Quantitative nuclear histomorphometry predicts oncotype DX risk categories for early stage ER+ breast cancer.

BMC Cancer
Jon WhitneyAnant Madabhushi

Abstract

Gene-expression companion diagnostic tests, such as the Oncotype DX test, assess the risk of early stage Estrogen receptor (ER) positive (+) breast cancers, and guide clinicians in the decision of whether or not to use chemotherapy. However, these tests are typically expensive, time consuming, and tissue-destructive. In this paper, we evaluate the ability of computer-extracted nuclear morphology features from routine hematoxylin and eosin (H&E) stained images of 178 early stage ER+ breast cancer patients to predict corresponding risk categories derived using the Oncotype DX test. A total of 216 features corresponding to the nuclear shape and architecture categories from each of the pathologic images were extracted and four feature selection schemes: Ranksum, Principal Component Analysis with Variable Importance on Projection (PCA-VIP), Maximum-Relevance, Minimum Redundancy Mutual Information Difference (MRMR MID), and Maximum-Relevance, Minimum Redundancy - Mutual Information Quotient (MRMR MIQ), were employed to identify the most discriminating features. These features were employed to train 4 machine learning classifiers: Random Forest, Neural Network, Support Vector Machine, and Linear Discriminant Analysis, via 3-fold cross...Continue Reading

References

Jul 15, 2000·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·C B BrezdenI F Tannock
Jan 6, 2001·The American Journal of Pathology·D GisselssonN Mandahl
Nov 19, 2004·Nature·Neil A BhowmickHarold L Moses
Dec 14, 2004·The New England Journal of Medicine·Soonmyung PaikNorman Wolmark
Apr 27, 2005·Journal of Bioinformatics and Computational Biology·Chris Ding, Hanchuan Peng
Aug 27, 2005·IEEE Transactions on Pattern Analysis and Machine Intelligence·Hanchuan PengChris Ding
May 25, 2006·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Soonmyung PaikNorman Wolmark
Oct 14, 2006·Breast Cancer Research and Treatment·Lida MinaKathy D Miller
Jan 25, 2007·Breast Cancer : the Journal of the Japanese Breast Cancer Society·Shozo OhsumiHirohisa Imai
Feb 9, 2008·Journal of Clinical Oncology : Official Journal of the American Society of Clinical Oncology·Joseph A Sparano, Soonmyung Paik
Mar 25, 2008·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Melina B FlanaganRohit Bhargava
May 17, 2008·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Ben S WittnerSridhar Ramaswamy
Sep 15, 2010·Clinical Cancer Research : an Official Journal of the American Association for Cancer Research·Torsten O NielsenMatthew J Ellis
Nov 11, 2011·Science Translational Medicine·Andrew H BeckDaphne Koller
Feb 9, 2013·IEEE Transactions on Bio-medical Engineering·Ajay BasavanhallyAnant Madabhushi
Mar 19, 2013·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Molly E KleinRohit Bhargava
Oct 3, 2014·International Journal of Cancer. Journal International Du Cancer·Balázs GyőrffyLajos Pusztai
May 2, 2015·Modern Pathology : an Official Journal of the United States and Canadian Academy of Pathology, Inc·Bradley M TurnerDavid G Hicks
Sep 29, 2015·The New England Journal of Medicine·Joseph A SparanoGeorge W Sledge
May 1, 2016·Journal of the National Cancer Institute·John M S BartlettUNKNOWN OPTIMA TMG
Aug 27, 2016·Journal of Pathology Informatics·Andrew Janowczyk, Anant Madabhushi
Feb 14, 2017·Cytometry. Part a : the Journal of the International Society for Analytical Cytology·David Romo-BucheliAnant Madabhushi

❮ Previous
Next ❯

Citations

Mar 11, 2020·JCO Clinical Cancer Informatics·Yijiang ChenAnant Madabhushi
Jun 9, 2019·Nature Biomedical Engineering·Spyridon Bakas, Michael D Feldman
Aug 5, 2020·Nature Communications·Benoît SchmauchGilles Wainrib
Aug 11, 2019·Nature Reviews. Clinical Oncology·Kaustav BeraAnant Madabhushi
May 21, 2020·Frontiers in Oncology·Martin LiptaySven Rottenberg
Aug 25, 2020·Kidney International·Catherine P JayapandianUNKNOWN Nephrotic Syndrome Study Network (NEPTUNE)
Jan 15, 2020·The Breast : Official Journal of the European Society of Mastology·Asmaa IbrahimEmad A Rakha
Jul 22, 2021·The Journal of Pathology. Clinical Research·Runtian MiaoAndrew Janowczyk

❮ Previous
Next ❯

Methods Mentioned

BETA
biopsy
feature extraction

Software Mentioned

VIP
MID
CUDA
PCA
MIQ
Caffe
MRMR

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.