Summary

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Starting or Joining a Research Project

We are currently hosting calls in support of TCGA-BRCA research projects on Wednesdays at 4pm Eastern. Please contact us at cancerimagingarchive@mail.nih.gov if you would like to inquire about setting up a new research project, discuss potential collaborations with existing groups or be otherwise kept in the loop as this effort moves forward.

Group Projects

This is a listing of ongoing projects.  If you are working with the TCGA-BRCA data hosted on TCIA please let us know and we would be happy to add a section describing your project here.

• Breast Image Feature Scoring Project - This project is in the preliminary stages and is being collaborated on by group members from MSKCC, MDACC, Roswell Park, and UPMC.  Multiple readers are evaluating each subject's imaging features using a BIRADS inspired Breast Feature Key and then investigating potential correlations with the TCGA genomic and clinical data.  This project is being led by Liz Morris of MSKCC.
• Mapping of Multi-modality Breast Image-based Phenotypes to Histopathology and Genomics – This project seeks to advance and relate quantitative, computer-extracted tumor and parenchymal characteristics from multi-modality breast images (e.g, mammography, ultrasound, and MRI) to clinical outcomes (diagnosis, staging, and response to therapy), histopathology, and genomics.  This project is led by Maryellen Giger (University of Chicago), and TBN others.  The quantitative output from this project feeds other projects such as the Breast Image Feature Scoring Project.
• Correlating computer-extracted MRI features with clinical and genomic data - In this project, features are extracted from breast MR images using computer vision algorithms. These features are then correlated with clinical and genomic information. This project is being led by Maciej Mazurowski from Duke University.
• Clustering (supervised & unsupervised) of BRCA Data - Cases are clustered into semantically-distinct categories using image-derived features, followed by examination of genomic correlates from the obtained clusters.  This project is being led by Arvind Rao and Gary Whitman of MDACC.

Publications

There are currently no imaging based publications for TCGA-BRCA. However, the following links contain publications from the main TCGA project, as well as their posted publication guidelines.

Imaging Source Site (ISS) Groups are being formed and governed by participants from institutions that have provided imaging data to the archive for a given cancer type. Modeled after TCGA analysis groups, ISS groups are given the opportunity to publish a marker paper for a given cancer type per the guidelines in the table above. This opportunity will generate increased participation in building these multi-institutional data sets as they become an open community resource. Current (TCGA-BRCA) The Cancer Genome Atlas Breast Invasive Carcinoma Collection source sites include:

• Mayo Clinic
• Roswell Park Cancer Institute
• MemorialSloan-KetteringCancerCenter
• University of Pittsburgh/UPMC
• University of Miami Health System

The ISS group has also been collaborating with the University of Chicago to conduct quantitative MRI phenotyping efforts.  Please contact Dr. Elizabeth Morris (morrise@mskcc.org) if you have scientific questions for TCGA-BRCA ISS or are interested in collaborating with their group.

Publications

TCGA Breast Phenotype Research Group Publications

• Guo W, Li H, Zhu Y, Lan L, Yang S, Drukker K, Morris E, Burnside E, Whitman G, Giger ML*, Ji Y*:  Prediction of clinical phenotypes in invasive breast carcinomas from the integration of radiomics and genomics data.  J Medical Imaging 2(4), 041007 (Oct-Dec 2015).
• Burnside E, Drukker K, Li H, Bonaccio E, Zuley M, Ganott M, Net JM, Sutton E, Brandt K, Whitman G, Conzen S, Lan L, Ji Y, Zhu Y, Jaffe C, Huang E, Freymann J, Kirby J, Morris EA*, Giger ML*:  Using computer-extracted image phenotypes from tumors on breast MRI to predict breast cancer pathologic stage. Cancer doi: 10.1002/cncr.29791, 2015.
• Zhu Y, Li H, Guo W, Drukker K, Lan L, Giger ML*, Ji Y*:  Deciphering genomic underpinnings of quantitative MRI-based radiomic phenotypes of invasive breast carcinoma.  Nature – Scientific Reports 5:17787. doi: 10.1038/srep17787, 2015.
• Li H, Zhu Y, Burnside ES, …. Perou CM, Ji Y*, Giger ML*:  MRI radiomics signatures for predicting the risk of breast cancer recurrence as given by research versions of gene assays of MammaPrint, Oncotype DX, and PAM50.  Radiology DOI: http://dx.doi.org/10.1148/radiol.2016152110, 2016.
• Li H, Zhu Y, Burnside ES, …. Perou CM, Ji Y, Giger ML:  Quantitative MRI radiomics in the prediction of molecular classifications of breast cancer subtypes in the TCGA/TCIA Dataset. npj Breast Cancer (2016) 2, 16012; doi:10.1038/npjbcancer.2016.12; published online 11 May 2016.

Publications written by other members of the research community can be found on our TCIA Publications page.  If you have a manuscript you’d like to add please contact TCIA’s Helpdesk.

TCGA Genomics Publications

 Read the Cell paper about the TCGA-BRCA genomic study.  Additional TCGA publications can be found at: http://cancergenome.nih.gov/publications.

Publication Policies

Per TCGA and TCIA Guidelines, formal permission requests are no longer required to submit publications using TCGA-BRCA data.  Please see the following links for more information about the freedom-to-publish criteria for these data sets:

Please contact us at help@cancerimagingarchive.net if you have any questions about these policies.

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