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Comparing Copy Number Variations and SNPs02:26

Comparing Copy Number Variations and SNPs

Sequencing of the human genome has opened up several best-kept secrets of the genome. Scientists have identified thousands of genome variations that exist within a population. These variations can be a single nucleotide or a larger chromosomal variation.
Copy number variations or CNVs are the structural variations that cover more than 1kb of DNA sequence. The single nucleotide polymorphism (SNP), on the other hand, is a single nucleotide change or a point mutation that is found in more than 1%...

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Reproducibility in Radiomics: A Comparison of Feature Extraction Methods and Two Independent Datasets.

Hannah Mary T Thomas1, Helen Y C Wang2,3, Amal Joseph Varghese1

  • 1Department of Radiation Oncology, Christian Medical College Vellore, Vellore 632004, Tamil Nadu, India.

Applied Sciences (Basel, Switzerland)
|May 10, 2024
PubMed
Summary
This summary is machine-generated.

This study evaluated the reproducibility of radiomics (radiology + omics) texture features between two software tools, MATLAB and Pyradiomics. It identified reproducible features crucial for reliable treatment stratification and outcome prediction in medical imaging.

Keywords:
CT imaginghead and neck cancerlung cancerradiomicsrepeatabilityreproducibilityvalidation

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Area of Science:

  • Medical Imaging Analysis
  • Radiomics Feature Reproducibility
  • Computational Pathology

Background:

  • Radiomics extracts quantitative imaging features for clinical applications.
  • Reproducibility of radiomics features across studies is a significant concern.
  • Standardized validation of feature extraction methods is essential for clinical translation.

Purpose of the Study:

  • To assess the reproducibility of CT texture features between MATLAB and Pyradiomics implementations.
  • To identify radiomics features that are reproducible across different datasets and software.
  • To validate a methodology for evaluating radiomics feature reproducibility.

Main Methods:

  • Comparison of 43 common radiomics features from MATLAB and Pyradiomics.
  • Utilized independent CT datasets (RIDER and HN1) with Gross Tumor Volume (GTV).
  • Calculated Spearman's rank correlation coefficient (rs) to assess feature rank ordering consistency.

Main Results:

  • 29 out of 43 features demonstrated high reproducibility (rs > 0.8) between MATLAB and Pyradiomics.
  • 18 features were common across lung and head and neck cancer datasets, suggesting potential site-agnostic utility.
  • The study validated a robust methodology for assessing radiomics reproducibility.

Conclusions:

  • A subset of radiomics features exhibits high reproducibility between common software tools.
  • Reproducibility is a critical criterion for selecting reliable radiomics features for clinical use.
  • The findings support the use of validated, reproducible radiomics features for treatment stratification and outcome prediction.