# FocalAmplifications
Genomic alterations in metastatic prostate cancer remain incompletely characterized. 
Here we analyze 493 prostate cancer cases from the TCGA database and perform whole-genome 
plasma sequencing on 95 plasma samples derived from 43 patients with metastatic prostate cancer. 
From these samples, we identify established driver aberrations in a cancer-related gene in nearly all cases (97.7%), 
including driver gene fusions (TMPRSS2:ERG), driver focal deletions (PTEN, RYBP, SHQ1), and driver amplifications (AR, MYC). 
In serial plasma analyses, we observe changes in focal amplifications in 40% of cases. The mean time interval 
between new amplifications was 26.4 weeks (range: 5-52 weeks), suggesting that they represent rapid adaptations
 to selection pressure. An increase in neuron-specific enolase is accompanied by clonal pattern changes in the 
tumor genome, most consistent with subclonal diversification of the tumor. Our findings suggest a high plasticity of 
prostate cancer genomes with newly occurring focal amplifications as a driving force in progression.

*Focal_amplifications_in_R.ipynb*  
Use R to identify focal events in segmented copy-number data

*PanCancer_focal_statistics.ipynb*  
Get statistics of copy-numbers from the TCGA PanCancer dataset

*FocalAmplifications_Prostate_methods.ipynb*  
Compare Plasma-Seq data to copy-number data of TCGA prostate cancer data set