Third-generation cytogenetic analysis

Biography

Alberto Magi is Associate Professor of Bioengineering at the University of Florence. His research activities have primarily focused on computational genomics. Over the past 15 years, Alberto has developed numerous algorithms and software tools leveraging high-throughput sequencing data to study human genetic variability and cancer genomes.

Abstract

Copy number variants (CNVs) play important roles in the pathogenesis of several genetic syndromes. Traditional and molecular karyotyping are considered the first-tier diagnostic tests to detect macroscopic and cryptic deletions/duplications. However, their time-consuming and laborious experimental protocols protract diagnostic times from 3 to 15 days. Nanopore sequencing has the ability to reduce time to results for the detection of CNVs with the same resolution as current state-of-the-art diagnostic tests. To fully leverage the potential of nanopore sequencing technology, we developed a novel computational framework that is capable of exploiting nanopore sequencing data as it is being generated. This method enables the identification of CNVs in real time, significantly accelerating the diagnostic process while maintaining high accuracy and reliability. Our approach offers a transformative step in clinical genomics by combining the speed of nanopore sequencing with robust computational tools tailored for CNV detection. Our novel approach was compared to molecular karyotyping for the detection of pathogenic CNVs in several samples with previously diagnosed causative CNVs of different sizes and cellular fractions. Larger chromosomal anomalies included trisomy and monosomy, while among smaller CNVs we used samples with genomic imbalances around one megabase and smaller alterations of hundreds of kilobases. We also tested samples with mosaic deletions and duplications. DNA was sequenced and data generated during runs were analyzed in online mode. All pathogenic CNVs were identified with detection time inversely proportional to size and cellular fraction. Aneuploidies were called after only 30 minutes of sequencing, whereas 30 hours were needed to call small CNVs. These results demonstrate the clinical utility of our approach that allows the molecular diagnosis of genomic disorders within a 30-minute to 30-hour time frame and its easy implementation as a routinary diagnostic tool.