Noninvasive Whole-Genome Sequencing of a Human Fetus

Sequencing of cell-free fetal-derived DNA from maternal plasma provides a noninvasive way to predict the fetal genome sequence. Not Your Mother’s Genome There are more than 3000 single-gene (Mendelian) disorders that are individually rare but collectively affect ~1% of births. Currently, only a few specific disorders are screened for during pregnancy, and definitive diagnosis requires invasive procedures such as amniocentesis. An ideal prenatal genetic diagnostic would noninvasively screen for all Mendelian disorders early in pregnancy. Exploiting the observation that ~10% of DNA floating freely in a pregnant woman’s plasma originates from the fetus she carries, several groups have developed DNA sequencing–based tests for conditions such as trisomy 21, the genetic cause of Down syndrome. Although these tests may readily detect gross abnormalities such as an extra copy of an entire chromosome, the noninvasive determination of a complete fetal genome sequence has remained out of reach. Here, Kitzman et al. reconstruct the whole-genome sequence of a human fetus using samples obtained noninvasively during the second trimester, including DNA from the pregnant mother, DNA from the father, and “cell-free” DNA from the pregnant mother’s plasma (a mixture of the maternal and fetal genomes). A big challenge for the authors was to be able to predict which genetic variants were passed from mother to fetus, because the overwhelming majority of DNA in the pregnant mother’s plasma derives from her genome rather than that of the fetus. To overcome this problem, the authors applied a recently developed technique to resolve the mother’s “haplotypes”—groups of genetic variants residing on the same chromosomes—and then used these groups to accurately predict inheritance. Another challenge was the identification of new mutations in the genome of the fetus. The authors demonstrate that, in principle, such mutations can be sensitively detected and triaged for validation. Although these methods must be refined and their costs driven down, this study hints that comprehensive, noninvasive prenatal screening for Mendelian disorders may be clinically feasible in the near future. Analysis of cell-free fetal DNA in maternal plasma holds promise for the development of noninvasive prenatal genetic diagnostics. Previous studies have been restricted to detection of fetal trisomies, to specific paternally inherited mutations, or to genotyping common polymorphisms using material obtained invasively, for example, through chorionic villus sampling. Here, we combine genome sequencing of two parents, genome-wide maternal haplotyping, and deep sequencing of maternal plasma DNA to noninvasively determine the genome sequence of a human fetus at 18.5 weeks of gestation. Inheritance was predicted at 2.8 × 106 parental heterozygous sites with 98.1% accuracy. Furthermore, 39 of 44 de novo point mutations in the fetal genome were detected, albeit with limited specificity. Subsampling these data and analyzing a second family trio by the same approach indicate that parental haplotype blocks of ~300 kilo–base pairs combined with shallow sequencing of maternal plasma DNA is sufficient to substantially determine the inherited complement of a fetal genome. However, ultradeep sequencing of maternal plasma DNA is necessary for the practical detection of fetal de novo mutations genome-wide. Although technical and analytical challenges remain, we anticipate that noninvasive analysis of inherited variation and de novo mutations in fetal genomes will facilitate prenatal diagnosis of both recessive and dominant Mendelian disorders.