Detecting fetal subchromosomal aberrations by MPS: An unexpected discrepancy between amniocyte DNA and ccffDNA

摘要

Because of apoptosis of placental cytotrophoblast cells, cell-free fetal DNA is released into the blood circulation of pregnant women. This circulating cell-free fetal DNA (ccffDNA) comprises about 10% of DNA in maternal plasma, making it a valuable source for noninvasive prenatal testing (NIPT).1 With the advent of massively parallel sequencing (MPS), it became feasible to overcome the challenge of analyzing fetal DNA in a predominant maternal background,2'3 opening the way for implementation of NIPT for whole chromosome aneuploidy detection in clinical practice. To date, the NIPT focus has been primarily on the detection of fetal whole chromosome aneuploidies, especially trisomy 21 (Down syndrome), trisomy 18 (Edwards syndrome), and trisomy 13 (Patau syndrome). The detection of subchromosomal aberrations is more challenging as it requires a higher sequencing depth and/or a relatively high percentage of fetal DNA in order to be feasible.4'5 A first proof-of-concept study6 used -243 x 10~6 reads to detect a 4.2-Mb deletion on chromosome 12, whereas in a second study, a 3-Mb 22qll.2 deletion was detected in two samples with 18% fetal DNA at a fourfold genomic coverage.7 However, in routine clinical practice, the genome-wide sequencing depth for fetal aneuploidy detection may be onefold or less. Chen et al. developed a bioinformatic approach for the detection of large deletions and duplications in such low coverage sequencing data.