Data from: Fetal genome profiling at 5 weeks of gestation after noninvasive isolation of trophoblast cells from the endocervical canal

Single-gene mutations account for more than 6000 diseases, 10% of all
pediatric hospital admissions, and 20% of infant deaths. Down syndrome and
other aneuploidies occur in more than 0.2% of births worldwide and are on
the rise because of advanced reproductive age. Birth defects of genetic
origin can be diagnosed in utero after invasive extraction of fetal
tissues. Noninvasive testing with circulating cell-free fetal DNA is
limited by a low fetal DNA fraction. Both modalities are unavailable until
the end of the first trimester. We have isolated intact trophoblast cells
from Papanicolaou smears collected noninvasively at 5 to 19 weeks of
gestation for next-generation sequencing of fetal DNA. Consecutive matched
maternal, placental, and fetal samples (n = 20) were profiled by multiplex
targeted DNA sequencing of 59 short tandem repeat and 94 single-nucleotide
variant sites across all 24 chromosomes. The data revealed fetal DNA
fractions of 85 to 99.9%, with 100% correct fetal haplotyping. This
noninvasive platform has the potential to provide comprehensive fetal
genomic profiling as early as 5 weeks of gestation.