Selective analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy.
OBJECTIVE
To develop a novel prenatal assay based on selective analysis of cell-free DNA in maternal blood for evaluation of fetal Trisomy 21 (T21) and Trisomy 18 (T18).


METHODS
Two hundred ninety-eight pregnancies, including 39 T21 and seven T18 confirmed fetal aneuploidies, were analyzed using a novel, highly multiplexed assay, termed digital analysis of selected regions (DANSR™). Cell-free DNA from maternal blood samples was analyzed using DANSR assays for loci on chromosomes 21 and 18. Products from 96 separate patients were pooled and sequenced together. A standard Z-test of chromosomal proportions was used to distinguish aneuploid samples from average-risk pregnancy samples. DANSR aneuploidy discrimination was evaluated at various sequence depths.


RESULTS
At the lowest sequencing depth, corresponding to 204,000 sequencing counts per sample, average-risk cases where distinguished from T21 and T18 cases, with Z statistics for all cases exceeding 3.6. Increasing the sequencing depth to 410,000 counts per sample substantially improved separation of aneuploid and average-risk cases. A further increase to 620,000 counts per sample resulted in only marginal improvement. This depth of sequencing represents less than 5% of that required by massively parallel shotgun sequencing approaches.


CONCLUSIONS
Digital analysis of selected regions enables highly accurate, cost efficient, and scalable noninvasive fetal aneuploidy assessment.
Aria Diagnostics Inc., 5945 Optical Court, San Jose, CA 95138, USA.
Andrew B
AB
Sparks
Eric T
ET
Wang
Craig A
CA
Struble
Wade
W
Barrett
Renee
R
Stokowski
Celeste
C
McBride
Jacob
J
Zahn
Kevin
K
Lee
Naiping
N
Shen
Jigna
J
Doshi
Michel
M
Sun
Jill
J
Garrison
Jay
J
Sandler
Desiree
D
Hollemon
Patrick
P
Pattee
Aoy
A
Tomita-Mitchell
Michael
M
Mitchell
John
J
Stuelpnagel
Ken
K
Song
Arnold
A
Oliphant
D000328:Adult; D002887:Chromosomes, Human, Pair 18 / Q000235:genetics; D002891:Chromosomes, Human, Pair 21 / Q000235:genetics; D003362:Cost-Benefit Analysis; D004247:DNA / Q000097:blood*; D004314:Down Syndrome / Q000097:blood / Q000175:diagnosis* / Q000235:genetics; D005260:Female; D005333:Fetus; D005820:Genetic Testing / Q000379:methods; D006801:Humans; D007091:Image Processing, Computer-Assisted; D011247:Pregnancy / Q000097:blood*; D011248:Pregnancy Complications / Q000175:diagnosis* / Q000235:genetics; D011296:Prenatal Diagnosis / Q000191:economics / Q000379:methods*; D011446:Prospective Studies; D015203:Reproducibility of Results; D014314:Trisomy / Q000175:diagnosis* / Q000235:genetics
D004247:DNA