Cell-free DNA testing of an extended range of chromosomal anomalies: clinical experience with 6,388 consecutive cases

Abstract

Purpose: Cell-free DNA (cfDNA) testing for fetal aneuploidies was broadly implemented for common trisomies and sex-chromosome anomalies (SCAs). However, such an approach identifies only 75 to 85% of clinically relevant aneuploidies.

Methods: We present a consecutive series of 6,388 cases, thus uncovering a broader array of aneuploidies, including the rare autosomal trisomies (RATs) and the maternally inherited deletion and duplication copy-number variations (CNVs), with complete and stratified follow-up by amniocentesis. Combined measurements of z-scores and the fetal fraction, in conjunction with fetal cfDNA enrichment, were used to stratify the likelihood of true and false results.

Results: We obtained an incremental diagnostic yield of 50%; RATs and CNVs were found to be significant causes of fetal pathology. Scrutinizing z-scores and the fetal fraction made it possible to distinguish the sources of false-negative results; predict the likelihood of false-positive results for major trisomies and SCAs; classify maternal mosaic SCAs and CNVs, preventing false-positive results; and robustly identify maternally inherited CNVs and detect recurrent genomic disorders as a standardized function of the fetal fraction.

Conclusion: With the clinical pertinence of this broader detection scheme confirmed, we offer recommendations for its implementation.Genet Med 19 2, 169-175.

Figure 1

The detected aneuploidy classes. The absolute numbers of the aneuploidy classes are shown from left to right: the common trisomies (trisomy 21, 18, and 13), the sex-chromosome anomalies (monosomy X, triple X, and Klinefelter syndromes), the rare autosomal trisomies, and the deletion and duplication copy-number variations.

Figure 2

The detected individual rare autosomal trisomies. The absolute numbers of the individual rare autosomal trisomies are shown from left to right in decreasing order of frequency found.

Figure 3

Standardization of detection of Di George syndrome duplication. Average (±1 SD) signal intensities of the negative control (left) and of serial dilutions (from left to right: 5%, 10%, 15%, 20%, 25%) of the chromosomal microarray-validated fetal case of maternal origin with a 3-Mb duplication of 22q11.2 (shown as 100% dosage on the far right). The detection thresholds are shown as dashed lines, the lower line represents the 99% confidence level (z-score +2.575829), and the upper line reflects the 99.9% confidence level (z-score +3.290527).