Noninvasive whole-genome sequencing of a human fetus.
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 × 10(6) 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.
Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Jacob O
JO
Kitzman
Matthew W
MW
Snyder
Mario
M
Ventura
Alexandra P
AP
Lewis
Ruolan
R
Qiu
Lavone E
LE
Simmons
Hilary S
HS
Gammill
Craig E
CE
Rubens
Donna A
DA
Santillan
Jeffrey C
JC
Murray
Holly K
HK
Tabor
Michael J
MJ
Bamshad
Evan E
EE
Eichler
Jay
J
Shendure
D004247:DNA / Q000097:blood* / Q000235:genetics; D005260:Female; D005333:Fetus / Q000378:metabolism*; D005865:Gestational Age; D006239:Haplotypes / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D011247:Pregnancy; D011296:Prenatal Diagnosis / Q000379:methods*
D004247:DNA