Streamlined glioma diagnosis from FFPE tissue: one assay, lower cost, and faster turnaround time | LC 25

Biography

Mashiat Mimosa is a PhD student in the Department of Laboratory Medicine and Pathobiology at the University of Toronto in Canada, under the supervision of Dr Rola Saleeb and Dr Ramzi Fattouh. She earned her BSc (Honours) in Neuroscience and Molecular Biology, Immunology, and Disease from the University of Toronto, where she developed a deep interest in genomics and oncology.

Mashiat’s PhD research focuses on developing novel brain cancer diagnostic and classification tests to improve the lives of cancer patients.

Abstract

We developed a single diagnostic assay to detect glioma biomarkers, including chromosomal and gene copy number variations (CNVs) and single nucleotide variations (SNVs). CNVs and SNVs are traditionally tested using different large platforms in large genomic facilities creating delays in testing and increasing cost. To streamline glioma diagnosis and address these challenges, we used nanopore sequencing with a PCR-based assay to create clean, nanopore-compatible formalin-fixed paraffin-embedded (FFPE) DNA copies. We adapted a single-nucleotide polymorphism (SNP) microarray-based approach that uses nanopore sequencing to detect the CNVs. We also optimized the testing conditions and reduced cost and turn-around, including streamlining the data analysis using custom shell script. Lastly, we conducted a mini validation with a cost and turnaround time analysis using 40 glioma FFPE samples. All our samples had a concordant molecular classification status with the reference results. A loss status was determined via a loss of heterozygosity (LOH), and gain status was observed as a 2:1 allele frequency pattern. Our total turnaround time (from DNA extraction to data analysis) was three business days for an entire batch of samples, which is at least one third of the turnaround time of conventional methods. Our material cost was approximately $200 CAD/sample (from DNA extraction to sequencing), which was approximately 10% of the existing assay costs. This is the first single streamlined diagnostic test to detect CNVs and SNVs in gliomas using FFPE DNA. Our assay will increase healthcare equity by allowing smaller laboratories to adopt molecular testing due to its low assay/capital cost, shorter testing time, and streamlined workflow.