Sample Specific Fetal Fraction Threshold for Non-Invasive Prenatal Testing

SNR separates meaningful information (signal) from background information (noise). In statistical applications of SNR, signal is equivalent to a random variable expectation, and noise is equivalent to its variance. Here, cell-free DNA material (containing both maternal and fetal DNA) from pregnant plasma is tested for detection of genomic events in fetal DNA. The fractional fetal DNA in a sample determined by a linear model, as described in Kim et al., 2015, is treated as the signal in the QC procedure. The normalized number of sequencing reads falling in equally spaced bins across the genome (bin count), serves as a base variable in the QC and classification procedures. Median absolute deviation (MAD) of the bin counts across autosomal chromosomes is treated as the noise. Finally, SNR is termed as the ratio of fetal fraction less its measurement error and autosomal MAD: Sample Specific Fetal Fraction Threshold for Non-Invasive Prenatal Testing Amin R. Mazloom1, Andrey Koch1, Youting Sun1, Jennifer Geis1, Mark Whidden1, Eyad Almasri1, John Tynan1, Timothy Burcham1, Mathias Ehrich1 1. Sequenom, Laboratory Corporation of America® Holdings, San Diego, California 92121 777