High Levels of Sample-to-Sample Variation Confound Data Analysis for Non-Invasive Prenatal Screening of Fetal Microdeletions

• Published in: PloS one Vol. 11; no. 6; p. e0153182
• Main Authors: Chu, Tianjiao, Yeniterzi, Suveyda, Yatsenko, Svetlana A, Dunkel, Mary, Shaw, Patricia A, Bunce, Kimberly D, Peters, David G
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 01.06.2016; Public Library of Science (PLoS)
• Subjects: Amniocentesis; Analysis; Biology and Life Sciences; Care and treatment; Chromosome 5; Chromosome Deletion; Chromosomes; Coefficient of variation; Complications and side effects; Confounding Factors (Epidemiology); Copy number; Data analysis; Data processing; Deoxyribonucleic acid; Diagnosis; DNA; DNA - genetics; DNA sequencing; Down syndrome; Female; Fetus; Fetuses; Gene sequencing; Genetics; Genome, Human; Genomes; Gynecology; Humans; Hybridization; Intermetallic compounds; Medical screening; Medicine; Medicine and Health Sciences; Nickel base alloys; Nickel compounds; Nucleotide sequence; Obstetrics; Plasma; Platinum compounds; Pregnancy; Prenatal development; Prenatal Diagnosis; Reproducibility of Results; Research and Analysis Methods; Systematic review; Ultrasonic imaging; Variation
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0153182

Our goal was to test the hypothesis that inter-individual genomic copy number variation in control samples is a confounding factor in the non-invasive prenatal detection of fetal microdeletions via the sequence-based analysis of maternal plasma DNA. The database of genomic variants (DGV) was used to determine the "Genomic Variants Frequency" (GVF) for each 50kb region in the human genome. Whole genome sequencing of fifteen karyotypically normal maternal plasma and six CVS DNA controls samples was performed. The coefficient of variation of relative read counts (cv.RTC) for these samples was determined for each 50kb region. Maternal plasma from two pregnancies affected with a chromosome 5p microdeletion was also sequenced, and analyzed using the GCREM algorithm. We found strong correlation between high variance in read counts and GVF amongst controls. Consequently we were unable to confirm the presence of the microdeletion via sequencing of maternal plasma samples obtained from two sequential affected pregnancies. Caution should be exercised when performing NIPT for microdeletions. It is vital to develop our understanding of the factors that impact the sensitivity and specificity of these approaches. In particular, benign copy number variation amongst controls is a major confounder, and their effects should be corrected bioinformatically.