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McGowan EC, O'Brien H, Sarri ME, Lopez GH, Daly JJ, Flower RL, Gardener GJ, Hyland CA. Feasibility for non-invasive prenatal fetal blood group and platelet genotyping by massively parallel sequencing: A single test system for multiple atypical red cell, platelet and quality control markers. Br J Haematol 2024; 204:694-705. [PMID: 37984869 DOI: 10.1111/bjh.19197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 10/30/2023] [Accepted: 10/30/2023] [Indexed: 11/22/2023]
Abstract
Non-invasive prenatal tests (NIPT) to predict fetal red cell or platelet antigen status for alloimmunised women are provided for select antigens. This study reports on massively parallel sequencing (MPS) using a red cell and platelet probe panel targeting multiple nucleotide variants, plus individual identification single nucleotide polymorphisms (IISNPs). Maternal blood samples were provided from 33 alloimmunised cases, including seven with two red cell antibodies. Cell-free and genomic DNA was sequenced using targeted MPS and bioinformatically analysed using low-frequency variant detection. The resulting maternal genomic DNA allele frequency was subtracted from the cell-free DNA counterpart. Outcomes were matched against validated phenotyping/genotyping methods, where available. A 2.5% subtractive allele frequency threshold was set after comparing MPS predictions for K, RhC/c, RhE/e and Fya /Fyb against expected outcomes. This threshold was used for subsequent predictions, including HPA-15a, Jka /Jkb , Kpa /Kpb and Lua . MPS outcomes were 97.2% concordant with validated methods; one RhC case was discordantly negative and lacked IISNPs. IISNPs were informative for 30/33 cases as controls. NIPT MPS is feasible for fetal blood group genotyping and covers multiple blood groups and control targets in a single test. Noting caution for the Rh system, this has the potential to provide a personalised service for alloimmunised women.
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Affiliation(s)
- Eunike C McGowan
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
| | - Helen O'Brien
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- Red Cell Reference Laboratory, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
| | - Mia E Sarri
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
| | - Genghis H Lopez
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- School of Health, University of the Sunshine Coast, Sippy Downs, Queensland, Australia
| | - James J Daly
- Pathology Services, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
| | - Robert L Flower
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Glenn J Gardener
- Maternal Fetal Medicine, Mater Mothers' Hospital, South Brisbane, Queensland, Australia
| | - Catherine A Hyland
- Research and Development, Australian Red Cross Lifeblood, Kelvin Grove, Queensland, Australia
- School of Biomedical Sciences, Faculty of Health, Queensland University of Technology, Brisbane, Queensland, Australia
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2
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Rieneck K. Cell-Free DNA and Next-Generation Sequencing for Prenatal Diagnosis. Methods Mol Biol 2024; 2753:583-609. [PMID: 38285369 DOI: 10.1007/978-1-0716-3625-1_38] [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] [Indexed: 01/30/2024]
Abstract
Deep sequencing by NGS of targeted amplicons can identify rare genetic variants in a pool of DNA where the vast majority of genomic DNA does not contain the variant. This approach can be used to detect a previously described paternally inherited, fetal variant in cell-free DNA (cfDNA) in maternal plasma. This is useful in cases where risk for the fetus is contingent upon inheritance of a paternal variant that the woman does not have. Both pathogenic and non-pathogenic variants that the woman does not have can be detected. In cases of compound heterozygosity, presence of the paternal pathogenic variant also requires detection of the maternal variant for risk assessment, which requires a chorion villus biopsy.We have used this approach to focus on detection of fetal blood groups in cases of presence of maternal alloantibodies against blood group antigens in pregnancy, to predict whether the fetus has inherited a blood group antigen that is targeted by the alloantibodies. In cases of maternal alloantibodies against blood group antigens, the fetus is at risk of hemolytic disease of the fetus and newborn (HDFN). With a known specificity of the maternal antibodies and if the fetal blood group can be determined in the pregnancy, then it can be ascertained if the fetus is at risk of HDFN and rational pregnancy care can be instituted. A noninvasive procedure avoids risks for the fetus. We have reported a procedure based on NGS analysis of PCR amplified cfDNA from maternal plasma. Some fetuses may die as early as week 18. We use this approach to predict fetal K, k, RhC, Rhc, RhE, and ABO blood groups in cases with a risk of HDFN due to the corresponding maternally produced antibodies.The NGS-based analysis can predict the presence or absence of incompatible antigens on the fetal RBCs.In this chapter, a noninvasive method for predicting some fetal blood groups early in pregnancy is described. There is a clinical need for such assays, and they may be a useful tool for management of pregnancies complicated by these alloantibodies within the field of precision medicine.
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Affiliation(s)
- Klaus Rieneck
- Department of Clinical Immunology, Laboratory of Blood Genetics, Copenhagen University Hospital, Copenhagen, Denmark.
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Pei XM, Yeung MHY, Wong ANN, Tsang HF, Yu ACS, Yim AKY, Wong SCC. Targeted Sequencing Approach and Its Clinical Applications for the Molecular Diagnosis of Human Diseases. Cells 2023; 12:493. [PMID: 36766834 PMCID: PMC9913990 DOI: 10.3390/cells12030493] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 01/19/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The outbreak of COVID-19 has positively impacted the NGS market recently. Targeted sequencing (TS) has become an important routine technique in both clinical and research settings, with advantages including high confidence and accuracy, a reasonable turnaround time, relatively low cost, and fewer data burdens with the level of bioinformatics or computational demand. Since there are no clear consensus guidelines on the wide range of next-generation sequencing (NGS) platforms and techniques, there is a vital need for researchers and clinicians to develop efficient approaches, especially for the molecular diagnosis of diseases in the emergency of the disease and the global pandemic outbreak of COVID-19. In this review, we aim to summarize different methods of TS, demonstrate parameters for TS assay designs, illustrate different TS panels, discuss their limitations, and present the challenges of TS concerning their clinical application for the molecular diagnosis of human diseases.
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Affiliation(s)
- Xiao Meng Pei
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Martin Ho Yin Yeung
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Alex Ngai Nick Wong
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
| | - Hin Fung Tsang
- Department of Health Technology and Informatics, The Hong Kong Polytechnic University, Hong Kong 999077, China
- Department of Clinical Laboratory and Pathology, Hong Kong Adventist Hospital, Hong Kong, China
| | - Allen Chi Shing Yu
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Aldrin Kay Yuen Yim
- Codex Genetics Limited, Unit 212, 2/F., Building 16W, No. 16 Science Park West Avenue, The Hong Kong Science Park, Hong Kong 852, China
| | - Sze Chuen Cesar Wong
- Department of Applied Biology & Chemical Technology, The Hong Kong Polytechnic University, Hong Kong 999077, China
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Orzińska A, Kluska A, Balabas A, Piatkowska M, Kulecka M, Ostrowski J, Mikula M, Dębska M, Uhrynowska M, Guz K. Prediction of fetal blood group antigens from maternal plasma using Ion AmpliSeq HD technology. Transfusion 2022; 62:458-468. [PMID: 34997618 DOI: 10.1111/trf.16780] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 09/24/2021] [Accepted: 11/18/2021] [Indexed: 12/22/2022]
Abstract
BACKGROUND Fetal blood group (BG) and platelet (HPA) antigens may trigger maternal immunization, causing a fetal disease. Noninvasive prenatal diagnostics (NIPT) predicts fetal genotype, identifying pregnancies with no risk. All current techniques detect fetal antigen alleles with unspecific background and without estimation of fetal fraction, thus new protocols for detection of fetal BG/HPA alleles with ultrahigh sensitivity still need to be tested to improve NIPT. AIM To design NIPT of clinically important antigens using Ion AmpliSeq HD technology. METHODS Plasma DNA from 36 pregnant women (9-33 week of gestation, 24 immunized with anti-HPA-1a,-3b,-15a, -K, or -D+C+S), with known BG/HPA genotypes of their neonates/partners, was tested on Ion S5 System using the Ion AmpliSeq HD designer custom gene panel. NGS contained 25 rs-targets encoding relevant BG/HPA antigens and 10 markers. RESULTS Using the NGS protocol, 76 out of 85 differences in fetal/maternal BG/HPA genotypes were determined in concentration above 2% fetal paternally inherited allele chimerism. The level of unspecific reads for BG/HPA alleles was below 0.87%. In 24 immunized women NGS revealed feto-maternal incompatibility in 11 cases (from 2.44% to 7.41%) and excluded in 10 (<0.05%), three cases had inconclusive results (1.79%, 0.19%, 0.11%). The presence of fetal DNA was confirmed in each case by detecting markers with at least 2% chimerism. CONCLUSION The use of Ion AmpliSeq HD technology improves the prediction of feto-maternal incompatibility, increasing the sensitivity of BG/HPA NIPT and serving confirmation of the fetal DNA at the same workflow.
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Affiliation(s)
- Agnieszka Orzińska
- Department of Hematological and Transfusion Immunology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Anna Kluska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Aneta Balabas
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Magdalena Piatkowska
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Medical Centre of Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland.,Medical Centre of Postgraduate Education, Department of Gastroenterology, Hepatology and Clinical Oncology, Warsaw, Poland
| | - Michal Mikula
- Department of Genetics, Maria Sklodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Marzena Dębska
- 1st Department of Obstetrics and Gynaecology, Medical University of Warsaw, Warsaw, Poland
| | - Małgorzata Uhrynowska
- Department of Hematological and Transfusion Immunology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
| | - Katarzyna Guz
- Department of Hematological and Transfusion Immunology, Institute of Hematology and Transfusion Medicine, Warsaw, Poland
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Dziegiel MH, Krog GR, Hansen AT, Olsen M, Lausen B, Nørgaard LN, Bergholt T, Rieneck K, Clausen FB. Laboratory Monitoring of Mother, Fetus, and Newborn in Hemolytic Disease of Fetus and Newborn. Transfus Med Hemother 2021; 48:306-315. [PMID: 34803574 DOI: 10.1159/000518782] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 07/27/2021] [Indexed: 01/12/2023] Open
Abstract
Background Laboratory monitoring of mother, fetus, and newborn in hemolytic disease of fetus and newborn (HDFN) aims to guide clinicians and the immunized women to focus on the most serious problems of alloimmunization and thus minimize the consequences of HDFN in general and of anti-D in particular. Here, we present the current approach of laboratory screening and testing for prevention and monitoring of HDFN at the Copenhagen University Hospital in Denmark. Summary All pregnant women are typed and screened in the 1st trimester. This serves to identify the RhD-negative pregnant women who at gestational age (GA) of 25 weeks are offered a second screen test and a non-invasive fetal RhD prediction. At GA 29 weeks, and again after delivery, non-immunized RhD-negative women carrying an RhD-positive fetus are offered Rh immunoglobulin. If the 1st trimester screen reveals an alloantibody, antenatal investigation is initiated. This also includes RhD-positive women with alloantibodies. Specificity and titer are determined, the fetal phenotype is predicted by non-invasive genotyping based on cell-free DNA (RhD, K, Rhc, RhC, RhE, ABO), and serial monitoring of titer commences. Based on titers and specificity, monitoring with serial peak systolic velocity measurements in the fetal middle cerebral artery to detect anemia will take place. Intrauterine transfusion is given when fetal anemia is suspected. Monitoring of the newborn by titer and survival of fetal red blood cells by flow cytometry will help predict the length of the recovery of the newborn.
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Affiliation(s)
- Morten Hanefeld Dziegiel
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Grethe Risum Krog
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Anne Todsen Hansen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Marianne Olsen
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Birgitte Lausen
- Department of Pediatrics and Adolescent Medicine, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Lone Nikoline Nørgaard
- Department of Obstetrics, Center of Fetal Medicine and Ultrasound, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Thomas Bergholt
- Department of Obstetrics, Rigshospitalet, Copenhagen, Denmark
| | - Klaus Rieneck
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
| | - Frederik Banch Clausen
- Department of Clinical Immunology, Copenhagen University Hospital, Rigshospitalet, Copenhagen, Denmark
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Clausen FB, Barrett AN, Advani HV, Choolani M, Dziegiel MH. Impact of long-term storage of plasma and cell-free DNA on measured DNA quantity and fetal fraction. Vox Sang 2020; 115:586-594. [PMID: 32342989 DOI: 10.1111/vox.12923] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2019] [Revised: 03/25/2020] [Accepted: 03/27/2020] [Indexed: 01/06/2023]
Abstract
BACKGROUND AND OBJECTIVE Optimal sample storage conditions are essential for non-invasive prenatal testing of cell-free fetal and total DNA. We investigated the effect of long-term storage of plasma samples and extracted cfDNA using qPCR. MATERIALS AND METHODS Fetal and total cfDNA yield and fetal fraction were calculated before and after storage of plasma for 0-6 years at -25°C. Dilution experiments were performed to investigate PCR inhibition. Extraction with or without proteinase K was used to examine protein dissociation. Storage of extracted cfDNA was investigated by testing aliquots immediately, and after 18 months and 3 years of storage at -25°C. RESULTS We observed a marked increase in the levels of amplifiable fetal and total DNA in plasma stored for 2-3 years, and fetal fraction was slightly decreased after 3 years of storage. cfDNA detection was independent of proteinase K during DNA extraction in plasma samples stored >2 years, indicating a loss of proteins from DNA over time, which was likely to account for the observed increase in DNA yields. Measured fetal and total DNA quantities, as well as fetal fraction, increased in stored, extracted cfDNA. CONCLUSION Fetal and total cell-free DNA is readily detectable in plasma after long-term storage at -25°C. However, substantial variation in measured DNA quantities and fetal fraction means caution may be required when using stored plasma and extracted cfDNA for test development or validation purposes.
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Affiliation(s)
- Frederik Banch Clausen
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Angela N Barrett
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Henna V Advani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mahesh Choolani
- Department of Obstetrics and Gynaecology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Morten Hanefeld Dziegiel
- Department of Clinical Immunology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
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Abstract
PURPOSE OF REVIEW To summarize recent advances in red blood cell (RBC) blood group genotyping, with an emphasis on advances in the use of NGS next generation sequencing (NGS) to detect clinically relevant blood group gene variation. RECENT FINDINGS Genetic information is useful in predicting RBC blood group antigen expression in several clinical contexts, particularly, for patients at high-risk for allosensitization, such as multiple transfused patients. Blood group antigen expression is directed by DNA variants affecting multiply genes. With over 300 known antigens, NGS offers the attractive prospect of comprehensive blood group genotyping. Recent studies from several groups show that NGS reliably detects blood group gene single nucleotide variants (SNVs) with good correlation with other genetic methods and serology. Additionally, new custom NGS methods accurately detect complex DNA variants, including hybrid RH alleles. Thus, recent work shows that NGS detects known and novel blood group gene variants in patients, solves challenging clinical cases, and detects relevant blood group variation in donors. SUMMARY New work shows that NGS is particularly robust in identifying SNVs in blood group genes, whereas custom genomic tools can be used to identify known and novel complex structural variants, including in the RH system.
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8
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Clausen FB. Lessons learned from the implementation of non-invasive fetalRHDscreening. Expert Rev Mol Diagn 2018; 18:423-431. [DOI: 10.1080/14737159.2018.1461562] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Frederik Banch Clausen
- Laboratory of Blood Genetics, Department of Clinical Immunology, Copenhagen University Hospital, Copenhagen, Denmark
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9
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Daniels G, Finning K, Lozano M, Hyland CA, Liew YW, Powley T, Castilho L, Bonet Bub C, Kutner JM, Banch Clausen F, Christiansen M, Sulin K, Haimila K, Legler TJ, Lambert M, Ryan H, Ní Loingsigh S, Matteocci A, Pierelli L, Dovc Drnovsek T, Bricl I, Nogués N, Muñiz-Diaz E, Olsson ML, Wikman A, de Haas M, van der Schoot CE, Massey E, Westhoff CM. Vox Sanguinis International Forum on application of fetal blood grouping. Vox Sang 2017; 113:e26-e35. [DOI: 10.1111/vox.12615] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | | | | | - C. A. Hyland
- Australian Red Cross Blood Service, Research and Development; 44 Musk Avenue, Kelvin Grove Brisbane Qld 4059 Australia
| | - Y.-W. Liew
- Australian Red Cross Blood Service, Research and Development; 44 Musk Avenue, Kelvin Grove Brisbane Qld 4059 Australia
| | - T. Powley
- Australian Red Cross Blood Service, Research and Development; 44 Musk Avenue, Kelvin Grove Brisbane Qld 4059 Australia
| | - L. Castilho
- Departamento de Hemoterapia; Hospital Israelita Albert Einstein; Avenida Albert Einstein, 627-3° andar Bloco E CEP: 05651-901 São Paulo SP Brazil
| | - C. Bonet Bub
- Departamento de Hemoterapia; Hospital Israelita Albert Einstein; Avenida Albert Einstein, 627-3° andar Bloco E CEP: 05651-901 São Paulo SP Brazil
| | - J. M. Kutner
- Departamento de Hemoterapia; Hospital Israelita Albert Einstein; Avenida Albert Einstein, 627-3° andar Bloco E CEP: 05651-901 São Paulo SP Brazil
| | - F. Banch Clausen
- Laboratory of Blood Genetics, Rigshospitalet, Section 2034, Department of Clinical Immunology; Copenhagen University Hospital; Blegdamsvej 9 Copenhagen Denmark
| | - M. Christiansen
- Department of Clinical Immunology; Aarhus University Hospital; Palle Juul-Jensens Boulevard 99 8200 Aarhus N Denmark
| | - K. Sulin
- Blood Group Unit; Finnish Red Cross Blood Service; Kivihaantie 7 FI-00310 Helsinki Finland
| | - K. Haimila
- Blood Group Unit; Finnish Red Cross Blood Service; Kivihaantie 7 FI-00310 Helsinki Finland
| | - T. J. Legler
- Department of Transfusion Medicine; University Medical Center Göttingen; Georg-August-Universität; Robert-Koch-Str. 40 Göttingen 37075 Germany
| | - M. Lambert
- Irish Blood Transfusion Service; Blood Group Genetics; National Blood Centre; James's Street Dublin 8 Ireland
| | - H. Ryan
- Irish Blood Transfusion Service; Blood Group Genetics; National Blood Centre; James's Street Dublin 8 Ireland
| | - S. Ní Loingsigh
- Irish Blood Transfusion Service; Blood Group Genetics; National Blood Centre; James's Street Dublin 8 Ireland
| | - A. Matteocci
- Department of Transfusion Medicine; San Camillo Forlanini Hospital; Circonvallazione Gianicolense 87 00152 Roma Italy
| | - L. Pierelli
- Department of Experimental Medicine; Sapienza University of Rome; Piazzale Aldo Moro 5 00185 Roma Italy
- Department of Transfusion Medicine; San Camillo Forlanini Hospital; Circonvallazione Gianicolense 87 00152 Roma Italy
| | - T. Dovc Drnovsek
- Department of Immunohematology; Blood Transfusion Centre of Slovenia; Slajmerjeva 6 SI-Ljubljana Slovenia
| | - I. Bricl
- Department of Immunohematology; Blood Transfusion Centre of Slovenia; Slajmerjeva 6 SI-Ljubljana Slovenia
| | - N. Nogués
- Immunohematology Department; Banc de Sang i Teixits; Passeig de Taulat 116 08005 Barcelona Spain
| | - E. Muñiz-Diaz
- Immunohematology Department; Banc de Sang i Teixits; Passeig de Taulat 116 08005 Barcelona Spain
| | - M. L. Olsson
- Department of Laboratory Medicine; Lund University; Lund Sweden
- Department of Clinical Immunology and Transfusion Medicine; LabMedicine; Office of Medical Services; Region Skåne Lund Sweden
| | - A. Wikman
- Department of Clinical Immunology and Transfusion Medicine; Karolinska University Hospital and Karolinska Institutet; Stockholm Sweden
| | - M. de Haas
- Sanquin Diagnostic Services; Department of Immunohematology Diagnostics; Sanquin Research; Plesmanlaan 125 1066 CX Amsterdam The Netherlands
- Center for Clinical Transfusion Research; Leiden The Netherlands
- Department of Immunohematology and Blood Transfusion; Leiden University Medical Center; Leiden The Netherlands
| | - C. E. van der Schoot
- Sanquin Research; Plesmanlaan 125 1066 CX Amsterdam The Netherlands
- Department of Experimental Immunohematology; Sanquin Research; Amsterdam The Netherlands
- Landsteiner Laboratory; Academic Medical Centre; University of Amsterdam; Amsterdam The Netherlands
| | - E. Massey
- Diagnostic and Therapeutic Services; NHS Blood and Transplant; North Bristol Park, Northway Filton Bristol BS34 7QH UK
| | - C. M. Westhoff
- Immunohematology and Genomics; New York Blood Center; 310 E 67th St New York NY 10065 USA
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Thierry AR, El Messaoudi S, Gahan PB, Anker P, Stroun M. Origins, structures, and functions of circulating DNA in oncology. Cancer Metastasis Rev 2017; 35:347-76. [PMID: 27392603 PMCID: PMC5035665 DOI: 10.1007/s10555-016-9629-x] [Citation(s) in RCA: 526] [Impact Index Per Article: 75.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
While various clinical applications especially in oncology are now in progress such as diagnosis, prognosis, therapy monitoring, or patient follow-up, the determination of structural characteristics of cell-free circulating DNA (cirDNA) are still being researched. Nevertheless, some specific structures have been identified and cirDNA has been shown to be composed of many “kinds.” This structural description goes hand-in-hand with the mechanisms of its origins such as apoptosis, necrosis, active release, phagocytosis, and exocytose. There are multiple structural forms of cirDNA depending upon the mechanism of release: particulate structures (exosomes, microparticles, apoptotic bodies) or macromolecular structures (nucleosomes, virtosomes/proteolipidonucleic acid complexes, DNA traps, links with serum proteins or to the cell-free membrane parts). In addition, cirDNA concerns both nuclear and/or mitochondrial DNA with both species exhibiting different structural characteristics that potentially reveal different forms of biological stability or diagnostic significance. This review focuses on the origins, structures and functional aspects that are paradoxically less well described in the literature while numerous reviews are directed to the clinical application of cirDNA. Differentiation of the various structures and better knowledge of the fate of cirDNA would considerably expand the diagnostic power of cirDNA analysis especially with regard to the patient follow-up enlarging the scope of personalized medicine. A better understanding of the subsequent fate of cirDNA would also help in deciphering its functional aspects such as their capacity for either genometastasis or their pro-inflammatory and immunological effects.
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Affiliation(s)
- A R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France.
| | - S El Messaoudi
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France
| | - P B Gahan
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, F-34298, Montpellier, France
| | - P Anker
- , 135 route des fruitières, 74160, Beaumont, France
| | - M Stroun
- , 6 Pedro-meylan, 1208, Geneva, Switzerland
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