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Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies
Published on: April 11, 2016
11.8K
Nanopore-based random genomic sampling for intraoperative molecular diagnosis.
Francesco E Emiliani1,2, Abdol Aziz Ould Ismail1, Edward G Hughes1
1Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, 03756, USA.
Genome Medicine
|January 20, 2025
Summary
iSCORED enables rapid, high-resolution copy number variation (CNV) detection and methylation classification for brain tumors. This integrated approach improves intraoperative diagnosis and surgical planning for improved patient outcomes.
Area of Science:
- Neuro-oncology
- Genomics
- Molecular Diagnostics
Background:
- Central nervous system tumors are highly lethal, necessitating accurate preoperative and intraoperative diagnosis for effective surgical resection.
- Current intraoperative diagnostic methods, including methylation classification, can be limited by low tumor purity and challenging morphology-based assessments.
- Copy number variations (CNVs) are sensitive molecular biomarkers that offer insights into oncogenic pathways and potential therapeutic targets.
Purpose of the Study:
- To develop and validate iSCORED, a novel method for rapid, high-resolution genome-wide copy number variation (CNV) quantification.
- To integrate CNV detection with methylation profiling for a comprehensive intraoperative brain tumor diagnostic approach.
- To assess the accuracy and efficiency of iSCORED in comparison to established diagnostic techniques.
Main Methods:
- iSCORED utilizes a one-step random genomic DNA reconstruction method to concatenate genomic fragments into long reads for low-pass sequencing.
- The method achieves ultrafast (1-hour) high-resolution (50 kb) CNV analysis by generating approximately 1-2 million genomic fragments.
- Concurrent methylation profiling is performed to enable brain tumor classification and identify promoter methylation in amplified oncogenes.
Main Results:
- iSCORED demonstrated 100% concordance with Next-Generation Sequencing and Chromosomal Microarray for CNV detection in a retrospective cohort of 26 malignant brain tumors.
- Real-time validation in 15 challenging primary brain tumors showed 100% concordance in aberrant CNV detection, including gains/losses and oncogene amplifications.
- The complete workflow, from tissue arrival to report generation, was completed within 105 minutes, with 14 out of 15 methylation classifications aligning with final pathological diagnoses.
Conclusions:
- iSCORED is the first method providing high-resolution CNV detection within the intraoperative timeframe.
- The integrated CNV detection and methylation classification offers a rapid and comprehensive molecular diagnostic tool for intraoperative decision-making.
- This approach enhances diagnostic accuracy, optimizes surgical planning, and identifies potential molecular therapies during surgery.
