http://dx.doi.org/10.1186/1479-7364-5-1-5">
 

Document Type

Journal Article

Department/Unit

Department of Mathematics

Title

Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis

Language

English

Abstract

© 2010 Henry Stewart Publications. Breast cancer tumours among African Americans are usually more aggressive than those found in Caucasian populations. African-American patients with breast cancer also have higher mortality rates than Caucasian women. A better understanding of the disease aetiology of these breast cancers can help to improve and develop new methods for cancer prevention, diagnosis and treatment. The main goal of this project was to identify genes that help differentiate between oestrogen receptor-positive and -negative samples among a small group of African-American patients with breast cancer. Breast cancer microarrays from one of the largest genomic consortiums were analysed using 13 African-American and 201 Caucasian samples with oestrogen receptor status. We used a shrinkage-based classification method to identify genes that were informative in discriminating between oestrogen receptor-positive and -negative samples. Subset analysis and permutation were performed to obtain a set of genes unique to the African-American population. We identified a set of 156 probe sets, which gave a misclassification rate of 0.16 in distinguishing between oestrogen receptor-positive and -negative patients. The biological relevance of our findings was explored through literature-mining techniques and pathway mapping. An independent dataset was used to validate our findings and we found that the top ten genes mapped onto this dataset gave a misclassification rate of 0.15. The described method allows us best to utilise the information available from small sample size microarray data in the context of ethnic minorities.

Keywords

African Americans, breast cancer, discriminant analysis, health disparities, microarrays, oestrogen receptor

Publication Date

2010

Source Publication Title

Human Genomics

Volume

5

Start Page

5

End Page

16

Publisher

BioMed Central

ISSN (print)

14739542

ISSN (electronic)

14797364

This document is currently not available here.

Share

COinS