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| Status |
Public on Oct 01, 2018 |
| Title |
An assessment of prognostic immunity markers in breast cancer |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
We used Targeted RNA-seq to generate a gene expression data set of the 72-gene panel (TARGETSEQ) including 483 targeted RNA-seq data of 225 breast cancer FFPE samples from Shanghai and 258 breast cancer FFPE samples from UNC at Chapel Hill. The identified gene panel and risk evaluation model iRDM were developed in training data set AFFY1951 (p<0.0001, n=1951) and further validated in two other published gene expression datasets including Illumina beads array data METABRIC (p<0.0001, n=1997) and whole transcriptomic mRNA-seq data TCGA (p=0.00019, n=996) and in our own targeted RNA-seq data TARGETSEQ (p<0.0001, n=303) (of 483 RNA-seq samples, 303 with survival data). In conclusion, immunity gene expression were an important parameter for prognosis and therefore can be incorporated into current multi-gene assays to improve assessment of risk of distant metastasis in breast cancer.
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| Overall design |
Gene expression were detected using Targeted RNA-seq. The fastq files were mapped to know region of human genome and gene expression raw counts were obtained and further processed using edgeR and DWD software. The normalized expression data were used for breast cancer subtype classification and risk stratification.
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| Contributor(s) |
Hu Z, Yang B, Chou J, Tao Y, Wu D, Wu X, Li X, Li Y, Chu Y, Zhou T, Kaufmann W, Carey LA, Wu J |
| Citation(s) |
30393759 |
| Submission date |
Apr 30, 2018 |
| Last update date |
Mar 26, 2019 |
| Contact name |
Zhiyuan Hu |
| E-mail(s) |
HUZI1111@OUTLOOK.COM
|
| Phone |
9195274295
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| Organization name |
University of North Carolina at Chapel Hill
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| Department |
Lineberger Comprehensive Cancer Center
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| Lab |
RAM lab
|
| Street address |
450 West Dr
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| City |
Chapel Hill |
| State/province |
NC |
| ZIP/Postal code |
27502 |
| Country |
USA |
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| Platforms (2) |
| GPL15520 |
Illumina MiSeq (Homo sapiens) |
| GPL18573 |
Illumina NextSeq 500 (Homo sapiens) |
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| Samples (483)
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| Relations |
| BioProject |
PRJNA454288 |
| SRA |
SRP144041 |
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