A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
A novel bioinformatics pipeline for identification and characterization of fusion transcripts in breast cancer and normal cell lines.
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DOI：
10.1093/nar/gkr362
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发表时间：
2011-08
影响因子：
14.9
通讯作者：
Thompson EA
中科院分区：
文献类型：
--
作者：
Asmann YW;Hossain A;Necela BM;Middha S;Kalari KR;Sun Z;Chai HS;Williamson DW;Radisky D;Schroth GP;Kocher JP;Perez EA;Thompson EA
雪鞋-FTD是为在配对的末端mRNA-Seq数据中检测融合转录而开发的，它使用多个步骤的假阳性过滤来提名融合转录本，其置信度接近100%。独特的特征包括：(I)从两个基因对中鉴定多种融合异构体；(Ii)基因组重排的预测；(Iii)外显子融合边界的鉴定；(Iv)用于PCR验证的5‘-3’融合跨越序列的产生；以及(V)蛋白质序列的预测，包括移码和氨基酸插入。我们应用雪鞋-FTD在22个乳腺癌和9个未转化的细胞系中鉴定了50个融合候选细胞。另外五个具有两种异构体的融合候选被确认。总体而言，55个融合候选者中有30个拥有框内蛋白产物。未转化细胞中未检测到融合转录本。对预测的融合蛋白子集的可能功能的考虑表明，在转化过程中有几个潜在的重要功能，包括可能在HER阳性细胞系中过度表达ERBB2的新机制。雪鞋-FTD的源代码以两种格式提供：一种被配置为在Sun网格引擎上运行以实现并行化，另一种被格式化为在单个Linux节点上运行。可以从我们的网站下载perl的可执行文件：http://mayoresearch.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.
SnowShoes-FTD, developed for fusion transcript detection in paired-end mRNA-Seq data, employs multiple steps of false positive filtering to nominate fusion transcripts with near 100% confidence. Unique features include: (i) identification of multiple fusion isoforms from two gene partners; (ii) prediction of genomic rearrangements; (iii) identification of exon fusion boundaries; (iv) generation of a 5′–3′ fusion spanning sequence for PCR validation; and (v) prediction of the protein sequences, including frame shift and amino acid insertions. We applied SnowShoes-FTD to identify 50 fusion candidates in 22 breast cancer and 9 non-transformed cell lines. Five additional fusion candidates with two isoforms were confirmed. In all, 30 of 55 fusion candidates had in-frame protein products. No fusion transcripts were detected in non-transformed cells. Consideration of the possible functions of a subset of predicted fusion proteins suggests several potentially important functions in transformation, including a possible new mechanism for overexpression of ERBB2 in a HER-positive cell line. The source code of SnowShoes-FTD is provided in two formats: one configured to run on the Sun Grid Engine for parallelization, and the other formatted to run on a single LINUX node. Executables in PERL are available for download from our web site: http://mayoresearch.mayo.edu/mayo/research/biostat/stand-alone-packages.cfm.
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DOI：
10.1038/nrc1299
发表时间：
2004-03
期刊：
Nature reviews. Cancer
影响因子：
--
作者：
通讯作者：
--
DOI：
10.1073/pnas.0505337102
发表时间：
2005-08-09
影响因子：
11.1
作者：
Huh, KW;DeMasi, J;Münger, K
通讯作者：
Münger, K
影响因子：
7
作者：
Pflueger, Dorothee;Terry, Stephane;Rubin, Mark A.
通讯作者：
Rubin, Mark A.
影响因子：
56.9
作者：
Tomlins, SA;Rhodes, DR;Chinnaiyan, AM
通讯作者：
Chinnaiyan, AM
影响因子：
4.8
作者：
Xiong, HB;Li, HX;Unkeless, JC
通讯作者：
Unkeless, JC