Abstract
Non-invasive prenatal testing (NIPT) of cell-free DNA in maternal plasma, which is a mixture of maternal DNA and a low percentage of fetal DNA, can detect fetal aneuploidies using massively parallel sequencing. Because of the low percentage of fetal DNA, methods with high sensitivity and precision are required. However, sequencing variation lowers sensitivity and hampers detection of trisomy samples. Therefore, we have developed three algorithms to improve sensitivity and specificity: the chi-squared-based variation reduction (χ2VR), the regression-based Z-score (RBZ) and the Match QC score. The χ2VR reduces variability in sequence read counts per chromosome between samples, the RBZ allows for more precise trisomy prediction, and the Match QC score shows if the control group used is representative for a specific sample. We compared the performance of χ2VR to that of existing variation reduction algorithms (peak and GC correction) and that of RBZ to trisomy prediction algorithms (standard Z-score, normalized chromosome value and median-absolute-deviation-based Z-score). χ2VR and the RBZ both reduce variability more than existing methods, and thereby increase the sensitivity of the NIPT analysis. We found the optimal combination ...Continue Reading
References
Apr 25, 1995·Nucleic Acids Research·G L Mutter, K A Boynton
Aug 16, 1997·Lancet·Y M LoJ S Wainscoat
Aug 15, 2003·The Cochrane Database of Systematic Reviews·Z AlfirevicS Brigham
May 3, 2006·Ultrasound in Obstetrics & Gynecology : the Official Journal of the International Society of Ultrasound in Obstetrics and Gynecology·P WegrzynK H Nicolaides
Jul 29, 2008·Nucleic Acids Research·Juliane C DohmHeinz Himmelbauer
Oct 8, 2008·Proceedings of the National Academy of Sciences of the United States of America·H Christina FanStephen R Quake
Dec 17, 2008·Proceedings of the National Academy of Sciences of the United States of America·Rossa W K ChiuY M Dennis Lo
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Jan 19, 2010·Bioinformatics·Heng Li, Richard Durbin
May 11, 2010·PloS One·H Christina Fan, Stephen R Quake
Oct 29, 2010·Nature·Gonçalo R AbecasisGil A McVean
Feb 23, 2011·Genome Biology·Daniel AirdAndreas Gnirke
Apr 27, 2011·Clinical Chemistry·Amy J SehnertRichard P Rava
Jul 15, 2011·PloS One·Eric Z ChenY M Dennis Lo
Nov 11, 2011·The Journal of Maternal-fetal & Neonatal Medicine : the Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians·Tze Kin LauXiuqing Zhang
Jan 10, 2012·Prenatal Diagnosis·Andrew B SparksArnold Oliphant
Jan 28, 2012·Genetics in Medicine : Official Journal of the American College of Medical Genetics·Glenn E PalomakiJacob A Canick
May 11, 2012·Fetal Diagnosis and Therapy·Ghalia AshoorKypros H Nicolaides
Sep 22, 2012·Ultrasound in Obstetrics & Gynecology : the Official Journal of the International Society of Ultrasound in Obstetrics and Gynecology·G AshoorK H Nicolaides
Oct 31, 2012·Prenatal Diagnosis·Bernhard ZimmermannMatthew Rabinowitz
Dec 1, 2012·Science Translational Medicine·Rebecca J LearyVictor E Velculescu
Jan 10, 2013·Prenatal Diagnosis·Desheng LiangLingqian Wu
Jan 15, 2013·Clinical Chemistry·Jessica M E van den OeverElles M J Boon
Nov 14, 2013·Prenatal Diagnosis·Markus StummWera Hofmann
Feb 4, 2014·PloS One·Dineika ChandranandaMelanie Bahlo
Feb 24, 2015·Bioinformatics·Artem TarasovPjotr Prins
Jun 2, 2016·BJOG : an International Journal of Obstetrics and Gynaecology·F L MackieM D Kilby
Citations
Jun 6, 2018·The Journal of Maternal-fetal & Neonatal Medicine : the Official Journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians·Minh-Duy PhanHoai-Nghia Nguyen
Sep 17, 2018·Bioinformatics·Jaroslav BudisTomas Szemes
Jul 13, 2019·Gene Therapy·Eddy N de BoerHidde J Haisma
Feb 6, 2019·Prenatal Diagnosis·Minh-Duy PhanHoa Giang
Jul 10, 2019·PloS One·Hindrek TederPriit Palta
Dec 12, 2019·Frontiers in Genetics·Anna A PendinaIgor Yu Kogan
Mar 16, 2019·Human Genomics·Hua HuYing Yang
Dec 19, 2018·BMC Bioinformatics·Lennart F JohanssonMorris A Swertz