Next Generation Sequencing Technologies in Medical Genetics by C. Alexander Valencia M. Ali Pervaiz Ammar Husami Yaping Qian & Kejian Zhang

Author:C. Alexander Valencia, M. Ali Pervaiz, Ammar Husami, Yaping Qian & Kejian Zhang
Language: eng
Format: epub
Publisher: Springer New York, New York, NY

5.4 Principle of Aneuploidy Detection with Next-Generation–Sequencing

The principle of the use of NGS for noninvasive fetal chromosomal aneuploidy detection in maternal plasma is shown in Fig. 5.1 (Chiu et al. 2008). Maternal plasma DNA (maternal and fetal) is naturally fragmented and further fragmentation is unnecessary for the next steps (Chan et al. 2004). The plasma DNA fragments are sequenced by an Illumina sequencer and processed by the Efficient Large-Scale Alignment of Nucleotide Databases (ELAND) software to determine the chromosomal origin, but the details about their gene-specific location are not required. Quantification of the number of sequence reads originating from any particular chromosome is performed for each human chromosome. Chiu et al. counted only sequences that could be mapped to just one location, unique sequences denoted as U0–1–0–0 on the basis of values in a number of fields in the data output files of the ELAND sequence alignment software, in the repeat-masked reference human genome with no mismatch. The percentage contribution of unique sequences mapped to each chromosome, %chrN, is determined by dividing the U0–1–0–0 count of a specific chromosome by the total number of U0–1–0–0 sequence reads generated in the sequencing run for the tested sample. Then, the z-score, defined as the number of standard deviations from the mean of a reference data set, of %chr21 of the tested sample is calculated to determine whether or not it was a T21 pregnancy. Hence, for a T21 fetus, a high z-score for %chr21 is expected when compared with the mean and standard deviation of %chr21 values obtained from maternal plasma of euploid pregnancies.

Fig. 5.1Schematic illustration for the noninvasive prenatal detection of fetal chromosomal aneuploidy using next-generation sequencing (adapted from Chiu et al. 2008)

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