Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Concept Videos

Modern Molecular Taxonomy01:29

Modern Molecular Taxonomy

861
Advancements in molecular biology have revolutionized the identification and characterization of bacteria, with multiple methods leveraging DNA sequencing for enhanced precision. As sequencing technologies improve and costs decline, these approaches are increasingly used in clinical, environmental, and evolutionary studies.Multilocus Sequence Typing (MLST) examines several housekeeping genes, essential chromosomal genes encoding cellular functions, to distinguish strains. Approximately...
861

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Cell Cycle Sensing Shapes Human T Cell Fate and Exhaustion Programs.

bioRxiv : the preprint server for biology·2026
Same author

Wavelet Decomposition-Based Genomic Analysis of the Human Electrocardiogram.

medRxiv : the preprint server for health sciences·2026
Same author

Structure-preserving multivariate hypothesis testing for mass spectrometry imaging and single-cell data.

Bioinformatics (Oxford, England)·2026
Same author

Temporal and spatial composition of the tumor microenvironment predicts response to immune checkpoint inhibition in metastatic TNBC.

Nature cancer·2026
Same author

Prognostic pan-cancer and single-cancer models: A large-scale analysis using a real-world clinico-genomic database.

PloS one·2026
Same author

Glaucoma Classification Through SSVEP-Derived ON- and OFF-Pathway Features.

Translational vision science & technology·2026

Related Experiment Video

Updated: Apr 15, 2026

Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
11:12

Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material

Published on: August 1, 2018

8.5K

Molecular subtyping for clinically defined breast cancer subgroups.

Xi Zhao, Einar Andreas Rødland, Robert Tibshirani

    Breast Cancer Research : BCR
    |April 8, 2015
    PubMed
    Summary

    A new subgroup-specific gene centering method improves breast cancer molecular subtyping accuracy, especially in cohorts with skewed characteristics. This approach enhances classification performance compared to standard gene centering for better clinical application.

    More Related Videos

    Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
    07:41

    Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases

    Published on: May 17, 2019

    9.7K
    High-Throughput Dissociation and Orthotopic Implantation of Breast Cancer Patient-Derived Xenografts
    06:06

    High-Throughput Dissociation and Orthotopic Implantation of Breast Cancer Patient-Derived Xenografts

    Published on: December 20, 2024

    1.4K

    Related Experiment Videos

    Last Updated: Apr 15, 2026

    Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material
    11:12

    Optimization of a Multiplex RNA-based Expression Assay Using Breast Cancer Archival Material

    Published on: August 1, 2018

    8.5K
    Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases
    07:41

    Performing Data Mining And Integrative Analysis Of Biomarker in Breast Cancer Using Multiple Publicly Accessible Databases

    Published on: May 17, 2019

    9.7K
    High-Throughput Dissociation and Orthotopic Implantation of Breast Cancer Patient-Derived Xenografts
    06:06

    High-Throughput Dissociation and Orthotopic Implantation of Breast Cancer Patient-Derived Xenografts

    Published on: December 20, 2024

    1.4K

    Area of Science:

    • Genomics and Molecular Biology
    • Oncology
    • Bioinformatics

    Background:

    • Breast cancer classification into intrinsic molecular subtypes is crucial for treatment.
    • Standard gene centering for subtyping can be inaccurate when study cohort characteristics differ from training data.
    • This discrepancy can lead to misclassification of breast cancer subtypes.

    Purpose of the Study:

    • To develop and evaluate a subgroup-specific gene-centering method for accurate molecular subtyping.
    • To address challenges in classifying breast cancer subtypes in cohorts with skewed clinicopathological distributions.
    • To improve the reliability of molecular subtyping classifiers like PAM50.

    Main Methods:

    • Proposed a subgroup-specific gene-centering technique, centering genes on a percentile derived from similar subgroups in the training cohort.
    • Applied the method to the PAM50 classifier and UNC training cohort.
    • Validated on study cohorts with skewed characteristics, including prototypic subtypes, ER-positive, and triple-negative external cohorts.

    Main Results:

    • Subgroup-specific gene centering significantly improved prediction accuracy (77–100%) compared to standard centering (17–33%) on prototypic subsets.
    • Reduced classification error rates for ER-positive (11% vs. 28%), ER-negative (5% vs. 41%), and triple-negative (11% vs. 56%) subgroups.
    • Increased accuracy for mixed ER-positive/ER-negative cohorts and improved subtype assignment for external ER-positive and triple-negative cohorts.

    Conclusions:

    • Subgroup-specific gene centering provides more accurate molecular subtype assignments than standard methods for skewed cohorts.
    • This refined method enhances the clinical utility of molecular subtyping classifiers.
    • Accurate subtyping is essential for effective breast cancer diagnosis and treatment strategies.