Authors contributed equally to the work.
Selective analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy
Article first published online: 6 JAN 2012
© 2012 John Wiley & Sons, Ltd.
Volume 32, Issue 1, pages 3–9, January 2012
How to Cite
Sparks, A. B., Wang, E. T., Struble, C. A., Barrett, W., Stokowski, R., McBride, C., Zahn, J., Lee, K., Shen, N., Doshi, J., Sun, M., Garrison, J., Sandler, J., Hollemon, D., Pattee, P., Tomita-Mitchell, A., Mitchell, M., Stuelpnagel, J., Song, K. and Oliphant, A. (2012), Selective analysis of cell-free DNA in maternal blood for evaluation of fetal trisomy. Prenat. Diagn., 32: 3–9. doi: 10.1002/pd.2922
Funding sources: None
Conflicts of interest: None declared
- Issue published online: 24 FEB 2012
- Article first published online: 6 JAN 2012
- Manuscript Accepted: 27 OCT 2011
- Manuscript Revised: 11 OCT 2011
- Manuscript Received: 8 SEP 2011
- DNA < fetal cells;
- nucleic acids and proteins;
- trisomy 21;
- trisomy 18;
- next-generation sequencing;
- cell-free DNA
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).
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.
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.
Digital analysis of selected regions enables highly accurate, cost efficient, and scalable noninvasive fetal aneuploidy assessment. © 2012 John Wiley & Sons, Ltd.