Evaluation of interpretation methods to improve accuracy of the prenatal BACs‑on‑Beads™ assay in prenatal diagnosis

Abstract

Prenatal BACs-on-Beads™ (PNBoBs™) technology has been approved for use in routine clinical prenatal diagnosis in numerous countries. However, the influence of data interpretation on the accuracy of the results remains to be evaluated. The present study aimed to determine the accuracy of existing data interpretation approaches and develop an optimization method to improve the performance of the PNBoBs™ assay in prenatal diagnosis. A total of 2,289 prenatal cases with known karyotypes and raw ratio data from PNBoBs™ assays were recruited for the present study. Positive results, according to the data interpretation methods used for the PNBoBs™ test, were validated against current gold-standard approaches. Statistical analyses were then performed to evaluate the accuracy of existing methods in data interpretation to provide a basis for the optimization of a follow-up approach. Among the existing methods, the 'trimmed standard deviation threshold' approach had the highest sensitivity and false-positive rates, with 98.1 and 4.2%, respectively. The 'n-1 or greater probes' rule had the highest specificity (99.7%) and the second-highest false-negative rate (11.5%). The method optimized in the present study provided a reasonable balance between sensitivity (98.1%) and specificity (99.6%) with regards to the interpretation of the data obtained from the PNBoBs™ assay. The results indicated that the present optimization method outperforms existing approaches in data interpretation for the PNBoBs™ assay, and as a result, may reduce unnecessary verification turnaround time and cost in prenatal diagnosis.

Clinical Utility of the Prenatal BACs-on-Beads™ Assay in Invasive Prenatal Diagnosis

“…In a recent study comparing the detection performance of genome-wide copy-number analysis to PNBoBs ™ in prenatal diagnosis (Xu et al, 2020), 10 cases of ambiguous results and two cases of sex-chromosome mosaicism were classified as false negatives by PNBoBs ™ . However, comparable types of karyotypes were accurately detected using PNBoBs ™ in our study, which may be due to our improved data interpretation method for the PNBoBs ™ assay (Jiang et al, 2021); If this hypothesis holds, then the rate of diagnostic agreement between CNV-seq and PNBoBs ™ in Xu's study would be 99.8% (1,873/1,876), indicating that the performance of PNBoBs ™ may not be inferior to that of genome-wide copy number analysis, without distinguishing clinical indications. Moreover, unexpected findings and/or variants of unknown significance (VUS) identified by genome-wide CNV testing are still very challenging in terms of diagnostic assessment and genetic counseling (Durham et al, 2019).…”

“…Raw data generated by the instrument were analyzed using BoBsoft ™ software (version 1.1; PerkinElmer, Inc.). Results were interpreted using the optimization method described in our previous report (Jiang et al, 2021).…”