RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data.

摘要: We introduce RNA2DNAlign, a computational framework for quantitative assessment of allele counts across paired RNA and DNA sequencing datasets. RNA2DNAlign is based on quantitation the relative abundance variant reference read counts, followed by binomial tests genotype allelic status at SNV positions between compatible sequences. detects with differential distribution, suggesting asymmetries due to regulatory/structural events. Based type asymmetry, outlines likely be implicated in editing, allele-specific expression or loss, somatic mutagenesis loss-of-heterozygosity (the first three also tumor-specific setting). applied 360 matching normal tumor exomes transcriptomes from 90 breast cancer patients TCGA. Under high-confidence settings, identified 2038 distinct sites associated one aforementioned asymetries, majority which have not been linked functionality before. The performance shows very high specificity sensitivity, corroboration signals multiple freely available http://github.com/HorvathLab/NGS as self-contained binary package 64-bit Linux systems.