Noninvasive Fetal Whole-Genome Sequencing from Maternal Plasma: Feasibility Studies and Future Directions

The discovery of cell-free fetal DNA in maternal plasma in 1997 has catalyzed the development of noninvasive prenatal diagnosis (1). Fetal DNA represents on average approximately 15% of the total circulating DNA in maternal plasma. The advent of massively parallel sequencing has made possible the analysis of circulating fetal DNA with unprecedented precision.In 2010, Lo et al. demonstrated that a fetal genomewide genetic map could be assembled by using a combination of DNA-sequencing data from maternal plasma and genetic maps of the parents (2). The latter data include a genotype map of the father and a haplotype-resolved genotype map of the mother. In this approach, the resolution of the deduced fetal genomic map is governed by the resolutions of the parental genetic maps. This approach was used to create a genomewide map of single-nucleotide polymorphism (SNP) alleles that the fetus had inherited from the father but that were absent in the mother's genome (Fig. 1A). The focus was then shifted to the maternally inherited half of the fetal genome and the SNP alleles that were heterozygous in the mother and homozygous in the father (Fig. 1B). These heterozygous SNPs would form 2 haplotypes within the mother's genome on each pair of homologous chromosomes. Analyzing DNA-sequencing data of the maternal plasma allowed comparisons of the relative dosages of these haplotypes in maternal plasma. One could then deduce which haplotypes had been passed on to the fetus, an approach termed “relative haplotype dosage analysis.” The maternal inheritance of the fetus was resolved as a series of >3000 haplotype blocks across the entire genome, and the approach was demonstrated to be useful for the noninvasive prenatal diagnosis of monogenic diseases such as β-thalassemia (2).Fig. 1. Schematic representation for elucidating paternally inherited and maternally inherited fetal genomic sequences in maternal plasma. This …