Noninvasive Detection of a Balanced Fetal Translocation from Maternal Plasma

Abstract

BACKGROUND Massively parallel sequencing of circulating cell free (ccf) DNA from maternal plasma has been demonstrated to be a powerful method for the detection of fetal copy number variations (CNVs). Although the detection of CNVs has been described by multiple independent groups, genomic aberrations resulting in copy number–neutral events including balanced translocations have proven to be more challenging to detect noninvasively from ccf DNA. METHODS Data modeling was initially performed to evaluate multiple methods, ultimately leveraging the short length of ccf DNA and paired-end sequencing to construct read-specific mapping characteristics. After testing in a model system, we evaluated the methods on ccf DNA isolated from the plasma of a donor known to be carrying a fetus with a balanced translocation [t(8;11)]. Sequencing was performed with Illumina sequencing technology. RESULTS Our methodology identified the known translocation (P = 1.21 × 10−8) and discounted the likelihood of others, enabling the base specific identification of the rearrangement positions. In total, 402 unique sequencing reads spanned the putative breakpoints, of which 76 contained the structural rearrangement. In addition, 38 of the chimeric reads were mapped to each of the resulting derivative chromosomes, supporting the presence of a reciprocal translocation. Finally, we identified a 6-bp deletion present within der(8) that was absent from the der(11) reciprocal rearrangement. CONCLUSIONS We have developed an algorithm to detect balanced rearrangements and applied our methodology to demonstrate the first proof-of-principle study on the noninvasive detection of a fetal-specific balanced translocation by sequencing ccf DNA from maternal plasma.

Clinical validation of a noninvasive prenatal test for genomewide detection of fetal copy number variants

“…Sequencing depth has been shown as the limiting factor in NIPT methods, with increased depth allowing improved detection of events in samples with lower fetal fractions or improved detection of smaller events. 9 High coverage sequencing has been used in multiple studies to unambiguously identify subchromosomal events 6,[10][11][12] and was used here as a reference for performance evaluation in discrepant amniocentesis samples.…”

Prenatal Diagnosis of Rare Familial Unbalanced Translocation of Chromosomes 7 and 12

“…In one recent study, the accuracy of prenatal diagnosis for abnormal chromosome diseases by chromosome microarray technology and karyotyping was compared. In the prenatal diagnosis test, compared with karyotyping, microarray technology could identify the extra cell genetic information with clinical significance, nonparallel translocations, and aneuploidy; however, its disadvantage was that it could not identify parallel translocations and triploidy [ 3 , 4 ].…”

Clinical Validation of a Non-Invasive Prenatal Test for Genome-Wide Detection of Fetal Copy Number Variants

“…Sequencing depth has been shown as the limiting factor in NIPT methods, with increased depth allowing improved detection of events in samples with lower fetal fractions or improved detection of smaller events [9]. High coverage sequencing has been used in multiple studies to unambiguously identify sub-chromosomal events ([6,10–12]) and was used here as a reference for performance evaluation in discrepant amniocentesis samples.…”