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Noninvasive Prenatal Screening and Diagnosis

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Noninvasive prenatal screening and diagnosis Citation for published version (APA): Mersy, E. (2016). Noninvasive prenatal screening and diagnosis: from bench to clinic. Maastricht University. https://doi.org/10.26481/dis.20161207em Document status and date: Published: 01/01/2016 DOI: 10.26481/dis.20161207em Document Version: Publisher's PDF, also known as Version of record Please check the document version of this publication: • A submitted manuscript is the version of the article upon submission and before peer-review. There can be important differences between the submitted version and the official published version of record. People interested in the research are advised to contact the author for the final version of the publication, or visit the DOI to the publisher's website. • The final author version and the galley proof are versions of the publication after peer review. • The final published version features the final layout of the paper including the volume, issue and page numbers. Link to publication General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. • Users may download and print one copy of any publication from the public portal for the purpose of private study or research. • You may not further distribute the material or use it for any profit-making activity or commercial gain • You may freely distribute the URL identifying the publication in the public portal. If the publication is distributed under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license above, please follow below link for the End User Agreement: www.umlib.nl/taverne-license Take down policy If you believe that this document breaches copyright please contact us at: [email protected] providing details and we will investigate your claim. Download date: 26 Sep. 2021 Noninvasive prenatal screening and diagnosis: from bench to clinic Elke Mersy Noninvasive prenatal screening and diagnosis: from bench to clinic The research presented in this thesis was conducted within GROW School for Oncology and Developmental Biology, at the Department of Clinical Genetics of the Maastricht University Medical Center (MUMC+). The studies described in this thesis were funded by The Netherlands Organisation for Health Research and Development (ZonMw Prevention Fund; projects 120510006 and 200320009). ISBN 978-94-6233-439-7 © Copyright Elke Mersy, Maastricht 2016 Cover: Petal Wijnen, Maastricht Lay-out: Elke Mersy, Maastricht Printed by: Gildeprint Drukkerijen, Enschede Noninvasive prenatal screening and diagnosis: from bench to clinic PROEFSCHRIFT ter verkrijging van de graad van doctor aan de Universiteit Maastricht, op gezag van de Rector Magnificus, Prof. dr. Rianne M. Letschert, volgens het besluit van het College van Decanen, in het openbaar te verdedigen op woensdag 7 december 2016 om 10.00 uur door Elke Mersy Geboren op 18 augustus 1986, te Kortrijk, België Promotores Prof. dr. ir. J.A. Veltman Prof. dr. C.E.M. de Die-Smulders Copromotor Dr. S.G.M. Frints Beoordelingscommissie Prof. dr. J.G. Nijhuis (voorzitter) Prof. dr. M.P. van Dieijen-Visser Dr. W.J. Dondorp Dr. K.D. Lichtenbelt (UMC Utrecht) Prof. dr. ir. J.R. Vermeesch (KU Leuven, België) "I look at myself doing science and I am almost like a tourist. Going places I have never been before – that I might be the first to see." Yuk Ming Dennis Lo , the Guardian, 2013 discovered fetal cell-free DNA Table of contents Abbreviations 8 Chapter 1 General introduction and outline of the thesis 11 Part I Design of noninvasive prenatal diagnostic tests 43 Chapter 2 Cell-free RNA is a reliable fetoplacental marker in noninvasive fetal sex determination 45 Chapter 3 Noninvasive prenatal diagnosis of myotonic dystrophy type 1 67 Part II Noninvasive prenatal screening for fetal chromosome disorders 89 Chapter 4 Noninvasive detection of fetal trisomy 21: Systematic review and report of quality and outcomes of diagnostic accuracy studies performed between 1997 and 2012 91 Chapter 5 Advantages and disadvantages of different implementation strategies of noninvasive prenatal testing in Down syndrome screening programs 119 Chapter 6 Noninvasive prenatal testing for sex chromosome trisomy: exploring opinions of pregnant women 145 Chapter 7 General discussion and future perspectives 167 Summary 201 Samenvatting 207 Addendum: valorization 213 Dankwoord 223 Curriculum vitae 227 Publications 229 Abbreviations 45,X Turner syndrome 47,XXX Triple X syndrome 47,XXY Klinefelter syndrome 95% CI 95% confidence interval AC amniocentesis AD autosomal dominant ADHD attention deficit hyperactivity disorder AFP alpha-fetoprotein AMELX X-linked amelogenin gene AMELY Y-linked amelogenin gene AR autosomal recessive ASHG American Society of Human Genetics BMI body mass index C21orf105 chromosome 21 open reading frame 105 gene cf(f)DNA cell-free (fetal) DNA cf(f)RNA cell-free (fetal) RNA CGB chorionic gonadotropin, beta polypeptide gene CGB1 chorionic gonadotropin, beta polypeptide 1 gene CGB2 chorionic gonadotropin, beta polypeptide 2 gene CGB5 chorionic gonadotropin, beta polypeptide 5 gene CGB7 chorionic gonadotropin, beta polypeptide 7 gene CGB8 chorionic gonadotropin, beta polypeptide 8 gene Co negative controls (non-trisomy 21 samples) CSH1 chorionic somatomammotropin hormone 1 (placental lactogen) gene CSH2 chorionic somatomammotropin hormone 2 gene CSHL1 chorionic somatomammotropin hormone-like 1 gene CVS chorionic villus sampling (CYP21) CAH congenital adrenal hyperplasia (due to 21-hydroxylase deficiency) DANSR digital analysis of selected regions DM1 myotonic dystrophy type 1 DMPK dystrophia myotonica protein kinase gene DS Down syndrome EDTA ethylenediaminetetraacetic acid 8 ESHG European Society of Human Genetics FCT first trimester combined test FISH interphase fluorescence in situ hybridization free-βhCG free beta human chorionic gonadotropin HBB hemoglobin beta gene hCG human chorionic gonadotropin IGV integrative genomics viewer IVF/ICSI in vitro fertilization/intracytoplasmic sperm injection KT karyotyping MAF minor allele frequency MeDiP methylated DNA immunoprecipitation MIPVAR MIP-based variant calling miRNA microRNA mRNA messenger RNA MLPA multiplex ligation-dependent probe amplification Mpa only paternal mutation detected MPS massively parallel sequencing NGS next-generation sequencing NIPD noninvasive prenatal diagnosis NIPT noninvasive prenatal testing NPV negative predictive value PAPP-A pregnancy-associated plasma protein-A PCR polymerase chain reaction PDE9A phosphodiesterases gene 9A PGD pre-implantation genetic diagnosis PL placental lactogen PLAC4 placenta-specific 4 gene PND prenatal diagnosis PPV positive predictive value QF-PCR quantitative fluorescent polymerase chain reaction qMSP quantitative methylation-specific polymerase chain reaction qPCR real-time quantitative polymerase chain reaction QUADAS-2 quality assessment of diagnostic accuracy (revised tool) RAD rapid aneuploidy detection RASSF1A Ras association domain family member 1 isoform A gene 9 RHD Rh blood group, D antigen gene RhD rhesus D RT(-PCR) reverse transcription (polymerase chain reaction) SCA sex chromosome aneuploidy SCT sex chromosome trisomy SD standard deviation SERPINB2 serpin peptidase inhibitor, clade B (ovalbumin), member 2 gene (sm)MIPs (single molecule) molecular inversion probes SNP single nucleotide polymorphism SRY sex-determining region Y gene sub substitution T13 trisomy 13, Edwards syndrome T18 trisomy 18, Patau syndrome T21 trisomy 21, Down syndrome TOP termination of pregnancy uE3 unconjugated estriol UI unmethylation index UTY ubiquitously transcribed tetratricopeptide repeat containing, Y-linked WES whole exome sequencing WGS whole genome sequencing WT wild-type nucleotide XL X-linked 10 Chapter 1 General introduction and outline of the thesis 11 Chapter 1 In Western countries the health of the pregnant woman and the unborn child are monitored in routine prenatal care. Prevention and early detection of birth defects are part of prenatal care. To prevent birth defects, pregnant women are taught to avoid known teratogens, for example alcohol. Furthermore, they are screened through blood tests for infections and a potential maternal immune response against fetal blood cells. Many birth defects become apparent during gestation because of reduced fetal growth or abnormalities, visible on ultrasound scan. Therefore, pregnant women are offered regular ultrasound examinations and a fetal anomaly ultrasound scan at 18 to 20 weeks of gestation. Additionally, prenatal screening and diagnostic tests for prenatally detectable genetic disorders are offered. In this thesis, I focus on the latter group of tests. 1.1 Prenatal screening and diagnosis: definitions Before describing the research upon which this doctoral dissertation is based, it is necessary to clarify exactly what is meant by the different terms referring to prenatal screening and diagnosis in this thesis. First and foremost, the terms screening and diagnostic will be used to describe the character of the test itself. The term prenatal diagnostic test will be used for any test providing a definite answer to a clinical question, not requiring a follow-up test to confirm the result. The term prenatal screening test will be applied for any test that offers a risk-assessment and requires
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