iSCORED: nanopore-based random genomic sampling for intraoperative molecular diagnosis

Abstract

Copy number variations (CNVs) are almost ubiquitous in cancer. In many cases, somatic CNV analysis has led to the identification of oncogenic pathways and suggested molecular-defined therapeutic targets. Here, we develop iSCORED, a one-step random genomic DNA reconstruction method that enables efficient, unbiased quantification of CNVs using a real-time Nanopore sequencer. By leveraging the long concatenated reads, we generate approximately 1-2 million genomic fragments within one hour of MinION sequencing, allowing for high-resolution genomic dosage comparisons. In our cohort of 26 malignant brain tumors, we demonstrated 100% concordance in CNV detections, including chromosomal alterations and oncogene amplifications when compared to clinically validated next generation sequencing and chromosomal microarray results. In addition, iSCORED allows concurrent brain tumor methylation classification without additional tissue preparation. The integrated methylation information revealed promoter hypomethylation in all detected amplified oncogenes. The entire workflow, including the automatic generation of CNV and methylation reports, can be accomplished within 120-140 minutes. Ultrafast molecular analysis can enhance clinical decision-making, optimize surgical planning and identify potential molecular therapies within surgical timeframes.