Atypical Chronic Myeloid Leukemia (aCML)

Vignette

More than 60 cross-sectional samples were collected and analyzed for mutations in a panel of less than 30 genes in
 Piazza et al.  (Nature Genetics). With this data, we show some basic data-processing operations in TRONCO, and exploit the CAPRI algorithm to infer a progression model for this cohort of leukemic patients. 
This is the example which comes along with the vignette of the stable release (2.0, Mantis Shrimp).





Colorectal Cancer (CRC)

Colorectal

We use the PiCnIc Pipeline for Cancer Inference to process  over 200 cross-sectional samples from the TCGA COADREAD project. We distinguish samples according to their microsatellite stability status, and exploit tools to detect groups of exclusive alterations in a pool of driver genes. Then, we use CAPRI algorithm to retrieve progression model for those subtypes, and assess their confidence with bootstrap and cross-validation techniques.

This is the first complete example of PiCnIc, our efficient pipeline to diminish  the confounding effects due to cancer heterogeneity.






Clear Cell Renal Cell Carcinoma (CCRCC)

Clonal architecture of Clear Cell Renal Cell Carcinoma (CCRCC)

Reconstruction of the clonal architecture in an individual patient (tree-phylogeny reconstruction) belonging to the study by Gerlinger et al., Nat Gen 46, 2014. We here show how the CAPRESE algorithm can be used to successfully resolve the genetic architecture and evolutionary histories of cancers from multi-region sequencing data.

This is the first example where we show the power of the selective advantage scores used in TRONCO's algorithms, at the individual cancer progression level.





Single-cell (synthetic data)

Single Cell Synthetic Data

We assess standard measures of performance - i.e., correctness of the inference process - with one of the algorithms implemented in TRONCO, CAPRESE, as if it were used to process single-cell data.

To make the problem realistic we account for noise in such data, an variable sample size - i.e., number of sequenced cells.



Processing data from the Cbio portal

Cbio-example.

We show how to access data available at the Cbio portal within TRONCO.