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2023 ACMG Annual Clinical Genetics Meeting Digital ...
Integrated Analysis of Cell-Free DNA for the Detec ...
Integrated Analysis of Cell-Free DNA for the Detection of Malignant Peripheral Nerve Sheath Tumors in Patients with Neurofibromatosis Type 1
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Pdf Summary
In this study, the researchers aimed to develop a way to detect malignant peripheral nerve sheath tumors (MPNST) in patients with Neurofibromatosis Type I (NF1) using cell-free DNA (cfDNA) analysis. They used a variety of fragmentomic features and machine learning classification techniques to analyze cfDNA samples from healthy controls, NF1 patients with plexiform neurofibromas, and NF1 patients with MPNST.<br /><br />The researchers found that NF1 patients had differential nucleosome footprints, which were further dysregulated in patients with MPNST. They also observed that patients with MPNST released shorter cfDNA fragments, while NF1 patients had increased release of di-nucleosome cfDNA fragments. This difference in fragment sizes allowed for the classification of healthy patients, patients with plexiform neurofibromas, and patients with MPNST.<br /><br />Moreover, the researchers developed a machine learning classifier that could robustly classify samples based on fragmentomic features. They applied this classifier to a validation cohort and found that it could accurately distinguish between samples from healthy patients, patients with plexiform neurofibromas, and patients with MPNST.<br /><br />The study also discussed future directions, including the development of a deep learning method for scoring plasma mutations, integration of genome-wide mutation data with fragmentation data, and follow-up studies on patients with plexiform neurofibromas for the development of MPNST.<br /><br />Overall, this study demonstrated the potential of using cfDNA analysis and fragmentomic features for the detection and classification of malignant peripheral nerve sheath tumors in patients with Neurofibromatosis Type I. The findings provide valuable insights for further research and potential clinical applications in the future.<br /><br />The study was supported by various grants and fellowships, and the researchers expressed their gratitude to the patients who participated in the study and donated their time, tissue, and plasma. The sequencing and analysis of the samples were performed by skilled technicians, and the analysis pipelines and discussions were contributed to by members of the research team.
Asset Subtitle
Presenting Author - Derek Wong, PhD; Co-Author - Ping Luo, PhD; Co-Author - Stephanie Pederson, BSc; Co-Author - Clarissa Chan, MSc; Co-Author - Kirsten M. Farncombe, PhD; Co-Author - Maia Norman, BSc; Co-Author - Leslie E. Oldfield, MSc; Co-Author - Raymond H. Kim, MD; Co-Author - Trevor J. Pugh, PhD;
Meta Tag
Bioinformatics
Cancer Syndromes
Cell free DNA/cfDNA
Genome sequencing
Genomic Methodologies
NextGen Sequencing
Oncogenesis
Co-Author
Ping Luo, PhD
Co-Author
Stephanie Pederson, BSc
Co-Author
Clarissa Chan, MSc
Co-Author
Kirsten M. Farncombe, PhD
Co-Author
Maia Norman, BSc
Co-Author
Leslie E. Oldfield, MSc
Co-Author
Raymond H. Kim, MD
Co-Author
Trevor J. Pugh, PhD
Presenting Author
Derek Wong, PhD
Keywords
malignant peripheral nerve sheath tumors
MPNST
Neurofibromatosis Type I
cell-free DNA analysis
fragmentomic features
machine learning classification
cfDNA samples
plexiform neurofibromas
nucleosome footprints
fragment sizes
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