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Human transcriptome array for high-throughput clinical studies.

http://www.ncbi.nlm.nih.gov/pubmed/21317363

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.

Pubmed ID: 21317363 RIS Download

Mesh terms: Alternative Splicing | Exons | Gene Expression Profiling | High-Throughput Screening Assays | Humans | Oligonucleotide Array Sequence Analysis | Organ Specificity | RNA, Untranslated | Reproducibility of Results | Sequence Analysis, RNA

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Associated grants

  • Agency: NHGRI NIH HHS, Id: P01HG000205
  • Agency: NHGRI NIH HHS, Id: R01HG004634
  • Agency: NIGMS NIH HHS, Id: U54 GM062119
  • Agency: NIGMS NIH HHS, Id: U54GM062119
  • Agency: NCRR NIH HHS, Id: UL1 RR025014

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