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Evolution of deletion/duplication calling in the era of clinical next-generation sequencing

Steve Lincoln, Bioinformatics at Invitae
September 09, 2014
Series: Leading with Science
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Compared to traditional approaches, next-generation sequencing (NGS) can simultaneously reduce the cost and increase the breadth of DNA assays, thus helping to make clinical genetic testing more accessible and more comprehensive. NGS was first introduced in 2005, and while it initially had limited performance and uses, continuous innovation has delivered robust NGS platforms that are widely accepted for clinical use.

NGS is most often used to detect relatively small DNA sequence alterations; however, NGS-based methods to detect larger deletions and duplications (del/dup events) were first published in 2009. Like NGS generally, these methods have evolved rapidly, and the most recent versions allow appropriately equipped laboratories to deliver high-quality results for both small and large DNA alterations from a single NGS assay.

In this seminar, we will briefly review approaches used for del/dup calling using NGS. We will focus on clinical data from our laboratory, which shows high concordance between our NGS-based approach and traditional del/dup test results. We also will illustrate cases in which the combination of NGS-based sequence and del/dup analysis resolves complex events that can be challenging for traditional approaches.