Hello everyone,
I am working on WGS data, and I am interested to do some copy number analysis. Particularly, I am looking to see what regions of genome has been applified (or deleted) recurrently in a specific cancer cohort. I know there is a tool for this called GISTIC 2.0, but it has been developed sometime around 2011.
I was wondering, has there been any new tools after GISTIC 2.0 that would do the same? Do they have better Sensitivity/Specificity?
Thank you.
•
written
by
enho •
1 answer
There are many tools to detect CNV (to be proper, in a somatic context, we should call them somatic copy number alterations (CNA)). To gauge the sensitivity/specificity of all of these would be a difficult task, but it would essentially require a comparison to a reference 'gold standard' dataset that contains known copy number variants and structural variants.
There is nothing 'wrong' with GISTIC 2.0. If you want a full pipeline for detecting recurrent somatic CNAs in the TCGA datasets, then take a look here:
- TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages adapted by me, here: A: How to extract the list of genes from TCGA CNV data )
Kevin
Log in to answer this question.
-
Harmonising WGS and SNP array data
written by FB1999 •
-
Optimizing mutect/sarek for somatic substitution variant calling
written by ramiro.barrantes •
-
GISTIC for tetraploid genomes
written by enho •
-
How to create a GSEA enrichment plot for the phenotypes in R?
written by newbie
-
identify highly mutated regions in WES/WGS samples
written by cocchi.e89
-
Germline CNV Databases for Healthy and/or Cancer Patients
written by tohc •
-
How to calculate the sensitivity and specificity of set of expression dataset used in a validation…
written by a.james
-
Driver mutation vs biomarker vs recurrent mutation
written by CY
-
how to detect mutation from viral RNA-seq data
written by babasaraki •
-
Is there a method as good/superior as GISTIC/JISTIC to detect cancer-driving copy number alteration…
written by Avro
