Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood

doi:10.1073/pnas.0808319105

Noninvasive diagnosis of fetal aneuploidy by shotgun sequencing DNA from maternal blood

*Department of Bioengineering, Stanford University and Howard Hughes Medical Institute, 318 Campus Drive, Clark Center, Room E300, Stanford, CA 94305;
^†Division of Maternal-Fetal Medicine, Department of Obstetrics and Gynecology, Stanford University, 300 Pasteur Drive, Room HH333, Stanford, CA 94305; and
^‡Division of Medical Genetics, Department of Pediatrics, Stanford University, 300 Pasteur Drive, Stanford, CA 94305

Communicated by Leonard A. Herzenberg, Stanford University School of Medicine, Stanford, CA, August 22, 2008 (received for review July 13, 2008)

Abstract

We directly sequenced cell-free DNA with high-throughput shotgun sequencing technology from plasma of pregnant women, obtaining, on average, 5 million sequence tags per patient sample. This enabled us to measure the over- and underrepresentation of chromosomes from an aneuploid fetus. The sequencing approach is polymorphism-independent and therefore universally applicable for the noninvasive detection of fetal aneuploidy. Using this method, we successfully identified all nine cases of trisomy 21 (Down syndrome), two cases of trisomy 18 (Edward syndrome), and one case of trisomy 13 (Patau syndrome) in a cohort of 18 normal and aneuploid pregnancies; trisomy was detected at gestational ages as early as the 14th week. Direct sequencing also allowed us to study the characteristics of cell-free plasma DNA, and we found evidence that this DNA is enriched for sequences from nucleosomes.

Footnotes

^§To whom correspondence should be addressed. E-mail: quake{at}stanford.edu
Author contributions: H.C.F., Y.J.B., U.C., L.H., and S.R.Q. designed research; H.C.F. performed research; H.C.F. analyzed data; Y.J.B., U.C., and L.H. designed the IRB-approved clinical protocol and coordinated patient recruitment and enrollment; and H.C.F., Y.J.B., and S.R.Q. wrote the paper.
Conflict of interest statement: S.R.Q. is a founder, shareholder, and consultant of Fluidigm Corporation. S.R.Q. and H.C.F. have applied for a patent relating to the method described in this study. Other authors declare no conflict of interest.
Freely available online through the PNAS open access option.