Y. Lo 1 .
1The Chinese University of Hong Kong, Li Ka Shing Institute of Health Sciences Prince of Wales Hospital, Shatin- New Territories, Hong Kong.
We explored the limit of noninvasive prenatal testing (NIPT) by sequencing the
plasma DNA of a pregnant woman to 270X haploid genome coverage. This
sequencing depth represents the deepest that any case has been sequenced to
date. By using such a depth of sequencing and a custom-built bioinformatics
pipeline, we were able to detect fetal de novo mutations on a genomewide level at
a sensitivity of 85% and a positive predictive value of 74%. These results indicate
that we have solved a hitherto unsolved challenge in NIPT. Furthermore, we
have shown that at such a depth of sequencing, we were also able to elucidate the
maternal inheritance of the fetus without using haplotype-based approaches. This
development has allowed us to increase the resolution of determining the
maternal inheritance of the fetus by 90-fold. Furthermore, we have observed that
there are recurrent DNA sites that plasma DNA molecules tend to preferentially
end on. We called such positions "preferred DNA ends". Interestingly, circulating
DNA fragments derived from the fetus and those derived from the pregnant
woman have sets of different preferred ends. This development allows one to
predict the likelihood that a plasma DNA fragment is of fetal or maternal origin
without using DNA polymorphisms. This approach also allows one to estimate the
fetal DNA fraction without using DNA polymorphisms or size analysis. We believe
that such 'second generation noninvasive fetal genomics' would have many
exciting diagnostic applications and may facilitate an increased understanding of
the biology of circulating DNA.