Second generation noninvasive fetal genome analysis reveals de novo mutations, single-base parental inheritance, and preferred DNA ends
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AbstractPlasma DNA obtained from a pregnant woman was sequenced to a depth of 270x 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 195x coverage. The causative de novo BRAF mutation was successfully detected through the maternal plasma DNA analysis.
All Author(s) ListChan KCA, Jiang PY, Sun K, Cheng YKY, Tong YK, Cheng SH, Wong AIC, Hudecova I, Leung TY, Chiu RWK, Lo YMD
Journal nameProceedings of the National Academy of Sciences
Year2016
Month12
Volume Number113
Issue Number50
PublisherNATL ACAD SCIENCES
PagesE8159 - E8168
ISSN0027-8424
LanguagesEnglish-United Kingdom
Keywordsnoninvasive prenatal testing,massively parallel sequencing,DNA fragmentation patterns
Web of Science Subject CategoriesMultidisciplinary Sciences;Science & Technology - Other Topics

Last updated on 2020-21-11 at 02:05