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Proc Natl Acad Sci U S A. 2016 Dec 13;113(50):E8159-E8168. Epub 2016 Oct 31.

Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends.

Author information

1
Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong.
2
Department of Chemical Pathology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong.
3
Department of Obstetrics and Gynaecology, The Chinese University of Hong Kong, Prince of Wales Hospital, Shatin, New Territories, Hong Kong.
4
Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, New Territories, Hong Kong; rossachiu@cuhk.edu.hk loym@cuhk.edu.hk.

Abstract

Plasma DNA obtained from a pregnant woman was sequenced to a depth of 270× haploid genome coverage. Comparing the maternal plasma DNA sequencing data with the parental genomic DNA data and using a series of bioinformatics filters, fetal de novo mutations were detected at a sensitivity of 85% and a positive predictive value of 74%. These results represent a 169-fold improvement in the positive predictive value over previous attempts. Improvements in the interpretation of the sequence information of every base position in the genome allowed us to interrogate the maternal inheritance of the fetus for 618,271 of 656,676 (94.2%) heterozygous SNPs within the maternal genome. The fetal genotype at each of these sites was deduced individually, unlike previously, where the inheritance was determined for a collection of sites within a haplotype. These results represent a 90-fold enhancement in the resolution in determining the fetus's maternal inheritance. Selected genomic locations were more likely to be found at the ends of plasma DNA molecules. We found that a subset of such preferred ends exhibited selectivity for fetal- or maternal-derived DNA in maternal plasma. The ratio of the number of maternal plasma DNA molecules with fetal preferred ends to those with maternal preferred ends showed a correlation with the fetal DNA fraction. Finally, this second generation approach for noninvasive fetal whole-genome analysis was validated in a pregnancy diagnosed with cardiofaciocutaneous syndrome with maternal plasma DNA sequenced to 195× coverage. The causative de novo BRAF mutation was successfully detected through the maternal plasma DNA analysis.

KEYWORDS:

DNA fragmentation patterns; massively parallel sequencing; noninvasive prenatal testing

Comment in

PMID:
27799561
PMCID:
PMC5167168
DOI:
10.1073/pnas.1615800113
[Indexed for MEDLINE]
Free PMC Article

Conflict of interest statement

R.W.K.C. and Y.M.D.L. received research support from Sequenom, Inc. R.W.K.C. and Y.M.D.L. were consultants to Sequenom, Inc. K.C.A.C., R.W.K.C., and Y.M.D.L. hold equities in Sequenom, Inc. K.C.A.C., R.W.K.C., and Y.M.D.L. are founders of Xcelom and Cirina. K.C.A.C., P.J., and R.W.K.C. are consultants to Xcelom. P.J. is a consultant to Cirina. K.C.A.C., P.J., R.W.K.C., and Y.M.D.L. have filed patent applications (PCT/CN2016/073753 and PCT/CN2016/091531) based on the data generated from this work, which have been licensed to Cirina.

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