Bayesian-Based Noninvasive Prenatal Diagnosis of Single-Gene Disorders
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The Accuracy of Cell-Free Fetal DNA Based
University of Birmingham The accuracy of cell-free fetal DNA based non- invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis Mackie, Fiona; Hemming, Karla; Allen, Stephanie; Morris, R. Katie; Kilby, Mark; MacKie, Fiona DOI: 10.1111/1471-0528.14050 License: Creative Commons: Attribution-NonCommercial-NoDerivs (CC BY-NC-ND) Document Version Peer reviewed version Citation for published version (Harvard): Mackie, F, Hemming, K, Allen, S, Morris, RK, Kilby, M & MacKie, F 2016, 'The accuracy of cell-free fetal DNA based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis', BJOG: An International Journal of Obstetrics & Gynaecology. https://doi.org/10.1111/1471-0528.14050 Link to publication on Research at Birmingham portal Publisher Rights Statement: Checked for eligibility: 27/04/2016. This is the peer reviewed version of the following article: Mackie FL, Hemming K, Allen S, Morris RK, Kilby MD. The accuracy of cell-free fetal DNA-based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis. BJOG 2016; DOI: 10.1111/1471-0528.14050. , which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/1471-0528.14050/full. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving." General rights Unless a licence is specified above, all rights (including copyright and moral rights) in this document are retained by the authors and/or the copyright holders. The express permission of the copyright holder must be obtained for any use of this material other than for purposes permitted by law. -
Applications of Cell-Free Fetal DNA in Maternal Serum Applications of Cell-Free Fetal DNA in Maternal Serum
IJIFM 10.5005/jp-journals-10016-1038 REVIEW ARTICLE Applications of Cell-Free Fetal DNA in Maternal Serum Applications of Cell-Free Fetal DNA in Maternal Serum Saeid Ghorbian ABSTRACT approaches, such as microfluidics digital polymerase chain Cell-free fetal DNA (cffDNA) is available in the maternal reaction (PCR), reveals a higher than expected circulation throughout pregnancy and can be used for non- concentrations of fetal DNA around 10 to 12% of total DNA invasive prenatal diagnosis including, determination of fetal sex, in maternal plasma.9 The size of circulating cffDNA identification of specific single gene disorders, typing of fetal blood groups (RhD), paternity determination and potentially predominantly of short DNA fragments, 193 base pairs in routine use for Down’s syndrome (DS) testing of all pregnancies. length10 and can be detected from the 4 weeks of gestation,11 I searched published literature on the PubMed and databases though only reliably from 7 weeks, and the concentration on Scopus interface systematically using keyword’s cffDNA, noninvasive diagnosis, fetal DNA in the maternal serum. increases with gestational age with a sharp peak during the 8,12 Reference lists from the papers were also searched. cffDNA last 8 weeks of pregnancy. The half-life of cffDNA is representing only 3% of the total cell-free circulating DNA in 16 minutes and is undetectable 2 hours after delivery, early and rising to 12% in late pregnancy, clinical investigations therefore, rapidly cleared from the maternal circulation.13 has already demonstrated the potential advantage, such as 14 improving safety, earlier diagnosis and comparative ease of cffDNA may be detectable for several days. -
Cffdna) Enrichment for Non-Invasive Prenatal Testing (NIPT
Cell-free fetal DNA (cffDNA) enrichment for non-invasive prenatal testing (NIPT): a comparison of molecular techniques by Kelly A Sillence A thesis submitted to the University of Plymouth in partial fulfilment for the degree of DOCTOR OF PHILOSOPHY (December 2015) School of Biomedical and Healthcare Sciences I Copyright Statement This copy of the thesis has been supplied on condition that anyone who consults it is understood to recognise that its copyright rests with its author and that no quotation from the thesis and no information derived from it may be published without the author's prior consent. II Cell-free fetal DNA (cffDNA) enrichment for non-invasive prenatal testing (NIPT): a comparison of molecular techniques Kelly Sillence ABSTRACT Prenatal assessment of fetal health is routinely offered throughout pregnancy to ensure that the most effective management can be provided to maintain fetal and maternal well-being. Currently, invasive testing is used for definitive diagnosis of fetal aneuploidy, which is associated with a 1% risk of iatrogenic fetal loss. Developing non-invasive prenatal testing (NIPT) is a key area of research and methods to increase the level of cell-free fetal DNA (cffDNA) within the maternal circulation have been discussed to improve accuracy of such tests. In this study, three strategies; co-amplification at lower denaturation temperature polymerase chain reaction (COLD-PCR), inverse-PCR and Pippin Prep™ gel electrophoresis, were analysed to identify a novel approach to selectively enrich shorter cffDNA fragments from larger maternal cell-free DNA (cfDNA). The sensitivity of droplet digital PCR (ddPCR) against real-time PCR (qPCR) was compared for fetal sex and RHD genotyping. -
Fetal Sex and RHD Genotyping with Digital PCR Demonstrates Greater Sensitivity Than Real-Time PCR
University of Plymouth PEARL https://pearl.plymouth.ac.uk Faculty of Health: Medicine, Dentistry and Human Sciences School of Biomedical Sciences 2015-11 Fetal Sex and RHD Genotyping with Digital PCR Demonstrates Greater Sensitivity than Real-time PCR. Sillence, KA http://hdl.handle.net/10026.1/3798 10.1373/clinchem.2015.239137 Clin Chem All content in PEARL is protected by copyright law. Author manuscripts are made available in accordance with publisher policies. Please cite only the published version using the details provided on the item record or document. In the absence of an open licence (e.g. Creative Commons), permissions for further reuse of content should be sought from the publisher or author. Clinical Chemistry 61:11 Molecular Diagnostics and Genetics 1399–1407 (2015) Fetal Sex and RHD Genotyping with Digital PCR Demonstrates Greater Sensitivity than Real-time PCR Kelly A. Sillence,1 Llinos A. Roberts,2 Heidi J. Hollands,2 Hannah P. Thompson,1 Michele Kiernan,1 Tracey E. Madgett,1 C. Ross Welch,2 and Neil D. Avent1* BACKGROUND: Noninvasive genotyping of fetal RHD inconclusive results, particularly when samples express (Rh blood group, D antigen) can prevent the unnecessary high levels of background maternal cell-free DNA. administration of prophylactic anti-D to women carry- © 2015 American Association for Clinical Chemistry ing RHD-negative fetuses. We evaluated laboratory methods for such genotyping. Diagnosis of fetal sex, RHD (Rh blood group, D anti- METHODS: Blood samples were collected in EDTA tubes gen)3 genotype, and chromosomal abnormalities can be and Streck® Cell-Free DNA™ blood collection tubes achieved only through analysis of fetal DNA. -
University of Birmingham the Accuracy of Cell-Free Fetal DNA
University of Birmingham The accuracy of cell-free fetal DNA based non- invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis Mackie, Fiona; Hemming, Karla; Allen, Stephanie; Morris, R. Katie; Kilby, Mark; MacKie, Fiona DOI: 10.1111/1471-0528.14050 License: Creative Commons: Attribution-NonCommercial-NoDerivs (CC BY-NC-ND) Document Version Peer reviewed version Citation for published version (Harvard): Mackie, F, Hemming, K, Allen, S, Morris, RK, Kilby, M & MacKie, F 2016, 'The accuracy of cell-free fetal DNA based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis', BJOG: An International Journal of Obstetrics & Gynaecology. https://doi.org/10.1111/1471-0528.14050 Link to publication on Research at Birmingham portal Publisher Rights Statement: Checked for eligibility: 27/04/2016. This is the peer reviewed version of the following article: Mackie FL, Hemming K, Allen S, Morris RK, Kilby MD. The accuracy of cell-free fetal DNA-based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis. BJOG 2016; DOI: 10.1111/1471-0528.14050. , which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/1471-0528.14050/full. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving." General rights Unless a licence is specified above, all rights (including copyright and moral rights) in this document are retained by the authors and/or the copyright holders. The express permission of the copyright holder must be obtained for any use of this material other than for purposes permitted by law. -
Noninvasive Fetal Genotyping of Paternally Inherited Alleles ISBN: 978-90-5335-545-9
Noninvasive fetal genotyping of paternally inherited alleles ISBN: 978-90-5335-545-9 Layout: Nikki Vermeulen, Ridderprint BV, Ridderkerk, The Netherlands Print: Ridderprint BV, Ridderkerk, The Netherlands Cover illustration: Lonneke Haer-Wigman and Peter Scheffer Centrifuged sample of blood in a test tube. Photographed at Sanquin Research Amsterdam. Noninvasive fetal genotyping of paternally inherited alleles Niet-invasieve foetale genotypering van paternaal overgeërfde allelen (met een samenvatting in het Nederlands) Proefschrift ter verkrijging van de graad van doctor aan de Universiteit Utrecht op gezag van de rector magnificus, prof.dr. G.J. van der Zwaan, ingevolge het besluit van het college voor promoties in het openbaar te verdedigen op dinsdag 22 mei 2012 des ochtends te 10.30 uur door Peter Gerhard Scheffer geboren op 15 februari 1981 te Utrecht Promotores: Prof. dr. C.E. van der Schoot Prof. dr. G.H.A. Visser Co-promotores: Dr. M. de Haas Dr. G.C.M.L. Page-Christiaens Aan mijn oma† Aan mijn ouders Contents Chapter 1 General introduction and scope of the thesis 9 Chapter 2 Reliability of fetal sex determination using maternal plasma 25 Chapter 3 Noninvasive fetal blood group genotyping of rhesus D, c, E and 41 of K in alloimmunised pregnant women: evaluation of a 7-year clinical experience Chapter 4 Noninvasive fetal genotyping of human platelet antigen-1a 61 Chapter 5 The controversy about controls for fetal blood group genotyping 69 by cell-free fetal DNA in maternal plasma Chapter 6 A nation-wide fetal RHD screening programme for targeted antenatal 81 and postnatal anti-D immunoglobulin prophylaxis: first-three-month analysis Chapter 7 Summary and concluding remarks 103 Nederlandse samenvatting 111 Dankwoord 117 Curriculum Vitae 123 Chapter 1 General introduction and scope of the thesis Chapter 1 Cell-free fetal nucleic acids in the blood of a pregnant woman are a source of fetal genetic material that can be obtained from the expectant mother by a simple venipuncture. -
Circulating Cell Free Tumor DNA Detection As a Routine Tool Forlung Cancer Patient Management
Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management Julie Vendrell, Frédéric Tran Mau-Them, Benoît Beganton, Sylvain Godreuil, Peter Coopman, Jérôme Solassol To cite this version: Julie Vendrell, Frédéric Tran Mau-Them, Benoît Beganton, Sylvain Godreuil, Peter Coopman, et al.. Circulating Cell Free Tumor DNA Detection as a Routine Tool forLung Cancer Patient Management. International Journal of Molecular Sciences, MDPI, 2017, 18 (2), pp.264. 10.3390/ijms18020264. hal-01784728 HAL Id: hal-01784728 https://hal.archives-ouvertes.fr/hal-01784728 Submitted on 25 May 2021 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. Distributed under a Creative Commons Attribution| 4.0 International License International Journal of Molecular Sciences Review Circulating Cell Free Tumor DNA Detection as a Routine Tool for Lung Cancer Patient Management Julie A. Vendrell 1, Frédéric Tran Mau-Them 1, Benoît Béganton 2,3,4,5, Sylvain Godreuil 6, Peter Coopman 2,3,4,5 and Jérôme Solassol 1,2,3,5,* 1 CHU Montpellier, Arnaud de Villeneuve -
Cell-Free Fetal DNA in Maternal Blood: New Possibilities in Prenatal Diagnostics1)
DOI 10.1515/labmed-2012-0078 J Lab Med 2012; aop Molecular-Genetic and Cytogenetic Diagnostics Editor: H.-G. Klein Markus Stumm *, Rolf-Dieter Wegner and Wera Hofmann Cell-free fetal DNA in maternal blood: new 1) possibilities in prenatal diagnostics Abstract: Cell free fetal DNA (cff-DNA) in maternal blood of prenatal diagnostics, it has been necessary so far to has given rise to the possibility of new non-invasive obtain placental or fetal material through chorionic villus approaches in prenatal genetic diagnoses. In contrast to sampling (CVS) in the first trimester of pregnancy or by the established invasive techniques chorionic villi sam- amniocentesis (AC) in the second trimester of pregnancy. pling and amniocentesis, both associated with specific Both methods, however, are invasive and fraught with a risk (0.5 % – 1 % ) for procedure-related abortions, cff-DNA procedure-related miscarriage risk of 0.5 % – 1 % , so that is simply gained by maternal venous blood sampling, they are performed only after a thorough clinical indica- without any risk for the embryo or fetus. Therefore, cff- tion [1] . For the detection of the most common fetal aneu- DNA offers the possibility for riskless genetic diagnoses ploidies (trisomy 13, 18 and 21), non-invasive screening of ongoing pregnancies. Molecular genetic techniques are tests are used additionally that are based on ultrasound already used for the qualitative detection of specific fetal and the determination of hormone and protein para- sequences, such as paternal inherited or spontaneous meters in maternal serum. This is not a diagnostic pro- originated (de novo) mutations. Until recently, the intro- cedure, but merely risk assessments that due to limited duction of digital PCR and next generation sequencing sensitivity and specificity result in a relatively large technologies has shown that a reliable quantitative detec- number of false positive and false negative results (about tion of mutant alleles as well as of clinical relevant aneu- 5 % ). -
The Accuracy of Cell-Free Fetal DNA Based
The accuracy of cell-free fetal DNA based non- invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis Mackie, Fiona; Hemming, Karla; Allen, Stephanie; Morris, R. Katie; Kilby, Mark; MacKie, Fiona DOI: 10.1111/1471-0528.14050 License: Creative Commons: Attribution-NonCommercial-NoDerivs (CC BY-NC-ND) Document Version Peer reviewed version Citation for published version (Harvard): Mackie, F, Hemming, K, Allen, S, Morris, RK, Kilby, M & MacKie, F 2016, 'The accuracy of cell-free fetal DNA based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis', BJOG: An International Journal of Obstetrics & Gynaecology. https://doi.org/10.1111/1471-0528.14050 Link to publication on Research at Birmingham portal Publisher Rights Statement: Checked for eligibility: 27/04/2016. This is the peer reviewed version of the following article: Mackie FL, Hemming K, Allen S, Morris RK, Kilby MD. The accuracy of cell-free fetal DNA-based non-invasive prenatal testing in singleton pregnancies: a systematic review and bivariate meta-analysis. BJOG 2016; DOI: 10.1111/1471-0528.14050. , which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1111/1471-0528.14050/full. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving." General rights Unless a licence is specified above, all rights (including copyright and moral rights) in this document are retained by the authors and/or the copyright holders. The express permission of the copyright holder must be obtained for any use of this material other than for purposes permitted by law. -
Circulating Tumor DNA As a Liquid Biopsy: Current Clinical Applicati…Ture Directions: Page 2 of 3 | Cancer Network | the Oncology Journal 11/19/17, 10(40 PM
Circulating Tumor DNA as a Liquid Biopsy: Current Clinical Applicati…ture Directions: Page 2 of 3 | Cancer Network | The Oncology Journal 11/19/17, 10(40 PM Circulating Tumor DNA as a Liquid Biopsy: Current Clinical Applications and Future Directions: Page 2 of 3 By Kimberly M. Komatsubara, MD and Adrian G. Sacher, MD, MMSc Tuesday, August 15, 2017 Issue: Volume: 31 8 Oncology Journal, Cancer and Genetics Abstract / Synopsis: Tumor genomic sequencing has become part of routine oncology practice in many tumor types, in order to identify potentially targetable mutations and to personalize cancer care. Plasma genotyping via circulating tumor DNA analysis is a noninvasive and rapid alternative method of detecting and monitoring genomic alterations throughout the course of disease. Multiple assays have been developed to date, each with different test characteristics and degrees of clinical validation. Here we review the clinical data supporting these different plasma genotyping methodologies, and present a practical approach to the interpretation of the results of these tests. While the clinical application of plasma genotyping has been most extensively validated in the metastatic setting—for the detection of targetable alterations at the time of initial diagnosis or disease progression— this technology holds significant promise across many tumor types and stages of disease. We will also review emerging applications of plasma genotyping that are currently under clinical investigation. http://www.cancernetwork.com/oncology-journal/circulating-tumor-dna-li…id-biopsy-current-clinical-applications-and-future-directions/page/0/1 Page 1 of 4 Circulating Tumor DNA as a Liquid Biopsy: Current Clinical Applicati…ture Directions: Page 2 of 3 | Cancer Network | The Oncology Journal 11/19/17, 10(40 PM Guide to Interpretation of Plasma Genotyping Results Oncology (Williston Park). -
Fetal Sex and RHD Genotyping with Digital PCR Demonstrates Greater Sensitivity Than Real-Time PCR Kelly A
Clinical Chemistry 61:11 Molecular Diagnostics and Genetics 1399–1407 (2015) Fetal Sex and RHD Genotyping with Digital PCR Demonstrates Greater Sensitivity than Real-time PCR Kelly A. Sillence,1 Llinos A. Roberts,2 Heidi J. Hollands,2 Hannah P. Thompson,1 Michele Kiernan,1 Tracey E. Madgett,1 C. Ross Welch,2 and Neil D. Avent1* BACKGROUND: Noninvasive genotyping of fetal RHD inconclusive results, particularly when samples express (Rh blood group, D antigen) can prevent the unnecessary high levels of background maternal cell-free DNA. administration of prophylactic anti-D to women carry- © 2015 American Association for Clinical Chemistry ing RHD-negative fetuses. We evaluated laboratory methods for such genotyping. Diagnosis of fetal sex, RHD (Rh blood group, D anti- METHODS: Blood samples were collected in EDTA tubes gen)3 genotype, and chromosomal abnormalities can be and Streck® Cell-Free DNA™ blood collection tubes achieved only through analysis of fetal DNA. Initially, (Streck BCTs) from RHD-negative women (n ϭ 46). this could be achieved through invasive procedures such Using Y-specific and RHD-specific targets, we investi- as amniocentesis and chorionic villus sampling, quoted as gated variation in the cell-free fetal DNA (cffDNA) frac- having a 1% risk of miscarriage (1). Since the discovery tion and determined the sensitivity achieved for optimal 4 and suboptimal samples with a novel Droplet Digital™ of cell-free fetal DNA (cffDNA) in maternal plasma, PCR (ddPCR) platform compared with real-time quan- noninvasive prenatal testing is now a clinical reality (1– titative PCR (qPCR). 5). Fetal sex determination is offered in the clinic for families at risk of X-linked disorders, such as Duchenne RESULTS: The cffDNA fraction was significantly larger for muscular dystrophy (6).