Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis
<p>Abstract</p> <p>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 aetiolog...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2010-10-01
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| Series: | Human Genomics |
| Subjects: | |
| Online Access: | http://www.humgenomics.com/content/5/1/5 |
| _version_ | 1798041576259190784 |
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| author | Pang Herbert Ebisu Keita Watanabe Emi Sue Laura Y Tong Tiejun |
| author_facet | Pang Herbert Ebisu Keita Watanabe Emi Sue Laura Y Tong Tiejun |
| author_sort | Pang Herbert |
| collection | DOAJ |
| description | <p>Abstract</p> <p>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.</p> |
| first_indexed | 2024-04-11T22:24:14Z |
| format | Article |
| id | doaj.art-1cd0b73e7a5d47c3ab8321e03ed5b448 |
| institution | Directory Open Access Journal |
| issn | 1479-7364 |
| language | English |
| last_indexed | 2024-04-11T22:24:14Z |
| publishDate | 2010-10-01 |
| publisher | BMC |
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| series | Human Genomics |
| spelling | doaj.art-1cd0b73e7a5d47c3ab8321e03ed5b4482022-12-22T03:59:53ZengBMCHuman Genomics1479-73642010-10-015151610.1186/1479-7364-5-1-5Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysisPang HerbertEbisu KeitaWatanabe EmiSue Laura YTong Tiejun<p>Abstract</p> <p>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.</p>http://www.humgenomics.com/content/5/1/5African Americansbreast cancerdiscriminant analysisoestrogen receptorhealth disparitiesmicroarrays |
| spellingShingle | Pang Herbert Ebisu Keita Watanabe Emi Sue Laura Y Tong Tiejun Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis Human Genomics African Americans breast cancer discriminant analysis oestrogen receptor health disparities microarrays |
| title | Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis |
| title_full | Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis |
| title_fullStr | Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis |
| title_full_unstemmed | Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis |
| title_short | Analysing breast cancer microarrays from African Americans using shrinkage-based discriminant analysis |
| title_sort | analysing breast cancer microarrays from african americans using shrinkage based discriminant analysis |
| topic | African Americans breast cancer discriminant analysis oestrogen receptor health disparities microarrays |
| url | http://www.humgenomics.com/content/5/1/5 |
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