591: Using targeted sequencing of SNPs to achieve a highly accurate non-invasive detection of fetal aneuploidy of 13, 18, 21 and sex chromosomes

Abstract

accurate non-invasive detection of fetal aneuploidy of 13, 18, 21 and sex chromosomes Matthew Rabinowitz, Matthew Hill, Zachary Demko, Sallie McAdoo, Bernhard Zimmermann, Brynn Levy Natera, Inc, Research and Development, San Carlos, CA, Columbia Univeristy, Department of Pathology and Cell Biology, New York, NY OBJECTIVE: To non-invasively detect all abnormalities of chromosomes 13, 18, 21, X and Y, in the fetus through analysis of cell-free fetal DNA in maternal blood. STUDY DESIGN: 500 maternal plasma samples (including 415 euploid and 85 aneuploid samples) were collected from patients at greater than 9 weeks of gestation under an institutional review board (IRB) approved protocol. Aneuploid samples included Trisomy 21, Trisomy 18, Trisomy 13, Turner syndrome (45,X), Klinefelter (47,XXY), and Triploidy. Cell free DNA was isolated, and a targeted multiplex PCR amplification of 19,000 SNP loci on 13, 18, 21, X, and Y was performed. Sequencing data was analyzed using novel Parental Support (PS) technology that uses Bayesian statistics to analyze multiple copy number hypotheses and determine the Maximum likelihood estimation (MLE) given the sequencing data. Unlike other reported methods, the PS method determines a confidence, or calculated accuracy, without requiring a reference chromosome. RESULTS: In those samples that passed quality control thresholds, all calls across all 5 chromosomes tested were correct. The mean calculated accuracy of calls in samples that passed the quality threshold was 99.8%. Samples that failed to meet this threshold (10%) were typically of poor DNA quality and/or low fetal fraction ( 4%). Identification of these samples enables a quick redraw and retesting of the patient rather than increasing the risk of false negatives/positives. CONCLUSION: The PS informatics approach is able to calculate a sample-specific accuracy and detect chromosomally abnormal fetuses from a maternal blood sample with high accuracy at chromosomes 13, 18, 21, X, and Y. Use of the calculated accuracy enables equivalent detection across the chromosomes, and permits maternal blood draws early in pregnancy without increasing the probability of false negatives or positives.