One for all at the Medical Genetics lab | LC26

Abstract
Short-read (SR) next-generation sequencing (NGS) is widely used but it has limitations in the analysis of structural variants (SVs) and repetitive regions. Together with the Pavia group, we compared the performance of Oxford Nanopore (ONT) sequencing with SR-NGS. In over 200 research samples, we found that Oxford Nanopore data matched short-read data for the detection of pathogenic variants (such as single nucleotide variants [SNVs]) and resolved previously undetected complex variants (such as SVs and short tandem repeats [STRs]). We wanted to expand this exercise using whole-genome sequencing (WGS) on the PromethION 24 device on an additional 200 cases. We have demonstrated that this device can replace all the techniques of a medical genetics laboratory from SR-NGS, to array comparative genomic hybridisation (aCGH) and multiplex ligation-dependent probe amplification (MLPA). The increased yield on undiagnosed cases was about 40%. Furthermore, even in cases already diagnosed (with SNV), a second pathogenic variant (of the SV or STR type) was detected in approximately 30% of cases, completing the diagnosis. Similarly, in cases diagnosed by aCGH (with copy number variants [CNV]), a second diagnosis was detected in approximately 30% of cases, sometimes more important than the first for patient management. From all the above, it emerges that making a prenatal, presymptomatic, or predictive diagnosis with the implementation of personalized preventive measures, based solely on SNVs (NGS) or solely on CNVs (aCGH), or both (at double the cost), renders the genetic diagnosis incomplete, leading to inaccurate conclusions by the clinical geneticist and even reaching the point of prognostic and therapeutic diagnostic errors.

Biography
Alessandra Renieri was born in 1965 and graduated in Medicine in 1989 at the University of Siena. She has a PhD in Human Genetics and an MS in Medical Genetics. She is currently Full Professor of Medical Genetics at the School of Medicine at the University of Siena and Director of the Medical Genetics Unit at the General Hospital of Siena.