Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer.
Targeted transcriptome analysis using synthetic long read sequencing uncovers isoform reprograming in the progression of colon cancer.
复制标题
使用合成长读测序的靶向转录组分析揭示了结肠癌进展中的异构体重编程。
DOI：
10.1038/s42003-021-02024-1
复制
发表时间：
2021-04-27
影响因子：
5.9
通讯作者：
Luo JH
中科院分区：
文献类型：
--
作者：
Liu S;Wu I;Yu YP;Balamotis M;Ren B;Ben Yehezkel T;Luo JH
人类基因表达的特征受到短阅读长度、高错误率和大输入要求的限制。在这里，我们使用了一种合成长读(SLR)测序方法LoopSeq，以使用标准的短读数据生成跨越全长转录本的准确测序读数。LoopSeq从对照样本中识别异构体的准确率为99.4%，每碱基错误率为0.01%，超过了其他长阅读技术报告的准确率。将LoopSeq应用于结肠癌和转移性结肠癌的靶向转录组测序，发现了从良性结肠粘膜到原发结肠癌和转移性癌的大规模异构体重新分布，并鉴定了几种先前未知的融合异构体。值得注意的是，单核苷酸变异(SNV)主要发生在特定的亚型中，一些SNV在癌症进展中经历了亚型转换。使用短阅读来生成准确的长阅读数据作为原始信息单元的能力有望成为转录组测序中一种广泛使用的方法。Silvia Liu等人。目前的LoopSeq是一种人工合成的长阅读测序方法，可以从Illumina短片段生成准确的长阅读转录组数据。作为一个可能应用的例子，他们使用LoopSeq来研究结肠癌多个阶段的差异异构体表达、异构体特异性单核苷酸变异和潜在的融合基因。总之，LoopSeq是分析复杂转录本和在异构体水平上研究基因表达的一种有价值的方法。
The characterization of human gene expression is limited by short read lengths, high error rates and large input requirements. Here, we used a synthetic long read (SLR) sequencing approach, LoopSeq, to generate accurate sequencing reads that span full length transcripts using standard short read data. LoopSeq identified isoforms from control samples with 99.4% accuracy and a 0.01% per-base error rate, exceeding the accuracy reported for other long-read technologies. Applied to targeted transcriptome sequencing from colon cancers and their metastatic counterparts, LoopSeq revealed large scale isoform redistributions from benign colon mucosa to primary colon cancer and metastatic cancer and identified several previously unknown fusion isoforms. Strikingly, single nucleotide variants (SNVs) occurred dominantly in specific isoforms and some SNVs underwent isoform switching in cancer progression. The ability to use short reads to generate accurate long-read data as the raw unit of information holds promise as a widely accessible approach in transcriptome sequencing. Silvia Liu et al. present LoopSeq, a synthetic long-read sequencing method that generates accurate long-read transcriptome data from short Illumina reads. As an example of possible applications, they use LoopSeq to investigate differential isoform expression, isoform-specific single nucleotide variants, and potential fusion genes in multiple stages of colon cancer. Altogether, LoopSeq is a valuable method for analyzing complex transcriptomes and investigating gene expression at the isoform level.
登录
查看更多内容
影响因子：
3.9
作者：
Dehm SM;Tindall DJ
通讯作者：
Tindall DJ
影响因子：
5.8
作者：
Li, Heng
通讯作者：
Li, Heng
影响因子：
4.8
作者：
Bibillo, A;Eickbush, TH
通讯作者：
Eickbush, TH
影响因子：
4.8
作者：
Ernst, Wayne L.;Shome, Kuntala;Aridor, Meir
通讯作者：
Aridor, Meir
MAN2A1-FER融合基因由人肝脏和其他肿瘤类型表达，并且在小鼠中具有致癌活性。
影响因子：
29.4
作者：
Chen ZH;Yu YP;Tao J;Liu S;Tseng G;Nalesnik M;Hamilton R;Bhargava R;Nelson JB;Pennathur A;Monga SP;Luketich JD;Michalopoulos GK;Luo JH
通讯作者：
Luo JH