W have been primarily based on the GC-corrected read counts.Gestational age at plasma collection Plasma sampling relative to Case no. (weeks) invasive procedure Invasive process 01 02 03 04 05 06 24 1/7 28 4/7 22 5/7 12 3/7 20 2/7 21 4/7 Post-invasive Post-invasive Post-invasive Pre-invasive Pre-invasive Pre-invasive Cordocentesis Cordocentesis AminocentesisChromosomal aberration 22q11.2 microdeletion 22q11.2 microdeletion 22q11.two microdeletionMethods used to confirm karyotype FISH FISH QF-PCR and FISH Array CGH Array CGHChorionic villus sampling 22q11.2 microduplication (2.4 Mb) Amniocentesis Aminocentesis 22q11.two microduplication (2.four Mb)3q29 microduplication (five.1 Mb); 4q32.1- Array CGH q35.two microdeletion (32.9 Mb)doi:ten.1371/journal.pone.0060968.tPLOS One | www.plosone.orgNoninvasive Prenatal Molecular KaryotypingFigure 1. Circos plot from the detected copy quantity aberrations across the genome in maternal plasma. From inside to outdoors: instances 01 to 06. Chromosome ideograms (outermost ring) are oriented pter to qter within a clockwise path. Every single bar represents a 1-Mb window. Regions with 3 or additional consecutive 1-Mb bins of increased or lowered representation in plasma are indicated by green and red bars, respectively. Red arrows highlight the approximate chromosomal areas on these aberrant regions. doi:ten.1371/journal.pone.0060968.gFor the detection of subchromosomal aberrations, we merged the 100-kb bins into 1-Mb bins and calculated the genomic representation of each and every 1-Mb bin (GRx2y), exactly where x and y denote the get started and end genomic coordinates in the 1-Mb bin. We determined the number of sequence reads originated from every 1Mb bin and calculated the GRx2y working with this equation [20]: GRx{y RCx{y RCtotalwhere RCx2y is the read counts for the 1-Mb bin; and RCtotal is the total read counts.IL-4 Protein, Mouse Calculation of z-scoresWe used the group of eight singleton pregnant cases with normal fetal karyotypes as the reference for the analysis of subchromosomal copy number aberrations.Daclatasvir dihydrochloride We determined the mean and the standard deviation of the genomic representation of each 1-Mb bin (GRx2y) of the reference group and calculated the z-score for each 1-Mb bin of the testPLOS ONE | www.plosone.orgNoninvasive Prenatal Molecular KaryotypingFigure 2. Copy number aberrations detected in maternal plasma. The chromosome(s) showing copy number aberrations for each case is shown. (A) Cases 01 to 04; (B) case 05; and (C) case 06. The genomic position is shown on the x-axis and the z-score is plotted on the y-axis. Each vertical bar represents a 1-Mb bin. Regions with three or more consecutive 1-Mb bins of increased or reduced representation in plasma are indicated by green and red bars, respectively.PMID:24377291 doi:10.1371/journal.pone.0060968.gsample using this equation: GRx{ytest {meanGRx{yreference SDx{yreferencez{scoreGRx{ywhere GRx{ytest is the genomic representation of the 1-Mb bin in the test sample; meanGRx{yreference and SDx{yreference are themean and the standard deviation of the genomic representation of the 1-Mb bin of the reference samples. To minimize the systematic inter-sample variations between different chromosomes, we performed median correction for each chromosome. Thus, the median genomic representation of all the bins on a particular chromosome was used as a baseline. For all bins located on that particular chromosome, the difference from this baseline value was used for the calculation of the z-score.PLOS ONE | www.plosone.orgNoninvasive Prenatal Molecular Karyoty.