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Graver AS, Lee D, Power DA, Whitlam JB. Understanding Donor-derived Cell-free DNA in Kidney Transplantation: An Overview and Case-based Guide for Clinicians. Transplantation 2023; 107:1675-1686. [PMID: 36579675 DOI: 10.1097/tp.0000000000004482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Kidney transplant recipients undergo lifelong monitoring of allograft function and evaluation for transplant complications. The current monitoring paradigm utilizes blood, urine, and tissue markers that are insensitive, nonspecific, or invasive to obtain. As a result, problems are detected late, after significant damage has accrued, and often beyond the time at which complete resolution is possible. Indeed, most kidney transplants eventually fail, usually because of chronic rejection and other undetected injury. There is a clear need for a transplant-specific biomarker that enables a proactive approach to monitoring via early detection of reversible pathology. A biomarker that supports timely and personalized treatment would assist in achieving the ultimate goal of improving allograft survival and limiting therapeutic toxicity to the recipient. Donor-derived cell-free DNA (ddcfDNA) has been proposed as one such transplant biomarker. Although the test is presently utilized most in the United States, it is conceivable that its use will become more widespread. This review covers aspects of ddcfDNA that support informed use of the test by general nephrologists, including the basic biology of ddcfDNA, methodological nuances of testing, and general recommendations for use in the kidney transplant population. Clinical contexts are used to illustrate evidence-supported interpretation of ddcfDNA results and subsequent management. Finally, knowledge gaps and areas for further study are discussed.
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Affiliation(s)
- Alison S Graver
- Kidney Transplant Service, Department of Nephrology, Austin Health, Heidelberg, VIC, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - Darren Lee
- Kidney Transplant Service, Department of Nephrology, Austin Health, Heidelberg, VIC, Australia
- Department of Renal Medicine, Eastern Health Clinical School, Monash University, Box Hill, VIC, Australia
| | - David A Power
- Kidney Transplant Service, Department of Nephrology, Austin Health, Heidelberg, VIC, Australia
- Department of Medicine, University of Melbourne, Parkville, VIC, Australia
| | - John B Whitlam
- Kidney Transplant Service, Department of Nephrology, Austin Health, Heidelberg, VIC, Australia
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Parkville, VIC, Australia
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Crompton K, Godler DE, Ling L, Elwood N, Mechinaud-Heloury F, Soosay Raj T, Hsiao KC, Fleming J, Tiedemann K, Novak I, Fahey M, Wang X, Lee KJ, Colditz PB, Edwards P, Reddihough D. Umbilical Cord Blood Cell Clearance Post-Infusion in Immune-Competent Children with Cerebral Palsy. Cells Tissues Organs 2022; 212:546-553. [PMID: 36261026 DOI: 10.1159/000527612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 09/13/2022] [Indexed: 11/19/2022] Open
Abstract
Umbilical cord blood cells have therapeutic potential for neurological disorders, through a paracrine mechanism of action. A greater understanding of the safety and immunological effects of allogeneic donor cord blood cells in the context of a healthy recipient immune system, such as in cerebral palsy, is needed. This study aimed to determine how quickly donor cord blood cells were cleared from the circulation in children with cerebral palsy who received a single intravenous infusion of 12/12 human leucocyte antigen (HLA)-matched sibling cord blood cells. Twelve participants with cerebral palsy aged 2-12 years received cord blood cell infusions as part of a phase I trial of umbilical blood infusion for cerebral palsy. Digital droplet PCR analysis of DNA copy number variants specific to donor and recipient was used to assess donor DNA clearance at five timepoints post-infusion, a surrogate measure of cell clearance. Donor cells were cleared by 3 months post-infusion in 11/12 participants. When detected, donor DNA was at a fraction of 0.01-0.31% of total DNA with no signs of graft-versus-host disease in any participant. The donor DNA clearance times provided by this study have important implications for understanding the safety of allogeneic cord blood cell infusion for cerebral palsy and translational tissue engineering or regenerative medicine research in other disorders.
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Affiliation(s)
- Kylie Crompton
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Neurodevelopment and Disability, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - David E Godler
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Diagnosis and Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Ling Ling
- Diagnosis and Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Ngaire Elwood
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Blood Development, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- The Royal Children's Hospital, Parkville, Victoria, Australia
- BMDI Cord Blood Bank, Parkville, Victoria, Australia
| | | | - Trisha Soosay Raj
- Children's Cancer Centre, The Royal Children's Hospital, Parkville, Victoria, Australia
- Oncology, Queensland Children's Hospital, South Brisbane, Queensland, Australia
| | - Kuang-Chih Hsiao
- Allergy Immunology, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Immunology, Starship Children's Hospital, Auckland, New Zealand
- Paediatrics, University of Auckland, Auckland, New Zealand
| | - Jacqueline Fleming
- Children's Cancer Centre, The Royal Children's Hospital, Parkville, Victoria, Australia
| | | | - Iona Novak
- Cerebral Palsy Alliance Research Institute, University of Sydney, Sydney, New South Wales, Australia
| | - Michael Fahey
- Paediatric Neurology, Monash Children's Hospital, Clayton, Victoria, Australia
- Medicine, Monash University, Melbourne, Victoria, Australia
| | - Xiaofang Wang
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Katherine J Lee
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
- Clinical Epidemiology and Biostatistics Unit, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Paul B Colditz
- Grantley Stable Neonatal Unit, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia
- Perinatal Research Centre, The University of Queensland, Brisbane, Queensland, Australia
| | - Priya Edwards
- Queensland Paediatric Rehabilitation Service, Queensland Children's Hospital, South Brisbane, Queensland, Australia
- Queensland Cerebral Palsy and Rehabilitation Research Centre, The Univeristy of Queensland, Brisbane, Queensland, Australia
| | - Dinah Reddihough
- Neurodisability and Rehabilitation, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
- Neurodevelopment and Disability, The Royal Children's Hospital, Parkville, Victoria, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
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Wu D, Kanaan SB, Penewit K, Waalkes A, Urselli F, Nelson JL, Radich J, Salipante SJ. Ultrasensitive Quantitation of Genomic Chimerism by Single-Molecule Molecular Inversion Probe Capture and High-Throughput Sequencing of Copy Number Deletion Polymorphisms. J Mol Diagn 2022; 24:167-176. [PMID: 34775030 PMCID: PMC8819186 DOI: 10.1016/j.jmoldx.2021.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 09/21/2021] [Accepted: 10/28/2021] [Indexed: 02/03/2023] Open
Abstract
Genomic chimerism represents co-existing cells with different genotypes and has diagnostic significance in transplant engraftment monitoring, residual cancer detection, and other contexts. We previously described an approach to chimerism detection by interrogating variably present or absent genomic loci using single-molecule molecular inversion probes (smMIPs) and next-generation sequencing, which provided ultrasensitive limits of detection (<1 in 10,000 cells) but was not reliably quantitative. Herein, smMIP testing was modified to accurately quantitate chimeric cells by incorporating copy number neutral control loci for data normalization and computationally modeling cell mixtures from individual-specific genotypes. Data demonstrate precision and accuracy over three orders of magnitude (0.01% to 50% chimerism). Seventy hematopoietic stem cell transplant specimens from single (n = 42) or double (n = 28) donors were evaluated, benchmarking smMIP against conventional variable number tandem repeat (VNTR) analysis and an unrelated, ultrasensitive polymorphism-specific quantitative PCR (PS-qPCR) assay. Quantitative concordance of all three assays was high (P < 0.0005, Pearson correlation coefficient), although smMIP correlated better with VNTR testing than PS-qPCR. smMIP and PS-qPCR collectively identified low-level chimerism in all specimens testing negative by VNTR (n = 41 and n = 45 of 48 specimens, respectively). This work demonstrates the feasibility of smMIP-based chimerism testing for quantitative and ultrasensitive measurement of genomic chimerism at practical levels approaching one in one million cells, and cross-validates the approach.
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Affiliation(s)
- David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington,Brotman Baty Institute for Precision Medicine, Seattle, Washington
| | - Sami B. Kanaan
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington,Chimerocyte, Inc., Seattle, Washington
| | - Kelsi Penewit
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Adam Waalkes
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington
| | - Francesca Urselli
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - J. Lee Nelson
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington,Chimerocyte, Inc., Seattle, Washington,Department of Medicine, University of Washington, Seattle, Washington
| | - Jerald Radich
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen J. Salipante
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington,Brotman Baty Institute for Precision Medicine, Seattle, Washington,Address correspondence to Stephen J. Salipante, M.D., Ph.D., University of Washington, Box 357110, 1959 NE Pacific St., Seattle, WA 98195.
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Jerič Kokelj B, Štalekar M, Vencken S, Dobnik D, Kogovšek P, Stanonik M, Arnol M, Ravnikar M. Feasibility of Droplet Digital PCR Analysis of Plasma Cell-Free DNA From Kidney Transplant Patients. Front Med (Lausanne) 2021; 8:748668. [PMID: 34692738 PMCID: PMC8531215 DOI: 10.3389/fmed.2021.748668] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/13/2021] [Indexed: 12/03/2022] Open
Abstract
Increasing research demonstrates the potential of donor-derived cell-free DNA (dd-cfDNA) as a biomarker for monitoring the health of various solid organ transplants. Several methods have been proposed for cfDNA analysis, including real-time PCR, digital PCR, and next generation sequencing-based approaches. We sought to revise the droplet digital PCR (ddPCR)-based approach to quantify relative dd-cfDNA in plasma from kidney transplant (KTx) patients using a novel pilot set of assays targeting single nucleotide polymorphisms that have a very high potential to distinguish cfDNA from two individuals. The assays are capable of accurate quantification of down to 0.1% minor allele content when analyzing 165 ng of human DNA. We found no significant differences in the yield of extracted cfDNA using the three different commercial kits tested. More cfDNA was extracted from the plasma of KTx patients than from healthy volunteers, especially early after transplantation. The median level of donor-derived minor alleles in KTx samples was 0.35%. We found that ddPCR using the evaluated assays within specific range is suitable for analysis of KTx patients' plasma but recommend prior genotyping of donor DNA and performing reliable preamplification of cfDNA.
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Affiliation(s)
- Barbara Jerič Kokelj
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Maja Štalekar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - David Dobnik
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | | | - Miha Arnol
- Department of Nephrology, University Medical Centre Ljubljana, Ljubljana, Slovenia.,Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Ravnikar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
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Wu D, Waalkes A, Penewit K, Salipante SJ. Ultrasensitive Detection of Chimerism by Single-Molecule Molecular Inversion Probe Capture and High-Throughput Sequencing of Copy Number Deletion Polymorphisms. Clin Chem 2018; 64:938-949. [PMID: 29549183 DOI: 10.1373/clinchem.2017.284737] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Accepted: 02/21/2018] [Indexed: 11/06/2022]
Abstract
BACKGROUND Genomic chimerism, the co-occurrence of cells from different genetic origins, provides important diagnostic information in diverse clinical contexts, including graft injury detection and longitudinal surveillance of hematopoietic stem cell transplantation patients, but existing assays are limiting. Here we applied single-molecule molecular inversion probes (smMIPs), a high-throughput sequencing technology combining multiplexed target capture with read quantification mediated by unique molecular identifiers, to detect chimerism based on the presence or absence of polymorphic genomic loci. METHODS We designed a 159-smMIP panel targeting 40 autosomal regions of frequent homozygous deletion across human populations and 2 sex-linked loci. We developed methods for detecting and quantitating loci absent from 1 cell population but present in another, which could be used to sensitively identify chimeric cell populations. RESULTS Unrelated individuals and first-degree relatives were highly polymorphic across the loci examined. Using synthetic DNA mixtures, limits of detection of at least 1 in 10000 chimeric cells were demonstrated without prior knowledge of genotypes, and mixtures of up to 4 separate donors could be deconvoluted. Quantitative linearity over 4 orders of magnitude and false-positive rates <1 in 85000 events were achieved. Eleven of 11 posttransplant clinical specimens from patients with hematological malignancies testing positive for residual cancer by conventional methods had detectable chimeric populations by smMIP, whereas 11 of 11 specimens testing negative by conventional methods were low-positive for chimerism by smMIP. CONCLUSIONS smMIPs are scalable to high sensitivity and large numbers of informative markers, enabling ultrasensitive chimerism detection for many clinical purposes.
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Affiliation(s)
- David Wu
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Adam Waalkes
- Department of Laboratory Medicine, University of Washington, Seattle, WA
| | - Kelsi Penewit
- Department of Laboratory Medicine, University of Washington, Seattle, WA
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