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A consensus prognostic gene expression classifier for ER positive breast cancer

Andrew E Teschendorff*, Ali Naderi, Nuno L Barbosa-Morais, Sarah E Pinder, Ian O Ellis, Sam Aparicio, James D Brenton and Carlos Caldas*

Genome Biology 2006, 7:R101  doi:10.1186/gb-2006-7-10-r101

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Why Sotiriou2006 did not use Wang et al dataset

Pratyaksha Wirapati   (2006-11-17 10:42)  Swiss Institute of Bioinformatics email

The authors wrote in the discussion:

"Intriguingly though, the grade-derived signature was not validated in a large available cohort [11], raising doubts as to its wider applicability."

The grade signature was not applied to Wang et al. cohort in the Sotirou 2006 paper because histologic grade data were not publicly available , and therefore the cohort can not be used to answer our main question. That is, figure 2 of Sotiriou et al. can not be produced without histologic grade information.

The grade-index can be applied to this cohort, with hazard ratio 2.53 (1.62-3.94), under the cutoff that gives the same ratio of "poor" and "good" prognostic groups as that in figure 3b of this commented paper (Teschendorff et al.), in order to make the hazard ratios comparable. The HR above is similar to the one reported in figure 3b (2.38 [1.38-3.69]). Note that we use all 209 ER+ patients, while figure 3b of Teschendorff et al. only used 144 patients.

Competing interests

Co-author of Sotiriou et al 2006 J Natl. Cancer Inst.

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