论文信息 - PurityEst: estimating purity of human tumor samples using next-generation sequencing data

PurityEst: estimating purity of human tumor samples using next-generation sequencing data

UNLABELLED We developed a novel algorithm, PurityEst, to infer the tumor purity level from the allelic differential representation of heterozygous loci with somatic mutations in a human tumor sample with a matched normal tissue using next-generation sequencing data. We applied our tool to a whole cancer genome sequencing datasets and demonstrated the accuracy of PurityEst compared with DNA copy number-based estimation. AVAILABILITY PurityEst has been implemented in PERL and is available at http://odin.mdacc.tmc.edu/~xsu1/PurityEst.html.

[1] Jianfeng Xu,et al. BACOM: in silico detection of genomic deletion types and correction of normal cell contamination in copy number data , 2011, Bioinform..

[2] Terence P. Speed,et al. TumorBoost: Normalization of allele-specific tumor copy numbers from a single pair of tumor-normal genotyping microarrays , 2010, BMC Bioinformatics.

[3] Fred A. Wright,et al. Integrated study of copy number states and genotype calls using high-density SNP arrays , 2009, Nucleic acids research.

[4] A. McKenna,et al. Absolute quantification of somatic DNA alterations in human cancer , 2012, Nature Biotechnology.

[5] Eric S. Lander,et al. The genomic complexity of primary human prostate cancer , 2010, Nature.

[6] C. Perou,et al. Allele-specific copy number analysis of tumors , 2010, Proceedings of the National Academy of Sciences.

[7] B. Rosner. Percentage Points for a Generalized ESD Many-Outlier Procedure , 1983 .

[8] Gabor T. Marth,et al. A general approach to single-nucleotide polymorphism discovery , 1999, Nature Genetics.

[9] Gabor T. Marth,et al. Whole-genome sequencing and variant discovery in C. elegans , 2008, Nature Methods.

[10] Henry M. Wood,et al. Correcting for cancer genome size and tumour cell content enables better estimation of copy number alterations from next-generation sequence data , 2012, Bioinform..