Human transcriptome array for high-throughput clinical studies
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 o...
| Main Authors: | , , , , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | en_US |
| Published: |
National Academy of Sciences (U.S.)
2011
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| Online Access: | http://hdl.handle.net/1721.1/66239 |
| _version_ | 1826196775446249472 |
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| author | Xu, Weihong Seok, Junhee Mindrinos, Michael N. Schweitzer, Anthony C. Jiang, Hui Wilhelmy, Julie Clark, Tyson A. Kapur, Karen Xing, Yi Faham, Malek Storey, John D. Moldawer, Lyle L. Maier, Ronald V. Tompkins, Ronald G. Wong, Wing Hung Davis, Ronald W. Xiao, Wenzhong Inflammation and Host Response to Injury Large-Scale Collaborative Research Program |
| author2 | Massachusetts Institute of Technology. Clinical Research Center |
| author_facet | Massachusetts Institute of Technology. Clinical Research Center Xu, Weihong Seok, Junhee Mindrinos, Michael N. Schweitzer, Anthony C. Jiang, Hui Wilhelmy, Julie Clark, Tyson A. Kapur, Karen Xing, Yi Faham, Malek Storey, John D. Moldawer, Lyle L. Maier, Ronald V. Tompkins, Ronald G. Wong, Wing Hung Davis, Ronald W. Xiao, Wenzhong Inflammation and Host Response to Injury Large-Scale Collaborative Research Program |
| author_sort | Xu, Weihong |
| collection | MIT |
| description | 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. |
| first_indexed | 2024-09-23T10:37:48Z |
| format | Article |
| id | mit-1721.1/66239 |
| institution | Massachusetts Institute of Technology |
| language | en_US |
| last_indexed | 2024-09-23T10:37:48Z |
| publishDate | 2011 |
| publisher | National Academy of Sciences (U.S.) |
| record_format | dspace |
| spelling | mit-1721.1/662392022-09-27T10:09:09Z Human transcriptome array for high-throughput clinical studies Xu, Weihong Seok, Junhee Mindrinos, Michael N. Schweitzer, Anthony C. Jiang, Hui Wilhelmy, Julie Clark, Tyson A. Kapur, Karen Xing, Yi Faham, Malek Storey, John D. Moldawer, Lyle L. Maier, Ronald V. Tompkins, Ronald G. Wong, Wing Hung Davis, Ronald W. Xiao, Wenzhong Inflammation and Host Response to Injury Large-Scale Collaborative Research Program Massachusetts Institute of Technology. Clinical Research Center Tompkins, Ronald G. Tompkins, Ronald G. 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. National Institutes of Health (U.S.) (grant U54GM062119) National Institutes of Health (U.S.) (grant P01HG000205) National Institutes of Health (U.S.) (grant R01HG004634) 2011-10-13T15:17:38Z 2011-10-13T15:17:38Z 2011-03 2010-11 Article http://purl.org/eprint/type/JournalArticle 1091-6490 http://hdl.handle.net/1721.1/66239 Xu, W. et al. “Human transcriptome array for high-throughput clinical studies.” Proceedings of the National Academy of Sciences 108 (2011): 3707-3712. ©2011 by the National Academy of Sciences. en_US http://dx.doi.org/10.1073/pnas.1019753108 Proceedings of the National Academy of Sciences of the United States of America Article is made available in accordance with the publisher's policy and may be subject to US copyright law. Please refer to the publisher's site for terms of use. application/pdf National Academy of Sciences (U.S.) PNAS |
| spellingShingle | Xu, Weihong Seok, Junhee Mindrinos, Michael N. Schweitzer, Anthony C. Jiang, Hui Wilhelmy, Julie Clark, Tyson A. Kapur, Karen Xing, Yi Faham, Malek Storey, John D. Moldawer, Lyle L. Maier, Ronald V. Tompkins, Ronald G. Wong, Wing Hung Davis, Ronald W. Xiao, Wenzhong Inflammation and Host Response to Injury Large-Scale Collaborative Research Program Human transcriptome array for high-throughput clinical studies |
| title | Human transcriptome array for high-throughput clinical studies |
| title_full | Human transcriptome array for high-throughput clinical studies |
| title_fullStr | Human transcriptome array for high-throughput clinical studies |
| title_full_unstemmed | Human transcriptome array for high-throughput clinical studies |
| title_short | Human transcriptome array for high-throughput clinical studies |
| title_sort | human transcriptome array for high throughput clinical studies |
| url | http://hdl.handle.net/1721.1/66239 |
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