Non-invasive prenatal testing of fetal whole chromosome aneuploidy by massively parallel sequencing

Objective To determine whether non-invasive prenatal testing by maternal plasma DNA sequencing can uncover all fetal chromosome aneuploidies in one simple sequencing event. Methods Plasma samples from 435 pregnant women at high risk for Down syndrome were collected prior to amniocentesis in three hospitals in China between March 2009 and June 2011. We sequenced the plasma DNA extracted from these samples at low coverage. We discovered that the genome representation of each of the 24 chromosomes obeyed a linear relationship to its GC content. Applying this relationship, we analysed the copy number of each of the 24 chromosomes. Full fetal karyotyping was compared with maternal plasma DNA sequencing results. Results Among the 435 samples, 412 samples (94.7%) have full karyotyping and sequencing results. Sixty-seven samples containing a fetal chromosome aneuploidy, including trisomy 21, trisomy 18, trisomy 13, trisomy 9, monosomy X or others, can be accurately identified with a detection sensitivity of 100% and a detection specificity of 99.71%. Normalization of the chromosome representation values against chromosomal guanine/cytosine base content is the key issue to ensure the accuracy. Conclusions Our results indicate that non-invasive detection of fetal chromosome aneuploidies for all 24 chromosomes in one single sequencing event is feasible. (c) 2013 John Wiley & Sons, Ltd.