Accurate and Fast Inference of Allele-specific Copy Number Alterations from Low-coverage Low-purity Tumor Sequencing Data
Introduction
Please use Accucopy instead, Accurity’s successor.
Accurity(Luo et al., 2018) is a computational method that infers tumor purity and tumor cell ploidy from tumor-normal WGS (whole exome will probably work too) data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy, and low-coverage (as low as 1X) settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased the signal/noise gaps between different copy numbers.
References
2018
Accurity
Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants
MOTIVATION: Tumor purity and ploidy have a substantial impact on next-gen sequence analyses of tumor samples and may alter the biological and clinical interpretation of results. Despite the existence of several computational methods that are dedicated to estimate tumor purity and/or ploidy from The Cancer Genome Atlas (TCGA) tumor-normal whole-genome-sequencing (WGS) data, an accurate, fast and fully-automated method that works in a wide range of sequencing coverage, level of tumor purity and level of intra-tumor heterogeneity, is still missing. RESULTS: We describe a computational method called Accurity that infers tumor purity, tumor cell ploidy and absolute allelic copy numbers for somatic copy number alterations (SCNAs) from tumor-normal WGS data by jointly modelling SCNAs and heterozygous germline single-nucleotide-variants (HGSNVs). Results from both in silico and real sequencing data demonstrated that Accurity is highly accurate and robust, even in low-purity, high-ploidy and low-coverage settings in which several existing methods perform poorly. Accounting for tumor purity and ploidy, Accurity significantly increased signal/noise gaps between different copy numbers. We are hopeful that Accurity is of clinical use for identifying cancer diagnostic biomarkers. AVAILABILITY: Accurity is implemented in C++/Rust, https://github.com/polyactis/Accurity.
@article{Luo2018Accurity,title={Accurity: accurate tumor purity and ploidy inference from tumor-normal WGS data by jointly modelling somatic copy number alterations and heterozygous germline single-nucleotide-variants},author={Luo, Z and Fan, X and Huang, YS},journal={Bioinformatics},year={2018},doi={10.1093/bioinformatics/bty043},url={https://doi.org/10.1093/bioinformatics/bty043},dimensions={true},}