Cancer Genomics Workshop

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# Cancer Genomics Workshop
## Advanced R for Bioinformatics. Visby, 2018.
### Markus Mayrhofer
### 19 June, 2018

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## Cancer Genomics:

In cancer research, NGS generates the majority of data for bioinformatic analysis:

* DNA sequencing of the whole genome, the whole exome, or known cancer-related genes to identify

+ point mutations
 + structural variants
 + copy number
 
--
 
* Epigenetic features

+ Bisulphite-treated DNA for methylation
 + ATAC-seq for open/active chromatin
 + ChIP-seq for DNA binding

* cDNA/RNA sequencing of the whole (or selected parts of the) transcriptome to

+ quantify gene expression (mRNA abundance)
 + detect fusion transcripts

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## Cancer Genomics: general aims

* Patient level (clinical analysis):
 + Find variants/features of **known** relevance for **diagnosis**, **prognosis** or **treatment**

--
 
 + e.g. somatic or germline mutations, mutational phenotypes, gene expression profiles,...

* Cohort level (research):
 + Find variants/features of **previously unknown** relevance for diagnosis, prognosis or treatment

+ e.g. somatic or germline mutations, mutational phenotypes, gene expression profiles,...

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## Exercises
(choose either exercise, or work on your own data analysis)

* Exercise 1: Explore whole genome sequencing data

+ Whole genome sequencing of single tumor-normal sample
 + Parse and explore VCF files and copy number data in R
 + Interpret variant multiplicity, somatic copy number and tumor purity

* Exercise 2: Model tumor grade from gene expression profiles

+ `cgdsr` package: Access wealth of published data from MSK cBioportal in your R session
 + Use machine learning to predict clinical features

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## Session

* This presentation was created in RStudio using [`remarkjs`](https://github.com/gnab/remark) framework through R package [`xaringan`](https://github.com/yihui/xaringan).
* For R Markdown, see <http://rmarkdown.rstudio.com>
* For R Markdown presentations, see <https://rmarkdown.rstudio.com/lesson-11.html>

```r
R.version
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```
##                _                           
## platform       x86_64-apple-darwin15.6.0   
## arch           x86_64                      
## os             darwin15.6.0                
## system         x86_64, darwin15.6.0        
## status                                     
## major          3                           
## minor          5.0                         
## year           2018                        
## month          04                          
## day            23                          
## svn rev        74626                       
## language       R                           
## version.string R version 3.5.0 (2018-04-23)
## nickname       Joy in Playing
```

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# Thank you