Use of targeted sequencing of SNPs to achieve highly accurate non-invasive detection of fetal aneuploidy of chromosomes 13, 18, 21, and sex chromosomes.

Figure 1: The PanoramaTM Non-Invasive Prenatal Test (NIPT)/NATUS Method. The NATUS algorithm considers parental genotypes, HapMap crossover frequency data, and possible fetal chromosome copy number to calculate expected allele distributions for a large number of hypothetical possible fetal genotypes and ploidy states (A-B). It then calculates a likelihood for each hypothesis by comparing the various predicted allele distributions to the actual allelic distributions measured in the cfDNA sample (C), sums the likelihoods for each hypothesis corresponding to the three ploidy states (monosomy, disomy, or trisomy) based on the sequencing data (D), and calls the ploidy state with maximum likelihood as the actual ploidy state, also giving the fetal fraction in the Maximum Likelihood optimization (E). 1. Zimmermann B, Hill M, Gemelos G, et al. Non-invasive prenatal aneuploidy testing of chromosomes 13, 18, 21, X, and Y using targeted sequencing of polymorphic loci. Prenat Diag. doi: 10.1002/pd.3993. 2. Savage M. Merging into Clinical Practice: Updates in Non-invasive Prenatal Testing. Abstract 304, 31st NSGC Annual Education Conference, October 26, 2012 in Boston, MA. 3. Rabinowitz M, Gemelos G, Hill M, et al. Non-Invasive Prenatal Aneuploidy Testing of Chromosomes 13, 18, 21, X, and Y Using Targeted Sequencing of Polymorphic Loci. American Society of Human Genetics Meeting, November 6-10, 2012, in San Francisco, CA. Panorama/NATUS-targeted analysis of SNPs represents a novel method for noninvasive prenatal aneuploidy testing. Here, the NATUS method identified chromosome copy number at chromosomes 13, 18, 21, X, and Y, detecting T13, T18, T21 with 100% sensitivity, 45,X with 92% sensitivity, and 100% specificity for all samples that passed the quality test. The method also detects 47,XXY, 47,XYY, and triploidy (data not shown) and is expected to be able to detect sub-chromosomal abnormalities. This method also obviates issues with amplification variability caused by GC bias, and generates a more powerful sample-specific calculated accuracy for samples with low fetal fractions of cfDNA . Together, this holds promise for a noninvasive screening test with unparalleled accuracy and scope, close to the ceiling of accuracy defined by mosaicism. Panorama TestTM Performance using NATUS Algorithm