A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.
A systematic comparison and evaluation of high density exon arrays and RNA-seq technology used to unravel the peripheral blood transcriptome of sickle cell disease.
复制标题
DOI：
10.1186/1755-8794-5-28
复制
发表时间：
2012-06-29
影响因子：
2.7
通讯作者：
Kato GJ
中科院分区：
文献类型：
--
作者：
Raghavachari N;Barb J;Yang Y;Liu P;Woodhouse K;Levy D;O'Donnell CJ;Munson PJ;Kato GJ
临床研究中的转录组学研究是破译基因组功能元件和揭示潜在疾病机制的重要工具。已经开发了各种技术来推断和量化转录组，包括杂交和基于测序的方法。最近，高密度外显子微阵列已经成功地用于检测差异表达基因和选择性剪接事件，用于生物标志物的发现和疾病诊断。转录组学领域目前正在通过高通量DNA测序方法进行革命，以绘制，表征和量化转录组。为了了解每种工具的优点和局限性，我们对镰状细胞病（单基因疾病）的转录组进行了研究，比较了Affymetrix Human Exon 1.0 ST微阵列（Exon array）和Illumina的深度测序技术（RNA-seq）对全血临床标本的影响。分析表明，外显子阵列与RNA-seq数据在基因水平和外显子水平转录物表达上具有很强的一致性（R = 0.64）。在RNA-seq中，差异表达的幅度普遍高于外显子微阵列。我们还首次证明了RNA-seq技术在镰状细胞病中发现新的转录物变体和先前未注释的基因组区域的差异表达的能力。除了检测表达水平的变化外，RNA-seq技术还能够鉴定表达转录本的序列变化。我们的研究结果表明，对于低输入要求的临床样本转录组学分析，微阵列仍然是有用和准确的，而RNA-seq技术补充并扩展了微阵列测量的新发现。
Transcriptomic studies in clinical research are essential tools for deciphering the functional elements of the genome and unraveling underlying disease mechanisms. Various technologies have been developed to deduce and quantify the transcriptome including hybridization and sequencing-based approaches. Recently, high density exon microarrays have been successfully employed for detecting differentially expressed genes and alternative splicing events for biomarker discovery and disease diagnostics. The field of transcriptomics is currently being revolutionized by high throughput DNA sequencing methodologies to map, characterize, and quantify the transcriptome. In an effort to understand the merits and limitations of each of these tools, we undertook a study of the transcriptome in sickle cell disease, a monogenic disease comparing the Affymetrix Human Exon 1.0 ST microarray (Exon array) and Illumina’s deep sequencing technology (RNA-seq) on whole blood clinical specimens. Analysis indicated a strong concordance (R = 0.64) between Exon array and RNA-seq data at both gene level and exon level transcript expression. The magnitude of differential expression was found to be generally higher in RNA-seq than in the Exon microarrays. We also demonstrate for the first time the ability of RNA-seq technology to discover novel transcript variants and differential expression in previously unannotated genomic regions in sickle cell disease. In addition to detecting expression level changes, RNA-seq technology was also able to identify sequence variation in the expressed transcripts. Our findings suggest that microarrays remain useful and accurate for transcriptomic analysis of clinical samples with low input requirements, while RNA-seq technology complements and extends microarray measurements for novel discoveries.
登录
查看更多内容
DOI：
10.1093/bioinformatics/btq033
发表时间：
2010-03-15
期刊：
Bioinformatics (Oxford, England)
影响因子：
--
作者：
Quinlan AR;Hall IM
通讯作者：
Hall IM
影响因子：
12.3
作者：
Cirulli ET;Singh A;Shianna KV;Ge D;Smith JP;Maia JM;Heinzen EL;Goedert JJ;Goldstein DB;Center for HIV/AIDS Vaccine Immunology (CHAVI)
通讯作者：
Center for HIV/AIDS Vaccine Immunology (CHAVI)
Affymetrix外显子和U133PLUS2 Genechip阵列的实验比较和评估。
影响因子：
3.7
作者：
Abdueva, Diana;Wing, Michele R.;Schaub, Betty;Triche, Timothy J.
通讯作者：
Triche, Timothy J.
DOI：
10.1111/j.2517-6161.1995.tb02031.x
发表时间：
1995-01-01
影响因子：
5.8
作者：
BENJAMINI, Y;HOCHBERG, Y
通讯作者：
HOCHBERG, Y
影响因子：
14.8
作者：
通讯作者：
--