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Fu X, Li X, Wang Y, Xie M, Wen D, Tang X, Wang C, Jia H, Liu Y, Chen S, Wang Y, Zha L, Li J. Discovery unbalanced DNA mixtures and evaluation mixing ratio via a droplet digital PCR method. Int J Legal Med 2024:10.1007/s00414-024-03306-z. [PMID: 39191920 DOI: 10.1007/s00414-024-03306-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2024] [Accepted: 08/05/2024] [Indexed: 08/29/2024]
Abstract
BACKGROUND Small amounts of DNA from a perpetrator collected during crime-scene investigations can be masked by large amounts of DNA from the victim. These samples can provide important information for the perpetrator's conviction. Short tandem repeat (STR) detection system is not sensitive enough to detect trace amounts of minor components in unbalanced mixed DNA. We developed a system using droplet digital polymerase chain reaction (ddPCR) capable of discovering trace components and accurately determining the ratio of mixed DNA in extremely unbalanced mixtures. METHODS The non-recombining regions of the X chromosome and Y chromosome were quantified in the DNA of male and female mixtures using duplex ddPCR. Absolute quantification of low-abundance portions of trace samples and unbalanced mixtures was done using different mixing ratios. RESULTS The ddPCR system could be used to detect low-abundance samples with < 5 copies of DNA components in an extremely unbalanced mixture at a mixing ratio of 10000:1. The high sensitivity and specificity of the system could identify the mixing ratio of mixed DNA accurately. CONCLUSIONS A ddPCR system was developed for evaluation of mixed samples of male DNA and female DNA. Our system could detect DNA quantities as low as 5 copies in extremely unbalanced mixed samples with good specificity and applicability. This method could assist forensic investigators in avoiding the omission of important physical evidence, and evaluating the ratio of mixed male/female trace samples.
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Affiliation(s)
- Xiaoyi Fu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Xueyun Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Xinjiang Medical University, Urumqi, 830017, Xinjiang PR, China
| | - Yuepeng Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Mingkun Xie
- Department of Obstetrics, Xiangya Hospital Central South University, Changsha, China
| | - Dan Wen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Xuan Tang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Chudong Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Hongtao Jia
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Yi Liu
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Siqi Chen
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Yue Wang
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Lagabaiyila Zha
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China
| | - Jienan Li
- Department of Forensic Medicine, School of Basic Medical Sciences, Central South University, No172. Tongzipo Road, Changsha, 410013, Hunan PR, China.
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Wang X, Lan Q, Lin Y, Yuan X, Mei S, Lei F, Dong B, Zhao M, Cai M, Shen C, Zhu B. Investigating the effectiveness of forensic genetics and population genetic diversity using a multi-InDel system in Chinese Hezhou and Southern Shaanxi Han populations. Ann Hum Genet 2024. [PMID: 38766954 DOI: 10.1111/ahg.12553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 01/21/2024] [Accepted: 01/29/2024] [Indexed: 05/22/2024]
Abstract
INTRODUCTION Multiple insertion-deletion (multi-InDel) has greater potential in forensic genetics than InDel, and its efficacy in kinship testing, individual identification, DNA mixture detection and ancestry inference remains to be explored. METHODS Consequently, we designed an efficient and robust system consisting of 41 multi-InDels to evaluate its efficacy in forensic applications in Chinese Hezhou Han (HZH) and Southern Shaanxi Han (SNH) populations and explore the genetic relationships between the SNH, HZH, and 26 reference populations. RESULTS AND CONCLUSION The obtained results showed that 38 out of the 41 multi-InDels had fairly high genetic variations. The the cumulative probability of discrimination and exclusion values of the multi-InDels (except MI38) in HZH and SNH populations both exceeded 1-e-25 and 1-e-6, correspondingly. The genetic compositions of HZH and SNH individuals were similar to that of East Asians and the Naive Bayes model could well distinguish East Asians, Africans and Americans. These results indicated that the multi-InDel systerm can serve as an effective tool to provide important evidence for the development of multi-InDels in forensic practice and better analyse the genetic background of the Han Chinese populations.
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Affiliation(s)
- Xi Wang
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Qiong Lan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Yifeng Lin
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Xi Yuan
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Shuyan Mei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Fanzhang Lei
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Bonan Dong
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Ming Zhao
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Meiming Cai
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
| | - Chunmei Shen
- Department of Laboratory Medicine, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Bofeng Zhu
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, China
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3
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Sel FA, Oğuz FS. Can novel methods replace the gold standard chimerism method after allogeneic hematopoietic stem cell transplantation? Ann Hematol 2024; 103:1035-1047. [PMID: 37801085 DOI: 10.1007/s00277-023-05448-3] [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: 12/15/2022] [Accepted: 09/07/2023] [Indexed: 10/07/2023]
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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Affiliation(s)
- Figen Abatay Sel
- Department of Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey.
- Institute of Graduate Studies in Health Science, Istanbul University, Istanbul, Turkey.
| | - Fatma Savran Oğuz
- Department of Biology, Istanbul University, Istanbul Faculty of Medicine, Istanbul, Turkey
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Häuser F, Mittler J, Hantal MS, Greulich L, Hermanns M, Shrestha A, Kriege O, Falter T, Immel UD, Herold S, Schuch B, Lackner KJ, Rossmann H, Radsak M. One fits all: a highly sensitive combined ddPCR/pyrosequencing system for the quantification of microchimerism after hematopoietic and solid organ transplantation. Clin Chem Lab Med 2023; 61:1994-2001. [PMID: 37167203 DOI: 10.1515/cclm-2023-0198] [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: 10/11/2022] [Accepted: 04/27/2023] [Indexed: 05/13/2023]
Abstract
OBJECTIVES A combined digital droplet PCR (ddPCR)/pyrosequencing assay system was developed that demonstrated advantages applicable to multiple qualitative and quantitative molecular genetic diagnostic applications. Data for characterizing this combined approach for hematologic stem cell transplantation (HSCT) and allele quantification from graft-derived cell-free (cf) DNA in solid organ transplantation (SOT) is presented. METHODS ddPCR and pyrosequencing assays targeting 32 SNPs/markers were established. ddPCR results from 72 gDNAs of 55 patients after allogeneic HSCT and 107 plasma-cfDNAs of 25 liver transplant recipients were compared with established methods/markers, i.e. short-tandem-repeat PCR and ALT, respectively. RESULTS The ddPCR results were in good agreement with the established marker. The limit of detection was 0.02 % minor allele fraction. The relationship between ddPCR and STR-PCR was linear with R2=0.98 allowing to transfer previously established clinical STR-PCR cut-offs to ddPCR; 50-fold higher sensitivity and a variation coefficient of <2 % enable the use of low DNA concentrations (e.g. pre-sorted cells). ddPCR detected liver allograft injury at least as sensitive as ALT suggesting that ddPCR is a reliable method to monitor the transplant integrity, especially when other biomarkers are lacking (e.g. kidney). CONCLUSIONS Combining pyrosequencing for genotyping and ddPCR for minor allele quantification enhances sensitivity and precision for the patient after HSCT and SOT. The assay is designed for maximum flexibility. It is expected to be suitable for other applications (sample tracking, prenatal diagnostics, etc.).
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Affiliation(s)
- Friederike Häuser
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Jens Mittler
- Department of General, Visceral, and Transplant Surgery, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Misra Simge Hantal
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Lilli Greulich
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Martina Hermanns
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Annette Shrestha
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Oliver Kriege
- Department of Medicine III, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Tanja Falter
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Uta D Immel
- Institute of Legal Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Stephanie Herold
- Department of Medicine III, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Brigitte Schuch
- Department of Medicine III, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Karl J Lackner
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Heidi Rossmann
- Institute of Clinical Chemistry and Laboratory Medicine, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - Markus Radsak
- Department of Medicine III, Johannes Gutenberg University Medical Center, Mainz, Germany
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5
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Picard C, Frassati C, Cherouat N, Maioli S, Moskovtchenko P, Cherel M, Chiaroni J, Pedini P. New methods for the quantification of mixed chimerism in transplantation. Front Immunol 2023; 14:1023116. [PMID: 36742303 PMCID: PMC9892455 DOI: 10.3389/fimmu.2023.1023116] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 01/05/2023] [Indexed: 01/20/2023] Open
Abstract
Background Quantification of chimerism showing the proportion of the donor in a recipient is essential for the follow-up of hematopoietic stem cell transplantation but can also be useful to document an immune tolerance situation after solid organ transplantation. Historically, chimerism has been quantified from genomic DNA, but with technological advances, chimerism from donor-derived cell-free DNA seems particularly relevant in solid organ transplantation. Methods The reference method was until recently the short tandem repeat technique, but new innovative techniques as digital PCR (dPCR) and NGS, have revolutionized the quantification of chimerism, such as the so-called microchimerism analysis. After a short review of chimerism methods, a comparison of chimerism quantification data for two new digital PCR systems (QIAcuity™ dPCR (Qiagen®) and QuantStudio Absolute Q (ThermoFisher®) and two NGS-based chimerism quantification methods (AlloSeq HCT™ (CareDx®) and NGStrack™ (GenDX®)) was performed. Results These new methods were correlated and concordant to routinely methods (r²=0.9978 and r²=0.9974 for dPCR methods, r²=0.9978 and r²=0.9988 for NGS methods), and had similar high performance (sensitivity, reproductibility, linearity). Conclusion Finally, the choice of the innovative method of chimerism within the laboratory does not depend on the analytical performances because they are similar but mainly on the amount of activity and the access to instruments and computer services.
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Affiliation(s)
- Christophe Picard
- Immunogenetic Laboratory, EFS PACC, Marseille, France,CNRS, EFS, ADES, Aix Marseille Université, Marseille, France
| | - Coralie Frassati
- Immunogenetic Laboratory, EFS PACC, Marseille, France,*Correspondence: Pascal Pedini, ; Coralie Frassati,
| | | | | | | | | | - Jacques Chiaroni
- Immunogenetic Laboratory, EFS PACC, Marseille, France,CNRS, EFS, ADES, Aix Marseille Université, Marseille, France
| | - Pascal Pedini
- Immunogenetic Laboratory, EFS PACC, Marseille, France,CNRS, EFS, ADES, Aix Marseille Université, Marseille, France,*Correspondence: Pascal Pedini, ; Coralie Frassati,
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Aravind Kumar N, Vishnuraj MR, Vaithiyanathan S, Srinivas C, Chauhan A, Barbuddhe SB. Droplet Digital PCR Assay with Linear Regression Models for Quantification of Buffalo-Derived Materials in Different Food Matrices. FOOD ANAL METHOD 2023. [DOI: 10.1007/s12161-022-02441-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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7
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Tozzo P, Delicati A, Zambello R, Caenazzo L. Chimerism Monitoring Techniques after Hematopoietic Stem Cell Transplantation: An Overview of the Last 15 Years of Innovations. Diagnostics (Basel) 2021; 11:diagnostics11040621. [PMID: 33808342 PMCID: PMC8065704 DOI: 10.3390/diagnostics11040621] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 03/22/2021] [Accepted: 03/29/2021] [Indexed: 01/14/2023] Open
Abstract
Chimerism analysis is a well-established method for monitoring the state of hematopoietic stem cell transplantation (HSCT) over time by analyzing peripheral blood or bone marrow samples of the recipient in several malignant and non-malignant hematologic diseases. From a clinical point of view, a continuous monitoring is fundamental for an effective early therapeutic intervention. This paper provides a comparative overview of the main molecular biology techniques which can be used to study chimerism after bone marrow transplantation, focusing on their advantages and disadvantages. According to the examined literature, short tandem repeats (STR) analysis through simple PCR coupled with capillary electrophoresis (STR-PCR) is the most powerful method which guarantees a high power of differentiation between different individuals. However, other methods such as real-time quantitative PCR (qPCR), digital PCR (dPCR), and next-generation sequencing (NGS) technology were developed to overcome the technical limits of STR-PCR. In particular, these other techniques guarantee a higher sensitivity, which allows for the detection of chimerism at an earlier stage, hence expanding the window for therapeutic intervention. After a comparative evaluation of the various techniques, it seems clear that STR-PCR still remains the gold standard option for chimerism study, even if it is likely that both dPCR and NGS could supplement or even replace the common methods of STR analysis.
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Affiliation(s)
- Pamela Tozzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy; (A.D.); (L.C.)
- Correspondence: ; Tel.: +39-049-827-2235
| | - Arianna Delicati
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy; (A.D.); (L.C.)
| | - Renato Zambello
- Department of Medicine (DIMED), Hematology and Clinical Immunology Section, Padova University School of Medicine, 35121 Padova, Italy;
| | - Luciana Caenazzo
- Department of Molecular Medicine, Laboratory of Forensic Genetics, University of Padova, 35121 Padova, Italy; (A.D.); (L.C.)
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8
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Coccaro N, Tota G, Anelli L, Zagaria A, Specchia G, Albano F. Digital PCR: A Reliable Tool for Analyzing and Monitoring Hematologic Malignancies. Int J Mol Sci 2020; 21:ijms21093141. [PMID: 32365599 PMCID: PMC7247671 DOI: 10.3390/ijms21093141] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
The digital polymerase chain reaction (dPCR) is considered to be the third-generation polymerase chain reaction (PCR), as it yields direct, absolute and precise measures of target sequences. dPCR has proven particularly useful for the accurate detection and quantification of low-abundance nucleic acids, highlighting its advantages in cancer diagnosis and in predicting recurrence and monitoring minimal residual disease, mostly coupled with next generation sequencing. In the last few years, a series of studies have employed dPCR for the analysis of hematologic malignancies. In this review, we will summarize these findings, attempting to focus on the potential future perspectives of the application of this promising technology.
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Affiliation(s)
| | | | | | | | | | - Francesco Albano
- Correspondence: ; Tel.: +39-(0)80-5478031; Fax: +39-(0)80-5508369
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9
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Sathirapatya T, Worrapitirungsi W, Sukawutthiya P, Rasmeepaisarn K, Vongpaisarnsin K. A SNP panel for early detection of artificial chimerism in HSCT patients using TaqMan technology. Int J Legal Med 2020; 134:1553-1561. [PMID: 32248307 DOI: 10.1007/s00414-020-02276-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Accepted: 03/12/2020] [Indexed: 11/26/2022]
Abstract
The monitoring of chimerism status in a hematopoietic stem cell transplantation patient is a crucial process and is performed periodically in a short time interval. A short tandem repeat marker is widely used for chimerism analysis due to its high discrimination power. However, the sensitivity of this approach was limited to 5% of a minor contributor and the interpretation is usually interrupted with PCR stochastic phenomena. Here, we developed an SNP panel for chimerism analysis using TaqMan technology. A set of SNPs was selected from Thai ancestry informative markers and open-access databases with proper criteria. We examined the 30 recipient-donor pairs that underwent HSCT and showed that the panel can provide an informative marker from 90% of all pairs. An early detection of artificial chimerism in post-HSCT samples was observed when compared with STR analysis. In addition, the detail of cases was discussed.
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Affiliation(s)
- Tikumphorn Sathirapatya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand
| | - Wikanda Worrapitirungsi
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand
| | - Poonyapat Sukawutthiya
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand
| | - Kawin Rasmeepaisarn
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand
| | - Kornkiat Vongpaisarnsin
- Department of Forensic Medicine, Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand.
- Forensic Serology and DNA, King Chulalongkorn Memorial Hospital and Thai Red Cross Society, Bangkok, Thailand.
- Forensic Genetics Research Unit, Ratchadapiseksompotch Fund, Faculty of Medicine, Chulalongkorn University, Bangkok, 10300, Thailand.
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Fortschegger M, Preuner S, Printz D, Poetsch AR, Geyeregger R, Pichler H, Lawitschka A, Lion T. Detection and Monitoring of Lineage-Specific Chimerism by Digital Droplet PCR-Based Testing of Deletion/Insertion Polymorphisms. Biol Blood Marrow Transplant 2020; 26:1218-1224. [PMID: 32092354 DOI: 10.1016/j.bbmt.2020.02.016] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 02/03/2020] [Accepted: 02/13/2020] [Indexed: 12/31/2022]
Abstract
Analysis of specific leukocyte subsets for post-transplantation monitoring of chimerism provides greater sensitivity and clinical informativeness on dynamic changes in donor- and recipient-derived cells. Limitations of the most commonly used approach to chimerism testing relying on PCR-based analysis of microsatellite markers prompted us to assess the applicability of digital droplet (dd) PCR amplification of deletion/insertion polymorphisms (DIPs) for lineage-specific chimerism testing in the related stem cell transplantation setting, where the identification of informative markers facilitating the discrimination between donor-derived and recipient-derived cells can be challenging. We analyzed 100 genetically related patient-donor pairs by ddPCR analysis using commercially available DIP kits including large sets of polymorphic markers. At least 1 informative marker was identified in all related pairs analyzed, and 2 or more discriminating markers were detected in the majority (82%) of instances. The achievable detection limit is dependent on the number of cells available for analysis and was as low as 0.1% in the presence of ≥20,000 leukocytes available for DNA extraction. Moreover, the reproducibility and accuracy of quantitative chimerism analysis compared favorably to highly optimized microsatellite assays. Thus, the use of ddPCR-based analysis of DIP markers is an attractive approach to lineage-specific monitoring of chimerism in any allogeneic transplantation setting.
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Affiliation(s)
| | - Sandra Preuner
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Dieter Printz
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - Anna R Poetsch
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | - René Geyeregger
- St Anna Children's Cancer Research Institute, Vienna, Austria
| | | | | | - Thomas Lion
- St Anna Children's Cancer Research Institute, Vienna, Austria; Department of Pediatrics, Medical University of Vienna, Vienna, Austria.
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11
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Sanz-Piña E, Santurtún A, Zarrabeitia MT. Forensic implications of the presence of chimerism after hematopoietic stem cell transplantation. Forensic Sci Int 2019; 302:109862. [DOI: 10.1016/j.forsciint.2019.06.020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Revised: 05/29/2019] [Accepted: 06/16/2019] [Indexed: 11/17/2022]
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12
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Szczerbal I, Nowacka-Woszuk J, Albarella S, Switonski M. Technical note: Droplet digital PCR as a new molecular method for a simple and reliable diagnosis of freemartinism in cattle. J Dairy Sci 2019; 102:10100-10104. [PMID: 31447157 DOI: 10.3168/jds.2019-17021] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 06/28/2019] [Indexed: 12/12/2022]
Abstract
Freemartinism is the most common type of disorder of sex development in cattle. It leads to sterility in the female co-twin in heterosexual twin pregnancy, and is thus a serious problem in cattle production. The incidence of freemartin syndrome is directly dependent on the prevalence of twinning, which has increased in dairy cattle populations in recent years. Thus, early and rapid identification of freemartins is needed to reduce economic loss. Of the various methods used to diagnose this condition, identifying the XX and XY cell lines in blood samples using cytogenetic techniques is the gold standard; however, this technique is time consuming. Faster and more reliable techniques are thus being sought. Droplet digital PCR (ddPCR) is a third-generation PCR method and it has not previously been used to detect XX/XY leukocyte chimerism in cattle. The aim of the present study was to verify the usefulness of ddPCR to detect and quantify leukocyte chimerism in this species. The X and Y copy numbers were estimated by identifying the copy numbers of 2 genes located on the sex chromosomes: amelogenin X-linked (AMELX) on the X chromosome and amelogenin Y-linked (AMELY) on the Y chromosome. In the first step, we performed ddPCR on samples prepared from female DNA mixed with male DNA in serially diluted proportions. We determined that the sensitivity of this method was sufficient to detect a low-frequency (<5%) cell line. In the next step, ddPCR was used to analyze 22 Holstein Friesian freemartins. Cytogenetic evaluation of these cases revealed leukocyte chimerism; the proportion of XX and XY metaphase spreads varied over a wide range, from XX (98%)/XY (2%) to XX (4%)/XY (96%). The use of ddPCR facilitated the precise estimation of the ratio of the copy number of X to Y sex chromosomes. In all cases, the XX/XY chimerism detected by cytogenetic analysis was confirmed using ddPCR. The method turned out to be very simple, accurate, and sensitive. In conclusion, we recommend the ddPCR method for fast and reliable detection of XX/XY leukocyte chimerism in cattle.
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Affiliation(s)
- I Szczerbal
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wołynska 33, 60-637, Poznan, Poland
| | - J Nowacka-Woszuk
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wołynska 33, 60-637, Poznan, Poland
| | - S Albarella
- Department of Veterinary Medicine and Animal Production, University of Naples Federico II, via Delpino 1, Naples 80137, Italy
| | - M Switonski
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Wołynska 33, 60-637, Poznan, Poland.
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Cao W, Li Y, Chen X, Chang Y, Li L, Shi L, Bai W, Ye L. Species identification and quantification of silver pomfret using the droplet digital PCR assay. Food Chem 2019; 302:125331. [PMID: 31404867 DOI: 10.1016/j.foodchem.2019.125331] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 07/30/2019] [Accepted: 08/04/2019] [Indexed: 11/30/2022]
Abstract
Adulteration of the high-value silver pomfret (Pampus argenteus) is a serious problem worldwide, necessitating accurate identification and quantification of the species. In this study, optimisation of the digital droplet PCR (ddPCR) assay for the identification and quantification of the silver pomfret was carried out. The primer and probe concentrations, melting temperature, and PCR cycle number were optimised by combining single-factor experiments with an orthogonal experimental design. The absolute limits of detection and quantification of the ddPCR were 2copies/μl and 21 copies/μl, respectively. Its sensitivity was 0.1% for meat mixtures and 0.5% for DNA mixtures. The ddPCR was 156 times more sensitive than the real-time PCR, although both methods had similar specificities. However, the overall time needed to complete the ddPCR method was twice that of the real-time PCR. Notwithstanding, the ddPCR methodology established in this study can be a valuable tool for addressing species adulteration issues.
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Affiliation(s)
- Weiwei Cao
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yiming Li
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou 510641, Guangdong, China
| | - Xun Chen
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Yanlei Chang
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Weibin Bai
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China
| | - Lei Ye
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou 510632, Guangdong, China.
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14
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Mika T, Baraniskin A, Ladigan S, Wulf G, Dierks S, Haase D, Schork K, Turewicz M, Eisenacher M, Schmiegel W, Schroers R, Klein-Scory S. Digital droplet PCR-based chimerism analysis for monitoring of hematopoietic engraftment after allogeneic stem cell transplantation. Int J Lab Hematol 2019; 41:615-621. [PMID: 31225701 DOI: 10.1111/ijlh.13073] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 04/25/2019] [Accepted: 05/29/2019] [Indexed: 11/29/2022]
Abstract
INTRODUCTION Allogeneic hematopoietic stem cell transplantation (alloHSCT) is a curative approach for multiple hematologic diseases. The success of alloHSCT is evaluated by analyzing the proportion of living donor cells in blood and bone marrow samples of the recipient (chimerism analysis). To monitor the engrafted cells, donor's individual genetic markers are analyzed in peripheral blood and bone marrow samples, usually by using short tandem repeat (STR) analysis. An alternative method to measure chimerism is based on insertion and deletion markers (InDels) analyzed by digital droplet PCR (ddPCR); however, this approach is rarely evaluated in clinical practice. METHODS In this study, we examined the usefulness of ddPCR-based chimerism analysis against the standard STR analysis in samples around day+30 after alloHSCT in clinical practice using peripheral blood and bone marrow samples. RESULTS The median absolute difference between ddPCR and STR analysis was 0.55% points for bone marrow chimerisms and 0.25% points for peripheral blood chimerisms, respectively, including variation in the range of maximum 2% for both methods. The results of every single sample gave the same clinical message. CONCLUSION According to our data, chimerism analysis by ddPCR has an excellent correlation with STR-based analyses. Due to its fast and easy applicability, the ddPCR technique is suitable for chimerism monitoring in clinical practice.
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Affiliation(s)
- Thomas Mika
- Department of Medicine, Ruhr-University Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Alexander Baraniskin
- Department of Medicine, Ruhr-University Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Swedlana Ladigan
- Department of Medicine, Ruhr-University Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Gerald Wulf
- Department of Hematology and Oncology, Georg-August University Göttingen, Göttingen, Germany
| | - Sascha Dierks
- Department of Hematology and Oncology, Georg-August University Göttingen, Göttingen, Germany
| | - Detlef Haase
- Department of Hematology and Oncology, Georg-August University Göttingen, Göttingen, Germany
| | - Karin Schork
- Medizinisches Proteom Center, Ruhr-University Bochum, Bochum, Germany
| | - Michael Turewicz
- Medizinisches Proteom Center, Ruhr-University Bochum, Bochum, Germany
| | - Martin Eisenacher
- Medizinisches Proteom Center, Ruhr-University Bochum, Bochum, Germany
| | - Wolff Schmiegel
- Department of Medicine, Ruhr-University Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany.,IMBL Medical Clinic, Ruhr-University Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Roland Schroers
- Department of Medicine, Ruhr-University Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
| | - Susanne Klein-Scory
- IMBL Medical Clinic, Ruhr-University Bochum, Universitätsklinikum Knappschaftskrankenhaus Bochum GmbH, Bochum, Germany
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15
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Sanz-Piña E, Santurtún A, Freire J, Gómez-Román J, Colorado M, Zarrabeitia MT. The genetic profile of bone marrow transplant patients in different samples of forensic interest. Forensic Sci Med Pathol 2018; 15:178-183. [DOI: 10.1007/s12024-018-0057-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/12/2018] [Indexed: 10/27/2022]
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16
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Kroth PG, Bones AM, Daboussi F, Ferrante MI, Jaubert M, Kolot M, Nymark M, Río Bártulos C, Ritter A, Russo MT, Serif M, Winge P, Falciatore A. Genome editing in diatoms: achievements and goals. PLANT CELL REPORTS 2018; 37:1401-1408. [PMID: 30167805 DOI: 10.1007/s00299-018-2334-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/07/2018] [Indexed: 05/20/2023]
Abstract
Diatoms are major components of phytoplankton and play a key role in the ecology of aquatic ecosystems. These algae are of great scientific importance for a wide variety of research areas, ranging from marine ecology and oceanography to biotechnology. During the last 20 years, the availability of genomic information on selected diatom species and a substantial progress in genetic manipulation, strongly contributed to establishing diatoms as molecular model organisms for marine biology research. Recently, tailored TALEN endonucleases and the CRISPR/Cas9 system were utilized in diatoms, allowing targeted genetic modifications and the generation of knockout strains. These approaches are extremely valuable for diatom research because breeding, forward genetic screens by random insertion, and chemical mutagenesis are not applicable to the available model species Phaeodactylum tricornutum and Thalassiosira pseudonana, which do not cross sexually in the lab. Here, we provide an overview of the genetic toolbox that is currently available for performing stable genetic modifications in diatoms. We also discuss novel challenges that need to be addressed to fully exploit the potential of these technologies for the characterization of diatom biology and for metabolic engineering.
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Affiliation(s)
- Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany.
| | - Atle M Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Fayza Daboussi
- LISBP, Université de Toulouse, CNRS, INSA, 135 Avenue de Rangueil, 31077, Toulouse, France
| | - Maria I Ferrante
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Marianne Jaubert
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France
| | - Misha Kolot
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
- Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Marianne Nymark
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | | | - Andrés Ritter
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France
| | - Monia T Russo
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Manuel Serif
- LISBP, Université de Toulouse, CNRS, INSA, 135 Avenue de Rangueil, 31077, Toulouse, France
| | - Per Winge
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Angela Falciatore
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France.
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17
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Santurtún A, Riancho JA, Santurtún M, Richard C, Colorado MM, García Unzueta M, Zarrabeitia MT. Genetic DNA profile in urine and hair follicles from patients who have undergone allogeneic hematopoietic stem cell transplantation. Sci Justice 2017; 57:336-340. [DOI: 10.1016/j.scijus.2017.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Revised: 05/12/2017] [Accepted: 05/12/2017] [Indexed: 11/26/2022]
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18
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Whitlam JB, Ling L, Swain M, Harrington T, Mirochnik O, Brooks I, Cronin S, Challis J, Petrovic V, Bruno DL, Mechinaud F, Conyers R, Slater H. Use of ubiquitous, highly heterozygous copy number variants and digital droplet polymerase chain reaction to monitor chimerism after allogeneic haematopoietic stem cell transplantation. Exp Hematol 2017; 49:39-47.e5. [PMID: 28147232 DOI: 10.1016/j.exphem.2017.01.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 01/12/2017] [Accepted: 01/17/2017] [Indexed: 12/12/2022]
Abstract
Chimerism analysis has an important role in the management of allogeneic hematopoietic stem cell transplantation. It informs response to disease relapse, graft rejection, and graft-versus-host disease. We have developed a method for chimerism analysis using ubiquitous copy number variation (CNV), which has the benefit of a "negative background" against which multiple independent informative markers are quantified using digital droplet polymerase chain reaction. A panel of up to 38 CNV markers with homozygous deletion frequencies of approximately 0.4-0.6 were used. Sensitivity, precision, reproducibility, and informativity were assessed. CNV chimerism results were compared against established fluorescence in situ hybridization, single nucleotide polymorphism, and short tandem repeat-based methods with excellent correlation. Using 30 ng of input DNA per well, the limit of detection was 0.05% chimerism and the limit of quantification was 0.5% chimerism. High informativity was seen with a median of four informative markers detectable per individual in 39 recipients and 43 donor genomes studied. The strength of this approach was exemplified in a multiple donor case involving four genomes (three related). The precision, sensitivity, and informativity of this approach recommend it for use in clinical practice.
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Affiliation(s)
- John B Whitlam
- Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia; Department of Nephrology, Austin Health, Heidelberg, Victoria, Australia
| | - Ling Ling
- Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Michael Swain
- Laboratory Services, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Tom Harrington
- Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Oksana Mirochnik
- Pathology West Institute of Clinical Pathology and Medical Research, Westmead Hospital, Westmead, New South Wales, Australia
| | - Ian Brooks
- Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Sara Cronin
- Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Jackie Challis
- Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Vida Petrovic
- Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Damien L Bruno
- Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Francoise Mechinaud
- Children's Cancer Centre, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Rachel Conyers
- Children's Cancer Centre, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Howard Slater
- Cyto-Molecular Diagnostic Research Group, Victorian Clinical Genetics Services and Murdoch Childrens Research Institute, Royal Children's Hospital, Parkville, Victoria, Australia; Department of Paediatrics, University of Melbourne, Parkville, Victoria, Australia.
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