Recurrent gene fusions in prostate cancer
A technology of prostate cancer and gene fusion, applied in the direction of fermentation, etc.
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Embodiment 1
[0305] Embodiment 1 ERG and ETV1 gene fusion
[0306] A. Materials and methods
[0307] Cancer Outlier Analysis (COPA)
[0308] COPA analysis was performed on 132 gene expression datasets in Oncomine 3.0 containing 10,486 microarray experiments. Additionally, data from 99 amplified laser capture microdissected prostate tissue samples were included in the COPA analysis. COPA has 3 steps. First, align the medians of gene expression values, setting the median expression value of each gene to 0. Second, the median absolute deviation (MAD) was calculated and scaled to 1 by dividing each gene expression value by its MAD. Median and MAD were used for transformations relative to mean and standard deviation so that outlier expression values do not unduly interfere with distribution estimates, thus maintaining post-normalization. In the third step, 75%, 90%, and 95% of the transformed expression values are listed for each gene, and the genes are then sorted according to their p...
Embodiment 2
[0357] Embodiment 2ETV4 gene fusion
[0358] A. Materials and methods
[0359] ETS family expression in mapping studies
[0360] To investigate the expression of ETS family members in prostate cancer, 2 prostate cancer mapping studies were used. (Lapointe et al., Proc Natl Acad Sci USA 2004; 101:811-6 and Tomlins et al., Science 2005; 310:644-8) are presented in the Oncomine database (Rhodes et al., Neoplasia 2004; 6:1-6). Genes with ETS domains were identified by Interpro filter 'Ets' (Interpro ID: IPR000418). Using the 'median-center per gene' option, a Heatmap diagram was created in Oncomine, and the color contrast was set to emphasize the differential expression of ERG and ETV1.
[0361] sample
[0362] Prostate cancer tissues (PCA1-5) were obtained from the MSU Radical Prostatectomy Series, which is part of the MSU Specialized Program of Prostate Cancer Research Excellence (S.P.O.R.E.) organizational core. All samples were collected from consenting patients, with pri...
Embodiment 3
[0378] The detection of embodiment 3 gene fusion RNA
[0379] This example describes target capture, amplification and qualitative detection of RNA (IVT) containing the sequence of 4 gene fusions in 4 separate qualitative assays: TMPRSS2 with APTIMA formulated reagents: ETV1a, TMPRSS2 :ETV1b, TMPRSS2:ERGa and TMPRSS2:ERGb, each HPA assay was performed with appropriate target-specific oligonucleotides, primers and probes. Table 5 shows the sequences of the oligonucleotides used in this assay.
[0380] table 5
[0381]
[0382] A. Materials and methods
[0383] RNA target capture
[0384] Lysis buffer contained 15 mM monobasic sodium phosphate monohydrate, 15 mM anhydrous sodium hydrogen phosphate, 1.0 mM disodium EDTA dihydrate, 1.0 mM EGTA free acid, and 110 mM lithium lauryl sulfate, pH 6.7.
[0385] The target capture reagent contained 250 mM HEPES, 310 mM lithium hydroxide, 1.88 M lithium chloride, 100 mM EDTA free acid, pH 6.4, and 250 μg / ml 1 micron magnetic partic...
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