Building a pipeline to assess effects of mutation burden based on tumor clonality. We will validate the clonality in pre-mixed cancer samples, separate the mutation burden based on segmented CNV calls, calculate clone-specific mutational burden and determine the potential benefit from immunotherapy treatment.
- Preprocessing: FASTQ files->BAM and VCF files
- CNV calling: CNV variants
- Mutational burden calculation: SNV calculation per clone of cells (comparison among different tools)
- Output: Appropriate for immunotherapy or not, which immunotherapy
Interval BED file for SureSelect Human All Exon V4 H. sapiens (hg19) is downloaded (S03723314). Recommended to use S03723314_AllTracks.bed which is uploaded at /gpfs/commons/projects/ncbi-nygc-hackathon/IntervalFiles.
Library construction for exam capture sequencing: http://www.nature.com/nbt/journal/v27/n2/full/nbt.1523.html
Clonality analysis tools:
List of CNV tools that might be used for variant calling:
ExomeCNV https://academic.oup.com/bioinformatics/article/27/19/2648/231564/Exome-sequencing-based-copy-number-variation-and download https://cran.r-project.org/src/contrib/Archive/ExomeCNV/ (currently removed from cran, the link is archived versions)