1. Quantification of within-sample genetic heterogeneity from SNP-array data
- Author
-
Pierre Martinez, Christopher Kimberley, Nicolai J. BirkBak, Andrea Marquard, Zoltan Szallasi, and Trevor A. Graham
- Subjects
Medicine ,Science - Abstract
Abstract Intra-tumour genetic heterogeneity (ITH) fosters drug resistance and is a critical hurdle to clinical treatment. ITH can be well-measured using multi-region sampling but this is costly and challenging to implement. There is therefore a need for tools to estimate ITH in individual samples, using standard genomic data such as SNP-arrays, that could be implemented routinely. We designed two novel scores S and R, respectively based on the Shannon diversity index and Ripley’s L statistic of spatial homogeneity, to quantify ITH in single SNP-array samples. We created in-silico and in-vitro mixtures of tumour clones, in which diversity was known for benchmarking purposes. We found significant but highly-variable associations of our scores with diversity in-silico (p
- Published
- 2017
- Full Text
- View/download PDF