RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data.
RNA2DNAlign: nucleotide resolution allele asymmetries through quantitative assessment of RNA and DNA paired sequencing data.
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DOI：
10.1093/nar/gkw757
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发表时间：
2016-12-15
影响因子：
14.9
通讯作者：
Horvath A
中科院分区：
文献类型：
--
作者：
Movassagh M;Alomran N;Mudvari P;Dede M;Dede C;Kowsari K;Restrepo P;Cauley E;Bahl S;Li M;Waterhouse W;Tsaneva-Atanasova K;Edwards N;Horvath A
我们介绍RNA 2DNAlign，一个用于定量评估配对RNA和DNA测序数据集等位基因计数的计算框架。RNA 2DNAlign是基于变体和参考读段计数的相对丰度的定量，随后是相容序列之间SNV位置处的基因型和等位基因状态的二项式检验。RNA 2DNAlign检测具有差异等位基因分布的位置，表明由于调节/结构事件导致的不对称性。基于不对称的类型，RNA 2DNAlign概述了可能涉及RNA编辑、等位基因特异性表达或缺失、体细胞诱变或杂合性缺失的位置（前三个也在肿瘤特异性环境中）。我们将RNA 2DNAlign应用于来自TCGA的90名乳腺癌患者的360个匹配的正常和肿瘤外显子组和转录组。在高置信度设置下，RNA 2DNAlign识别了2038个与上述不对称之一相关的不同SNV位点，其中大多数之前没有与功能相关。性能评估显示出非常高的特异性和灵敏度，这是由于多个匹配数据集之间的信号确证。RNA 2DNAlign作为一个自包含的二进制包，可从http://github.com/HorvathLab/NGS免费获得，用于64位Linux系统。
We introduce RNA2DNAlign, a computational framework for quantitative assessment of allele counts across paired RNA and DNA sequencing datasets. RNA2DNAlign is based on quantitation of the relative abundance of variant and reference read counts, followed by binomial tests for genotype and allelic status at SNV positions between compatible sequences. RNA2DNAlign detects positions with differential allele distribution, suggesting asymmetries due to regulatory/structural events. Based on the type of asymmetry, RNA2DNAlign outlines positions likely to be implicated in RNA editing, allele-specific expression or loss, somatic mutagenesis or loss-of-heterozygosity (the first three also in a tumor-specific setting). We applied RNA2DNAlign on 360 matching normal and tumor exomes and transcriptomes from 90 breast cancer patients from TCGA. Under high-confidence settings, RNA2DNAlign identified 2038 distinct SNV sites associated with one of the aforementioned asymetries, the majority of which have not been linked to functionality before. The performance assessment shows very high specificity and sensitivity, due to the corroboration of signals across multiple matching datasets. RNA2DNAlign is freely available from http://github.com/HorvathLab/NGS as a self-contained binary package for 64-bit Linux systems.
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影响因子：
4.9
作者：
Fontanillas P;Landry CR;Wittkopp PJ;Russ C;Gruber JD;Nusbaum C;Hartl DL
通讯作者：
Hartl DL
影响因子：
4.4
作者：
Main, Bradley J.;Bickel, Ryan D.;Nuzhdin, Sergey V.
通讯作者：
Nuzhdin, Sergey V.
影响因子：
3.5
作者：
Fogarty, Marie P.;Xiao, Rui;Mohlke, Karen L.
通讯作者：
Mohlke, Karen L.
影响因子：
24.5
作者：
Chan TH;Lin CH;Qi L;Fei J;Li Y;Yong KJ;Liu M;Song Y;Chow RK;Ng VH;Yuan YF;Tenen DG;Guan XY;Chen L
通讯作者：
Chen L
影响因子：
12.3
作者：
Mayba O;Gilbert HN;Liu J;Haverty PM;Jhunjhunwala S;Jiang Z;Watanabe C;Zhang Z
通讯作者：
Zhang Z