Computational protocol: 17β-Hydroxysteroid dehydrogenases involved in local oestrogen synthesis have prognostic significance in breast cancer

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Protocol publication

[…] We used the computer software Primer Express (PE Applied Biosystems, Foster City, CA, USA) to design primers and probes that recognised human 17β-HSD types 1 and 2 cDNA sequences. We conducted Blast searches (GenBank) to confirm the specificity of nucleotide sequences chosen for the primers and probes and the absence of DNA polymorphism. To avoid detection of contaminating genomic DNA, the probe was placed in the junction between two exons. The primer and probe sequences were; 17HSD type 1: forward primer: 5′-TAT GCG AGA GTC TGG CGG TT-3′, reverse primer: 5′-TGC ACT GGG CCG CAC T-3′, probe: 5′-CGA TCA GGC TCA AGT GGA CCC CAA-3′; 17HSD type 2: forward primer: 5′-TTA CCT GTG GAT CAG AAG GCA GT-3′, reverse primer: 5′-TTG CAC AAA GCA TGG CCA-3′, probe: 5′-CCC GCA ATC ACC ACC TGT CAC CA-3′. Both primers and probes were purchased from PE Applied Biosystems, as were the primers and probes for β-actin, which was used as endogenous control gene. [...] The relationships between grouped variables were analysed with the χ2 test. Survival curves were produced according to the life-table method described by Kaplan and Meier. Differences in recurrence-free survival were estimated with the log-rank test. Multivariate analysis of recurrence and mortality rates was performed with Cox proportional hazard regression. All the procedures are comprised in the statistical package STATISTICA 6.0 (StatSoft Scandinavia AB, Sweden). The criterion for statistical significance was P<0.05. […]

Pipeline specifications

Software tools Primer Express, Statistica
Applications Miscellaneous, qPCR
Organisms Homo sapiens
Diseases Breast Neoplasms, Neoplasms
Chemicals Estradiol, Steroids, Tamoxifen