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Tanja S Hartwig, Louise Ambye, Lene Werge, Martin Kenneth Weiergang, Pernille Nørgaard, Steen Sørensen, Finn Stener Jørgensen
OBJECTIVES: We have established an open source platform for non-invasive prenatal testing (NIPT) based on massively parallel whole-genome sequencing in a public setting. The objective of this study was to investigate factors of importance for correct interpretation of NIPT results to ensure a high sensitivity and specificity. STUDY DESIGN: This investigation is a retrospective case-control study performed in a public NIPT center. The study included 108 aneuploid cases and 165 euploid controls...
May 1, 2018: European Journal of Obstetrics, Gynecology, and Reproductive Biology
Karin Huijsdens-van Amsterdam, Roy Straver, Merel C van Maarle, Alida C Knegt, Diane Van Opstal, Frank Sleutels, Dominique Smeets, Erik A Sistermans
PurposeUsing genome-wide noninvasive prenatal screening (NIPS), we detected a 20-megabase specific deletion starting at 10q25 in eight pregnancies. The deletion could not be confirmed by invasive testing. Since all 10(q25→︀qter) deletions started close to the FRA10B fragile site in 10q25, we investigated whether the pregnant women were indeed carriers of FRA10B.MethodsWe performed NIPS analysis for all autosomes using single-read sequencing. Analysis was done with the WISECONDOR algorithm. Culture of blood lymphocytes with bromodeoxyuridine was used to detect FRA10B expansions...
March 1, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
Tianjiao Chu, Patricia A Shaw, Suveyda Yeniterzi, Mary Dunkel, Aleksander Rajkovic, W Allen Hogge, Kimberly D Bunce, David G Peters
Minimally Invasive Karyotyping (MINK) was communicated in 2009 as a novel method for the non-invasive detection of fetal copy number anomalies in maternal plasma DNA. The original manuscript illustrated the potential of MINK using a model system in which fragmented genomic DNA obtained from a trisomy 21 male individual was mixed with that of his karyotypically normal mother at dilutions representing fetal fractions found in maternal plasma. Although it has been previously shown that MINK is able to non-invasively detect fetal microdeletions, its utility for aneuploidy detection in maternal plasma has not previously been demonstrated...
2017: PloS One
Paul A Cohen, Nicola Flowers, Stephen Tong, Natalie Hannan, Mark D Pertile, Lisa Hui
BACKGROUND: Non-invasive prenatal testing (NIPT) identifies fetal aneuploidy by sequencing cell-free DNA in the maternal plasma. Pre-symptomatic maternal malignancies have been incidentally detected during NIPT based on abnormal genomic profiles. This low coverage sequencing approach could have potential for ovarian cancer screening in the non-pregnant population. Our objective was to investigate whether plasma DNA sequencing with a clinical whole genome NIPT platform can detect early- and late-stage high-grade serous ovarian carcinomas (HGSOC)...
August 24, 2016: BMC Medicine
Peter Johansen, Stine R Richter, Marie Balslev-Harder, Caroline B Miltoft, Ann Tabor, Morten Duno, Susanne Kjaergaard
OBJECTIVE: The objective of this study was to introduce non-invasive prenatal testing (NIPT) for fetal autosomal trisomies and gender in a Danish public health setting, using semi-conductor sequencing and published open source scripts for analysis. METHODS: Plasma-derived DNA from a total of 375 pregnant women (divided into three datasets) was whole-genome sequenced on the Ion Proton™ platform and analyzed using a pipeline based on WISECONDOR for fetal autosomal aneuploidy detection and SeqFF for fetal DNA fraction estimation...
June 2016: Prenatal Diagnosis
Kornelia Neveling, Djie Tjwan Thung, Lean Beulen, Wendy van Rens-Buijsman, Ingrid Gomes, Simone van den Heuvel, Hanneke Mieloo, Irma Derks-Prinsen, Ellen Kater-Baats, Brigitte H W Faas
OBJECTIVE: To validate Illumina's two-channel NextSeq 500 sequencing system for noninvasive prenatal testing (NIPT) of fetal whole chromosome and partial aberrations. METHODS: A total of 162 plasma samples, previously sequenced for NIPT on a SOLiD 5500xl platform, were sequenced on the NextSeq 500 using 75-bp single-end sequencing, followed by analysis using the WISECONDOR algorithm. RESULTS: For whole chromosome aneuploidy detection, all samples were classified correctly (in total 3× T13, 3× T18, 8× T21 and 145× euploid)...
March 2016: Prenatal Diagnosis
Roy Straver, Erik A Sistermans, Marcel J T Reinders
Noninvasive prenatal testing is a relatively new screening method for the detection of fetal chromosome abnormalities using next-generation sequencing (NGS) of fetal DNA in maternal blood. Recently, the introduction of a new tool called WIthin SamplE COpy Number aberration DetectOR (WISECONDOR) marked a new era in prenatal screening. WISECONDOR detects copy number aberrations at a resolution that is almost comparable to classic karyotyping and requires only shallow sequencing, making noninvasive prenatal screening cost-effective...
June 2014: Expert Review of Molecular Diagnostics
Roy Straver, Erik A Sistermans, Henne Holstege, Allerdien Visser, Cees B M Oudejans, Marcel J T Reinders
Genetic disorders can be detected by prenatal diagnosis using Chorionic Villus Sampling, but the 1:100 chance to result in miscarriage restricts the use to fetuses that are suspected to have an aberration. Detection of trisomy 21 cases noninvasively is now possible owing to the upswing of next-generation sequencing (NGS) because a small percentage of fetal DNA is present in maternal plasma. However, detecting other trisomies and smaller aberrations can only be realized using high-coverage NGS, making it too expensive for routine practice...
March 2014: Nucleic Acids Research
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