depends on the engraftment of donor cells and the elimination of recipient cells monitored through chimerism testing. We aimed to validate a next-generation sequencing (NGS)-based chimerism assay for engraftment monitoring and to emphasize the importance of including the most prevalent cell subsets in proficiency testing (PT) programs. We evaluated the analytical performance of NGS-based chimerism testing (AlloSeq-HCT and CareDx) with a panel of targeted 202 informative single-nucleotide polymorphisms (SNPs) (i.e., linearity and precision, analytical sensitivity and specificity, system accuracy, and reproducibility). We further compared the performance of our NGS panel with conventional short tandem repeat (STR) analysis in unfractionated whole blood and cell-subset-enriched CD3 and CD66. Our NGS-based chimerism monitoring assay has an impressive detection limit (0.3% host DNA) for minor alleles and analytical specificity (99.9%). Pearson's correlation between NGS- and STR-based chimerism monitoring showed a linear relationship with a slope of 0.8 and r = 0.973. The concordance of allo-HSCT patients using unfractionated whole blood, CD3, and CD66 was 0.95, 0.96, and 0.54, respectively. Utilization of CD3+ cell subsets for mixed chimerism detection yielded an average of 7.3 ± 7-fold higher donor percentage detection compared to their corresponding unfractionated whole blood samples. The accuracy of the NGS assay achieved a concordance of 98.6% on blinded external quality control STR samples. The reproducibility series showed near 100% concordance with respect to inter-assay, inter-tech, inter-instrument, cell flow kits, and AlloSeq-HCT software versions. Our study provided robust validation of NGS-based chimerism testing for accurate detection and monitoring of engraftment in allo-HSCT patients. By incorporating the cell subsets (CD3 and CD66), the sensitivity and accuracy of engraftment monitoring are significantly improved, making them an essential component of any PT program. Furthermore, the implementation of NGS-based chimerism testing shows potential to streamline high-volume transplant services and improve clinical outcomes by enabling early relapse detection and guiding timely interventions.
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Affiliation(s)
- Pramath Kakodkar
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Yayuan Zhao
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Henry Pan
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Fang Wu
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Twyla Pearce
- Histocompatibility and Immunogenetics Laboratory, St. Paul’s Hospital, Saskatoon, SK, Canada
| | - Destinie Webster
- Histocompatibility and Immunogenetics Laboratory, St. Paul’s Hospital, Saskatoon, SK, Canada
| | - Mohamed Elemary
- Department of Hematological Oncology, Saskatchewan Cancer Agency, Saskatoon, SK, Canada
| | - Waleed Sabry
- Department of Hematological Oncology, Saskatchewan Cancer Agency, Saskatoon, SK, Canada
| | - Luvinia Kwan
- HLA Laboratory, Cancer Care Manitoba, Winnipeg, MB, Canada
| | - Lindsay Pelzer
- Department of Hematological Oncology, Saskatchewan Cancer Agency, Saskatoon, SK, Canada
| | - Mark Bosch
- Department of Hematological Oncology, Saskatchewan Cancer Agency, Saskatoon, SK, Canada
| | - Karen R. Sherwood
- University of British Columbia, Vancouver Coastal Health, Vancouver, BC, Canada
| | - James Lan
- Department of Transplant Nephrology, Vancouver Coastal Health, Vancouver, BC, Canada
| | - Jenny Tran
- University of British Columbia, Vancouver Coastal Health, Vancouver, BC, Canada
| | - Robert Liwski
- Department of Pathology, Dalhousie University, Halifax, NS, Canada
| | - Paul Keown
- University of British Columbia, Vancouver Coastal Health, Vancouver, BC, Canada
| | - Ahmed Mostafa
- Department of Pathology and Laboratory Medicine, University of Saskatchewan, Saskatoon, SK, Canada
- Histocompatibility and Immunogenetics Laboratory, St. Paul’s Hospital, Saskatoon, SK, Canada
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Bendjelloul M, Usureau C, Etancelin P, Saidak Z, Lebon D, Garçon L, Marolleau J, Desoutter J, Guillaume N. Utility of assessing
CD3
+
cell chimerism within the first months after allogeneic hematopoietic stem‐cell transplantation for acute myeloid leukemia. HLA 2022; 100:18-23. [PMID: 35064642 PMCID: PMC9303291 DOI: 10.1111/tan.14557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/22/2021] [Accepted: 01/19/2022] [Indexed: 11/30/2022]
Affiliation(s)
- Mehdi Bendjelloul
- Department of Hematology and Histocompatibility Amiens University Medical Center Amiens France
- EA HEMATIM 4666, Jules Verne University of Picardie Amiens France
| | - Cédric Usureau
- Department of Hematology and Histocompatibility Amiens University Medical Center Amiens France
- EA HEMATIM 4666, Jules Verne University of Picardie Amiens France
| | | | - Zuzana Saidak
- Laboratory of Molecular Oncobiology, Center of Human Biology, Amiens‐Picardie University Medical Center Amiens France
| | - Delphine Lebon
- EA HEMATIM 4666, Jules Verne University of Picardie Amiens France
- Department of Clinical Hematology and Cellular Therapy Amiens University Medical Center Amiens France
| | - Loïc Garçon
- Department of Hematology and Histocompatibility Amiens University Medical Center Amiens France
- EA HEMATIM 4666, Jules Verne University of Picardie Amiens France
| | - Jean‐Pierre Marolleau
- EA HEMATIM 4666, Jules Verne University of Picardie Amiens France
- Department of Clinical Hematology and Cellular Therapy Amiens University Medical Center Amiens France
| | - Judith Desoutter
- Department of Hematology and Histocompatibility Amiens University Medical Center Amiens France
| | - Nicolas Guillaume
- Department of Hematology and Histocompatibility Amiens University Medical Center Amiens France
- EA HEMATIM 4666, Jules Verne University of Picardie Amiens France
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Blouin AG, Ye F, Williams J, Askar M. A practical guide to chimerism analysis: Review of the literature and testing practices worldwide. Hum Immunol 2021; 82:838-849. [PMID: 34404545 DOI: 10.1016/j.humimm.2021.07.013] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 06/30/2021] [Accepted: 07/26/2021] [Indexed: 12/17/2022]
Abstract
BACKGROUND AND PURPOSE Currently there are no widely accepted guidelines for chimerism analysis testing in hematopoietic cell transplantation (HCT) patients. The objective of this review is to provide a practical guide to address key aspects of performing and utilizing chimerism testing results. In developing this guide, we conducted a survey of testing practices among laboratories that are accredited for performing engraftment monitoring/chimerism analysis by either the American Society for Histocompatibility & Immunogenetics (ASHI) and/or the European Federation of Immunogenetics (EFI). We interpreted the survey results in the light of pertinent literature as well as the experience in the laboratories of the authors. RECENT DEVELOPMENTS In recent years there has been significant advances in high throughput molecular methods such as next generation sequencing (NGS) as well as growing access to these technologies in histocompatibility and immunogenetics laboratories. These methods have the potential to improve the performance of chimerism testing in terms of sensitivity, availability of informative genetic markers that distinguish donors from recipients as well as cost. SUMMARY The results of the survey revealed a great deal of heterogeneity in chimerism testing practices among participating laboratories. The most consistent response indicated monitoring of engraftment within the first 30 days. These responses are reflective of published literature. Additional clinical indications included early detection of impending relapse as well as identification of cases of HLA-loss relapse.
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Affiliation(s)
- Amanda G Blouin
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Fei Ye
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Jenifer Williams
- Department of Pathology & Laboratory Medicine, Baylor University Medical Center, Dallas, TX, United States
| | - Medhat Askar
- Department of Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, United States; Department of Pathology & Laboratory Medicine, Baylor University Medical Center, Dallas, TX, United States; Department of Pathology and Laboratory Medicine, Texas A&M Health Science Center College of Medicine, United States.
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Desoutter J, Usureau C, Jacob V, Lebon D, Caulier A, Da Costa C, Charbonnier A, Joris M, Marolleau JP, Guillaume N. A one-step assay for sorted CD3 + cell purity and chimerism after hematopoietic stem cell transplantation. HLA 2020; 97:183-187. [PMID: 33314632 DOI: 10.1111/tan.14168] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Revised: 10/06/2020] [Accepted: 12/11/2020] [Indexed: 11/30/2022]
Abstract
A hematopoietic chimerism assay is the laboratory test for monitoring engraftment and quantifying the proportions of donor and recipient cells after hematopoietic stem cell transplantation recipients. Flow cytometry is the reference method for determining the purity of CD3+ cells on the chimerism of selected CD3+ cells. In the present study, we developed a single-step procedure that combines the CD3+ purity assay (using the PCR-based Non-T Genomic Detection Kit from Accumol, Calgary, Canada) and the qPCR chimerism monitoring assay (the QTRACE qPCR assay from Jeta Molecular, Utrecht, the Netherlands). First, for the CD3+ purity assay, we used a PCR-friendly protocol by changing the composition of the ready-to-use reaction tubes (buffer and taq polymerase) and obtained a satisfactory calibration plot (R2 = 0.8924) with a DNA reference scale of 2 ng/μl. Next, 29 samples (before and after CD3 positive selection) were analyzed, the mean cell purity was, respectively, 19.6% ± 6.45 and 98.9% ± 1.07 in the flow cytometry assay; 26.8% ± 7.63 and 98.5% ± 1.79 in the PCR-based non-T genomic detection assay. Our results showed that the CD3+ purity assay using a qPCR kit is a robust alternative to the flow cytometry assay and is associated with time savings when combined with a qPCR chimerism assay.
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Affiliation(s)
- Judith Desoutter
- Department of Hematology and Histocompatibility, Amiens University Medical Center, Amiens, France.,EA HEMATIM 4666, Jules Verne University of Picardie, Amiens, France
| | - Cédric Usureau
- Department of Hematology and Histocompatibility, Amiens University Medical Center, Amiens, France.,EA HEMATIM 4666, Jules Verne University of Picardie, Amiens, France
| | - Valentine Jacob
- Department of Hematology and Histocompatibility, Amiens University Medical Center, Amiens, France.,EA HEMATIM 4666, Jules Verne University of Picardie, Amiens, France
| | - Delphine Lebon
- EA HEMATIM 4666, Jules Verne University of Picardie, Amiens, France.,Department of Clinical Hematology and Cellular Therapy, Amiens University Medical Center, Amiens, France
| | - Alexis Caulier
- EA HEMATIM 4666, Jules Verne University of Picardie, Amiens, France.,Department of Clinical Hematology and Cellular Therapy, Amiens University Medical Center, Amiens, France
| | - Cécilia Da Costa
- EA HEMATIM 4666, Jules Verne University of Picardie, Amiens, France
| | - Amandine Charbonnier
- Department of Clinical Hematology and Cellular Therapy, Amiens University Medical Center, Amiens, France
| | - Magalie Joris
- Department of Clinical Hematology and Cellular Therapy, Amiens University Medical Center, Amiens, France
| | - Jean-Pierre Marolleau
- EA HEMATIM 4666, Jules Verne University of Picardie, Amiens, France.,Department of Clinical Hematology and Cellular Therapy, Amiens University Medical Center, Amiens, France
| | - Nicolas Guillaume
- Department of Hematology and Histocompatibility, Amiens University Medical Center, Amiens, France.,EA HEMATIM 4666, Jules Verne University of Picardie, Amiens, France
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Dubois V, Alizadeh M, Bourhis JH, Etancelin P, Farchi O, Ferrand C, Goursaud L, Mollet I, Renac V, Varlet P, Yakoub-Agha I, Bay JO. Étude du chimérisme après allogreffe de cellules hématopoïétiques : recommandations de la Société francophone de greffe de moelle et de thérapie cellulaire (SFGM-TC). Bull Cancer 2017; 104:S59-S64. [DOI: 10.1016/j.bulcan.2017.08.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/31/2017] [Accepted: 08/10/2017] [Indexed: 11/30/2022]
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6
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Clemente I, Goncalo A, Faria C, Dias M, Barbosa I, Mendes C. Relevance of Chimerism Analysis After Allogeneic Stem Cell Transplantation. Transplant Proc 2017; 49:890-892. [DOI: 10.1016/j.transproceed.2017.01.065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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Clark JR, Scott SD, Jack AL, Lee H, Mason J, Carter GI, Pearce L, Jackson T, Clouston H, Sproul A, Keen L, Molloy K, Folarin N, Whitby L, Snowden JA, Reilly JT, Barnett D. 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 2014; 168:26-37. [PMID: 25145701 DOI: 10.1111/bjh.13073] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Analysis of short tandem repeats (STR) is the predominant method for post-transplant monitoring of donor engraftment. It can enable early detection of disease relapse, level of engraftment and provide useful information on the graft-versus-host disease (GVHD)/graft-versus-tumour (GVT) effect, facilitating therapeutic intervention. Harmonization and standardization of techniques and result interpretation is essential to reduce the impact of laboratory variability on both clinical management and the results of multi-centre clinical trials. However, the United Kingdom National External Quality Assessment Service for Leucocyte Immunophenotyping (UK NEQAS LI) has highlighted significant issues inherent in STR testing that impact upon inter- and intra- laboratory variation. We present here consensus best practice guidelines and recommendations for STR chimerism testing, data interpretation and reporting that have been drawn up and agreed by a consortium of 11 UK and Eire clinical laboratories. This document uses data obtained from the UK NEQAS LI Post-Stem Cell Transplant (SCT) Chimerism Monitoring Programme.
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Affiliation(s)
- Jordan R Clark
- UK NEQAS for Leucocyte Immunophenotyping, Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
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