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Hopeful · 10-18-2006, 02:35 PM

I went searching on the web and found the abstract for Lani's article:

Research Article
Gene expression in 16q is associated with survival and differs between Sørlie breast cancer subtypes

Kristian Wennmalm 1 *, Stefano Calza 2, Alexander Ploner 2, Per Hall 2, Judith Bjöhle 1, Sigrid Klaar 1, Johanna Smeds 1, Yudi Pawitan 2, Jonas Bergh 11Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden
2Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
email: Kristian Wennmalm (Kristian.Wennmalm@cgb.ki.se)
*Correspondence to Kristian Wennmalm, Cancer Center Karolinska R 8:3, Karolinska Institutet and University Hospital, S-171 76 Stockholm, Sweden

setDOI("ADOI=10.1002/gcc.20392")Funded by:

Swedish Cancer Society

Research Funds at Radiumhemmet

The Swedish Research Council

AbstractWe have investigated the relationship between gene expression and chromosomal positions in 402 breast cancer patients. Using an overrepresentation approach based on Fisher's exact test, we identified disproportionate contributions of specific chromosomal positions to genes associated with survival. Our major finding is that the gene expression in the long arm of chromosome 16 stands out in its relationship to survival. This arm contributes 36 (18%) and 55 (11%) genes to lists negatively associated with recurrence-free survival (set to sizes 200 and 500). This is a highly disproportionate contribution from the 313 (2%) genes in this arm represented on the used Affymetrix U133A and B microarray platforms (Bonferroni corrected Fisher test: P < 2.2 × 10-16). We also demonstrate differential expression in 16q across tumor subtypes, which suggests that the ERBB2, basal, and luminal B tumors progress along a high grade-poor prognosis path, while luminal A and normal-like tumors progress along a low grade-good prognosis path, in accordance with a previously proposed model of tumor progression. We conclude that important biological information can be extracted from gene expression data in breast cancer by studying non-random connections between chromosomal positions and gene expression. This article contains Supplementary Material available at http://www.interscience.wiley.com/jp...5-2257/suppmat. © 2006 Wiley-Liss, Inc.Received: 9 June 2006; Accepted: 18 September 2006

Hope this helps - Hopeful

10-18-2006, 02:35 PM	#75
Hopeful Senior Member Join Date: Aug 2006 Posts: 3,380	The abstract is a little easier to digest I went searching on the web and found the abstract for Lani's article: Research Article Gene expression in 16q is associated with survival and differs between Sørlie breast cancer subtypes Kristian Wennmalm 1 , Stefano Calza 2, Alexander Ploner 2, Per Hall 2, Judith Bjöhle 1, Sigrid Klaar 1, Johanna Smeds 1, Yudi Pawitan 2, Jonas Bergh 11Department of Oncology and Pathology, Cancer Center Karolinska, Radiumhemmet, Karolinska Institutet and University Hospital, Stockholm, Sweden 2Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden email:* Kristian Wennmalm (Kristian.Wennmalm@cgb.ki.se) Correspondence to Kristian Wennmalm, Cancer Center Karolinska R 8:3, Karolinska Institutet and University Hospital, S-171 76 Stockholm, Sweden setDOI("ADOI=10.1002/gcc.20392")Funded by:* Swedish Cancer Society Research Funds at Radiumhemmet The Swedish Research Council AbstractWe have investigated the relationship between gene expression and chromosomal positions in 402 breast cancer patients. Using an overrepresentation approach based on Fisher's exact test, we identified disproportionate contributions of specific chromosomal positions to genes associated with survival. Our major finding is that the gene expression in the long arm of chromosome 16 stands out in its relationship to survival. This arm contributes 36 (18%) and 55 (11%) genes to lists negatively associated with recurrence-free survival (set to sizes 200 and 500). This is a highly disproportionate contribution from the 313 (2%) genes in this arm represented on the used Affymetrix U133A and B microarray platforms (Bonferroni corrected Fisher test: P < 2.2 × 10-16). We also demonstrate differential expression in 16q across tumor subtypes, which suggests that the ERBB2, basal, and luminal B tumors progress along a high grade-poor prognosis path, while luminal A and normal-like tumors progress along a low grade-good prognosis path, in accordance with a previously proposed model of tumor progression. We conclude that important biological information can be extracted from gene expression data in breast cancer by studying non-random connections between chromosomal positions and gene expression. This article contains Supplementary Material available at http://www.interscience.wiley.com/jp...5-2257/suppmat. © 2006 Wiley-Liss, Inc.Received: 9 June 2006; Accepted: 18 September 2006 Hope this helps - Hopeful