Retrospective Breast Cancer Genomics Analysis

We performed an observational retrospective cohort analysis of women with breast cancer with publicly available clinical and primary tumor mRNA expression and mutation data from the METABRIC study. Data was retrieved using the cBioPortal implementation in R, package CGDS-R [25 (link), 26 (link), 70 (link)]. The METABRIC study included over 2,000 fresh-frozen breast cancer specimens and a subset of normal breast tissue from tumor banks in the UK and Canada. The METABRIC study reported 2,136 primary tumors with expression array (Affymetrix U133A microarray) data and 2,433 primary tumors with somatic mutation testing by sequencing for 173 genes. We also analyzed RNA sequencing data for mRNA expression from 1,100 primary breast cancer tumors from The Cancer Genome Atlas (TCGA) to validate our results for differentially expressed genes from the METABRIC study [27 (link)].

Free full text: Click here

Ann P., Seagle B.L., Shilpi A., Kandpal M, & Shahabi S. (2018). Association of increased primary breast tumor AGR2 with decreased disease-specific survival. Oncotarget, 9(33), 23114-23125.

Publication 2018

U133A microarray

Breast Breast cancer 2 Breast primary cancer Cgds Frozen Genes Genome Microarray Mrna Mutation Normal tissue Somatic Tumors Women

Corresponding Organization : Northwestern University

Top 5 similar protocols

Variable analysis

independent variables

Not explicitly mentioned

dependent variables

Breast cancer primary tumor mRNA expression
Breast cancer primary tumor somatic mutations

control variables

Not explicitly mentioned

controls

RNA sequencing data for mRNA expression from 1,100 primary breast cancer tumors from The Cancer Genome Atlas (TCGA) to validate results for differentially expressed genes from the METABRIC study
None specified

Annotations

Based on most similar protocols

Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.

As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.

About PubCompare

Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.

We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.

However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.

Ready to get started?

Revolutionizing how scientists
search and build protocols!