MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.
MMAPPR: mutation mapping analysis pipeline for pooled RNA-seq.
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DOI：
10.1101/gr.146936.112
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发表时间：
2013-04
期刊：
影响因子：
7
通讯作者：
Yost HJ
中科院分区：
文献类型：
--
作者：
Hill JT;Demarest BL;Bisgrove BW;Gorsi B;Su YC;Yost HJ
在模式生物中进行正向遗传筛选对于鉴定发育或疾病过程所必需的新基因至关重要。这些筛选的一个缺点是绘制致病突变的劳动密集型过程，有时是不确定的。为了利用高通量技术来改善这一映射过程，我们开发了一种用于合并RNA-seq（MMAPPR）的突变映射分析管道，该管道在没有亲本菌株信息或需要生物体的预先存在的SNP图谱的情况下工作，并适应整个基因组的差异重组频率。MMAPPR适应RNA-seq数据集中的大量噪声，通过欧氏距离计算等位基因频率，然后进行黄土回归分析，确定突变所在的区域，并生成连锁基因组片段中推定的编码区突变列表。MMAPPR可以利用来自分离组织或整个生物体的RNA-seq数据集，用于新突变体的基因表达和转录组分析。我们在斑马鱼的两个已知突变系nkx2.5和tbx 1上测试了MMAPPR，并用它来绘制两个新的ENU诱导的心血管突变体，在ctr 9和cds 2基因中发现了突变。MMAPPR可以直接应用于其他模式生物，如果蝇和秀丽隐杆线虫，这些模式生物可以进行正向遗传筛选和合并的RNA-seq实验。因此，MMAPPR是一种快速，具有成本效益和高度自动化的管道，可用于在任何具有良好组装基因组的生物体中进行突变作图。
Forward genetic screens in model organisms are vital for identifying novel genes essential for developmental or disease processes. One drawback of these screens is the labor-intensive and sometimes inconclusive process of mapping the causative mutation. To leverage high-throughput techniques to improve this mapping process, we have developed a Mutation Mapping Analysis Pipeline for Pooled RNA-seq (MMAPPR) that works without parental strain information or requiring a preexisting SNP map of the organism, and adapts to differential recombination frequencies across the genome. MMAPPR accommodates the considerable amount of noise in RNA-seq data sets, calculates allelic frequency by Euclidean distance followed by Loess regression analysis, identifies the region where the mutation lies, and generates a list of putative coding region mutations in the linked genomic segment. MMAPPR can exploit RNA-seq data sets from isolated tissues or whole organisms that are used for gene expression and transcriptome analysis in novel mutants. We tested MMAPPR on two known mutant lines in zebrafish, nkx2.5 and tbx1, and used it to map two novel ENU-induced cardiovascular mutants, with mutations found in the ctr9 and cds2 genes. MMAPPR can be directly applied to other model organisms, such as Drosophila and Caenorhabditis elegans, that are amenable to both forward genetic screens and pooled RNA-seq experiments. Thus, MMAPPR is a rapid, cost-efficient, and highly automated pipeline, available to perform mutant mapping in any organism with a well-assembled genome.
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影响因子：
3.7
作者：
Baird NA;Etter PD;Atwood TS;Currey MC;Shiver AL;Lewis ZA;Selker EU;Cresko WA;Johnson EA
通讯作者：
Johnson EA
影响因子：
--
作者：
Chen, J N;van Bebber, F;Goldstein, A M;Serluca, F C;Jackson, D;Childs, S;Serbedzija, G;Warren, K S;Mably, J D;Lindahl, P;Mayer, A;Haffter, P;Fishman, M C
通讯作者：
Fishman, M C
影响因子：
3.3
作者：
Bowen, Margot E.;Henke, Katrin;Harris, Matthew P.
通讯作者：
Harris, Matthew P.
影响因子：
7.2
作者：
Austin, Ryan S.;Vidaurre, Danielle;Guttman, David S.
通讯作者：
Guttman, David S.
影响因子：
3.7
作者：
Doitsidou M;Poole RJ;Sarin S;Bigelow H;Hobert O
通讯作者：
Hobert O