1
|
Clausen FB, Jørgensen KMCL, Wardil LW, Nielsen LK, Krog GR. Droplet digital PCR-based testing for donor-derived cell-free DNA in transplanted patients as noninvasive marker of allograft health: Methodological aspects. PLoS One 2023; 18:e0282332. [PMID: 36827438 PMCID: PMC9955980 DOI: 10.1371/journal.pone.0282332] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2022] [Accepted: 02/13/2023] [Indexed: 02/26/2023] Open
Abstract
In solid organ transplantation, donor-derived cell-free DNA (dd-cfDNA) is a promising universal noninvasive biomarker for allograft health, where high levels of dd-cfDNA indicate organ damage. Using Droplet Digital PCR (ddPCR), we aimed to develop an assay setup for monitoring organ health. We aimed to identify the least distinguishable percentage-point increase in the fraction of minute amounts of cfDNA in a large cfDNA background by using assays targeting single nucleotide polymorphisms (SNPs). We mimicked a clinical sample from a recipient in a number of spike-in experiments, where cfDNA from healthy volunteers were mixed. A total of 40 assays were tested and approved by qPCR and ddPCR. Limit of detection (LOD) was demonstrated to be approximately 3 copies per reaction, observed at a fraction of 0.002%, and which would equal 6 copies per mL plasma. Limit of quantification (LOQ) was 35 copies per reaction, estimated to 0.038%. The lowest detectable increase in percentage point of dd-cfDNA was approximately 0.04%. Our results demonstrated that ddPCR has great sensitivity, high precision, and exceptional ability to quantify low levels of cfDNA. The ability to distinguish small differences in mimicking dd-cfDNA was far beyond the desired capability. While these methodological data are promising, further prospective studies are needed to determine the clinical utility of the proposed method.
Collapse
Affiliation(s)
- Frederik Banch Clausen
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
- * E-mail:
| | - Kristine Mathilde Clara Lund Jørgensen
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Technology, Faculty of Health, University College Copenhagen, Copenhagen, Denmark
| | - Lasse Witt Wardil
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
- Department of Technology, Faculty of Health, University College Copenhagen, Copenhagen, Denmark
| | - Leif Kofoed Nielsen
- Department of Technology, Faculty of Health, University College Copenhagen, Copenhagen, Denmark
| | - Grethe Risum Krog
- Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
| |
Collapse
|
2
|
Qiao L, Cao X, Tang H, Yu Z, Shi J, Xue Y, Wang T, Liang Y, Huang C, Wang J. White blood cell count affects fetal fraction and test failure rates in noninvasive prenatal screening. Front Med (Lausanne) 2023; 10:1088745. [PMID: 36817785 PMCID: PMC9932807 DOI: 10.3389/fmed.2023.1088745] [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: 11/03/2022] [Accepted: 01/10/2023] [Indexed: 02/05/2023] Open
Abstract
Objective To investigate the effects of white blood cell (WBC) count on fetal fraction (FF), which is an essential quality control for obtaining reliable results, and on the rate of screen failures in noninvasive prenatal screening (NIPS). Methods Noninvasive prenatal screening, serum lipid and liver enzyme level measurements, and WBC count were performed for 4,281 pregnancies with male fetuses. After adjusting for confounders, including the maternal characteristics and alanine aminotransferase (ALT) levels, the effect of WBC count on FF and test failure rate was measured by linear and logistic regression analyses. Results Fetal fraction was negatively associated with BMI, ALT, IVF conceptions, and WBC count and positively correlated with gestational age in the multivariate linear regression model. Moreover, WBC count was the most important factor affecting FF after BMI according to the standardization coefficient analysis. In the 4,281 pregnancy samples with male fetuses, FF decreased with WBC count from 11.45% at ≤8 to 9.02% at >12, and FF markedly decreased to 7.40% in pregnancies with a higher WBC count (>12) and higher BMI (≥25 kg/m2). Meanwhile, the test failure rates were significantly higher in the WBC count > 12 group (4.29%) than in the WBC count ≤ 8 group (0.89%). Notably, when the BMI of pregnancies with a WBC count of >12 was >25, the rate reached 7.53%. Subsequently, multivariate logistic regression analysis further confirmed that an increased BMI and WBC count were independently and significantly associated with the test failure rates. Conclusion An increased WBC count was associated with lower FF and higher test failure rates, suggesting that these important factors should be carefully considered during genetic counseling in pregnant women who decide to undergo blood collection or resampling.
Collapse
Affiliation(s)
- Longwei Qiao
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China
| | - XiaoJu Cao
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Haoyu Tang
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Zheng Yu
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Jingye Shi
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ying Xue
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Ting Wang
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China
| | - Yuting Liang
- Center for Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu Province, China,*Correspondence: Yuting Liang, ; Chao Huang, ; Jiucun Wang,
| | - Chao Huang
- Suzhou Municipal Hospital, Center for Reproduction and Genetics, School of Gusu, The Affiliated Suzhou Hospital of Nanjing Medical University, Suzhou, China,*Correspondence: Yuting Liang, ; Chao Huang, ; Jiucun Wang,
| | - Jiucun Wang
- State Key Laboratory of Genetic Engineering, School of Life Sciences, and Human Phenome Institute, Fudan University, Shanghai, China,Collaborative Innovation Center for Genetics and Development, Fudan University, Shanghai, China,*Correspondence: Yuting Liang, ; Chao Huang, ; Jiucun Wang,
| |
Collapse
|
3
|
Sedej I, Štalekar M, Tušek Žnidarič M, Goričar K, Kojc N, Kogovšek P, Dolžan V, Arnol M, Lenassi M. Extracellular vesicle-bound DNA in urine is indicative of kidney allograft injury. J Extracell Vesicles 2022; 11:e12268. [PMID: 36149031 PMCID: PMC9503341 DOI: 10.1002/jev2.12268] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/29/2022] [Accepted: 09/09/2022] [Indexed: 11/11/2022] Open
Abstract
Extracellular vesicle‐bound DNA (evDNA) is an understudied extracellular vesicle (EV) cargo, particularly in cancer‐unrelated research. Although evDNA has been detected in urine, little is known about its characteristics, localization, and biomarker potential for kidney pathologies. To address this, we enriched EVs from urine of well‐characterized kidney transplant recipients undergoing allograft biopsy, characterized their evDNA and its association to allograft injury. The SEC‐based method enriched pure EVs from urine of kidney transplant recipients, regardless of the allograft injury. Urinary evDNA represented up to 29.2 ± 8% (mean ± SD) of cell‐free DNA (cfDNA) and correlated with cfDNA in several characteristics but was less fragmented (P < 0.001). Importantly, using DNase treatment and immunogold labelling TEM, we demonstrated that evDNA was bound to the surface of urinary EVs. Normalised evDNA yield (P = 0.042) and evDNA copy number (P = 0.027) significantly differed between patients with normal histology, rejection injury and non‐rejection injury, the later groups having significantly larger uEVs (mean diameter, P = 0.045) and more DNA bound per uEV. ddDNA is detectable in uEV samples of kidney allograft recipients, but its quantity is highly variable. In a proof‐of‐principle study, several evDNA characteristics correlated with clinical and histological parameters (P = 0.040), supporting that the potential of evDNA as a biomarker for kidney allograft injury should be further investigated.
Collapse
Affiliation(s)
- Ivana Sedej
- Department of Nephrology, Division of Internal Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia.,Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Maja Štalekar
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Magda Tušek Žnidarič
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Katja Goričar
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Nika Kojc
- Institute of Pathology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Polona Kogovšek
- Department of Biotechnology and Systems Biology, National Institute of Biology, Ljubljana, Slovenia
| | - Vita Dolžan
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Miha Arnol
- Department of Nephrology, Division of Internal Medicine, University Medical Center Ljubljana, Ljubljana, Slovenia.,Department of Internal Medicine, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| | - Metka Lenassi
- Institute of Biochemistry and Molecular Genetics, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
4
|
Galimberti S, Balducci S, Guerrini F, Del Re M, Cacciola R. Digital Droplet PCR in Hematologic Malignancies: A New Useful Molecular Tool. Diagnostics (Basel) 2022; 12:1305. [PMID: 35741115 PMCID: PMC9221914 DOI: 10.3390/diagnostics12061305] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Revised: 05/21/2022] [Accepted: 05/22/2022] [Indexed: 01/27/2023] Open
Abstract
Digital droplet PCR (ddPCR) is a recent version of quantitative PCR (QT-PCR), useful for measuring gene expression, doing clonality assays and detecting hot spot mutations. In respect of QT-PCR, ddPCR is more sensitive, does not need any reference curve and can quantify one quarter of samples already defined as "positive but not quantifiable". In the IgH and TCR clonality assessment, ddPCR recapitulates the allele-specific oligonucleotide PCR (ASO-PCR), being not adapt for detecting clonal evolution, that, on the contrary, does not represent a pitfall for the next generation sequencing (NGS) technique. Differently from NGS, ddPCR is not able to sequence the whole gene, but it is useful, cheaper, and less time-consuming when hot spot mutations are the targets, such as occurs with IDH1, IDH2, NPM1 in acute leukemias or T315I mutation in Philadelphia-positive leukemias or JAK2 in chronic myeloproliferative neoplasms. Further versions of ddPCR, that combine different primers/probes fluorescences and concentrations, allow measuring up to four targets in the same PCR reaction, sparing material, time, and money. ddPCR is also useful for quantitating BCR-ABL1 fusion gene, WT1 expression, donor chimerism, and minimal residual disease, so helping physicians to realize that "patient-tailored therapy" that is the aim of the modern hematology.
Collapse
Affiliation(s)
- Sara Galimberti
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Serena Balducci
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Francesca Guerrini
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Marzia Del Re
- Department of Clinical and Experimental Medicine, Section of Hematology, University of Pisa, 56126 Pisa, Italy; (S.G.); (S.B.); (F.G.); (M.D.R.)
| | - Rossella Cacciola
- Department of Clinical and Experimental Medicine, Section of Hemostasis, University of Catania, 95123 Catania, Italy
| |
Collapse
|