Leeds Institute of Cancer and Pathology

Pre-Cancer Genomics

GH index

This page provides code to calculate a G-stat, H-stat, and combined GH index using copy number data derived from low coverage whole genome sequencing data.
This code is described in the paper: A computational index derived from whole-genome copy number analysis is a novel tool for prognosis in early stage lung squamous cell carcinoma. Ornella Belvedere, Stefano Berri, Rebecca Chalkley, Caroline Conway, Fabio Barbone, Federica Pisa, Kenneth MacLennan, Catherine Daly, Melissa Alsop, Joanne Morgan, Jessica Menis, Peter Tcherveniakov, Kostas Papagiannopoulos, Pamela Rabbitts, Henry M Wood. Genomics. 2011, epub ahead of print.
A link to the data from this paper is also provided.

Code

The commands are available as zipped R code here:

get_GH.R

Requirements

The code uses functions from the CNAnorm package, and calculates GH using the example dataset LS041 provided with CNAnorm. Installation of CNAnorm is necessary to run the script.

Data

All the sequence data from the paper is stored at the European Nucleotide Archive under accession number ERP000834.

© Copyright Leeds 2017