76. Goals, methods and challenges in a clinical validation of a NGS-based platform for the detection of constitutional CNVs

Abstract

<h3>Background</h3> DNA microarrays are used in our institution since 2011 to evaluate copy number variants (CNVs) in both constitutional (prenatal and postnatal) and oncology applications. We are currently validating a NGS-based platform from the company OGT to replace our arrays in constitutional applications. <h3>Objectives</h3> In accordance with the 2013′s ACMG technical guidelines for constitutional cytogenomic microarray, our analysis evaluates separately, postnatal (blood) and prenatal (amniotic fluid, chorionic villi, fetal skin) specimens. Specifically for the prenatal, we will compare the results obtained from both uncultured and cultured specimens in a subset of patients. <h3>Design/ Method</h3> Minimally, 30 patients with CNVs observed on the array, are ran on the NGS platform to determine the clinical correlation, clinical sensitivity, and positive predictive values. Two patients are prepared three-times in successive library preparations to assess repeatability. Four patients with mosaics ranging between 15% and 60% are also assessed. <h3>Results</h3> Up to now, 24 postnatal patients containing 22 different CNVs, have been analyzed. While 95% expected CNVs have been observed with the NGS approach, we've been able to detect new CNVs: six (6) out-of-frame duplications and nine (9) exonic deletions (containing 1 to 3 exons). We are in the process of confirming these new CNVs. <h3>Conclusions</h3> We are pursuing our validation and expecting to conclude it by April 2022, so that final data will be presented at the meeting.