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| Content Provider | World Health Organization (WHO)-Global Index Medicus |
|---|---|
| Author | Schweitzer, Anthony C. Xing, Yi Moldawer, Lyle L. Clark, Tyson A. Faham, Malek Jiang, Hui Kapur, Karen Wong, Wing Hung Seok, Junhee Xu, Weihong Mindrinos, Michael N. Wilhelmy, Julie Xiao, Wenzhong Storey, John D. Tompkins, Ronald G. Maier, Ronald V. Davis, Ronald W. |
| Description | Author Affiliation: Xu W ( Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304, USA.); |
| Abstract | A 6.9 million-feature oligonucleotide array of the human transcriptome [Glue Grant human transcriptome (GG-H array)] has been developed for high-throughput and cost-effective analyses in clinical studies. This array allows comprehensive examination of gene expression and genome-wide identification of alternative splicing as well as detection of coding SNPs and noncoding transcripts. The performance of the array was examined and compared with mRNA sequencing (RNA-Seq) results over multiple independent replicates of liver and muscle samples. Compared with RNA-Seq of 46 million uniquely mappable reads per replicate, the GG-H array is highly reproducible in estimating gene and exon abundance. Although both platforms detect similar expression changes at the gene level, the GG-H array is more sensitive at the exon level. Deeper sequencing is required to adequately cover low-abundance transcripts. The array has been implemented in a multicenter clinical program and has generated high-quality, reproducible data. Considering the clinical trial requirements of cost, sample availability, and throughput, the GG-H array has a wide range of applications. An emerging approach for large-scale clinical genomic studies is to first use RNA-Seq to the sufficient depth for the discovery of transcriptome elements relevant to the disease process followed by high-throughput and reliable screening of these elements on thousands of patient samples using custom-designed arrays. |
| ISSN | 00278424 |
| e-ISSN | 10916490 |
| Journal | Proceedings of the National Academy of Sciences of the United States of America |
| Issue Number | 9 |
| Volume Number | 108 |
| Language | English |
| Publisher | National Academy of Sciences |
| Publisher Date | 2011-03-01 |
| Publisher Place | United States |
| Access Restriction | Open |
| Subject Keyword | Gene Expression Profiling High-Throughput Screening Assays Oligonucleotide Array Sequence Analysis Alternative Splicing Genetics Exons Organ Specificity RNA, Untranslated Reproducibility Of Results Sequence Analysis, RNA Research Support, N.I.H., Extramural Multidisciplinary |
| Content Type | Text |
| Resource Type | Article |
| Subject | Multidisciplinary |
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