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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.<\/jats:p>","DOI":"10.1073\/pnas.1019753108","type":"journal-article","created":{"date-parts":[[2011,2,12]],"date-time":"2011-02-12T04:35:33Z","timestamp":1297485333000},"page":"3707-3712","update-policy":"https:\/\/doi.org\/10.1073\/pnas.cm10313","source":"Crossref","is-referenced-by-count":111,"title":["Human transcriptome array for high-throughput clinical studies"],"prefix":"10.1073","volume":"108","author":[{"given":"Weihong","family":"Xu","sequence":"first","affiliation":[{"name":"Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304;"}]},{"given":"Junhee","family":"Seok","sequence":"additional","affiliation":[{"name":"Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304;"}]},{"given":"Michael N.","family":"Mindrinos","sequence":"additional","affiliation":[{"name":"Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304;"}]},{"given":"Anthony C.","family":"Schweitzer","sequence":"additional","affiliation":[{"name":"Assay and Application Product Development, Affymetrix, Inc., Santa Clara, CA 95051;"}]},{"given":"Hui","family":"Jiang","sequence":"additional","affiliation":[{"name":"Department of Statistics and Department of Health Research and Policy, Stanford University, Stanford, CA 94305;"}]},{"given":"Julie","family":"Wilhelmy","sequence":"additional","affiliation":[{"name":"Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304;"}]},{"given":"Tyson A.","family":"Clark","sequence":"additional","affiliation":[{"name":"Assay and Application Product Development, Affymetrix, Inc., Santa Clara, CA 95051;"}]},{"given":"Karen","family":"Kapur","sequence":"additional","affiliation":[{"name":"Department of Statistics and Department of Health Research and Policy, Stanford University, Stanford, CA 94305;"}]},{"given":"Yi","family":"Xing","sequence":"additional","affiliation":[{"name":"Department of Statistics and Department of Health Research and Policy, Stanford University, Stanford, CA 94305;"},{"name":"Department of Internal Medicine and Department of Biomedical Engineering, University of Iowa, Iowa City, IA 52242;"}]},{"given":"Malek","family":"Faham","sequence":"additional","affiliation":[{"name":"Assay and Application Product Development, Affymetrix, Inc., Santa Clara, CA 95051;"}]},{"given":"John D.","family":"Storey","sequence":"additional","affiliation":[{"name":"Lewis\u2013Sigler Institute and Department of Molecular Biology, Princeton University, Princeton, NJ 08544;"}]},{"given":"Lyle L.","family":"Moldawer","sequence":"additional","affiliation":[{"name":"Department of Surgery, University of Florida College of Medicine, Gainesville, FL 32610;"}]},{"given":"Ronald V.","family":"Maier","sequence":"additional","affiliation":[{"name":"Department of Surgery, University of Washington, Seattle, WA 98104; and"}]},{"given":"Ronald G.","family":"Tompkins","sequence":"additional","affiliation":[{"name":"Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston, MA 02114"}]},{"given":"Wing Hung","family":"Wong","sequence":"additional","affiliation":[{"name":"Department of Statistics and Department of Health Research and Policy, Stanford University, Stanford, CA 94305;"}]},{"given":"Ronald W.","family":"Davis","sequence":"additional","affiliation":[{"name":"Stanford Genome Technology Center and Department of Biochemistry, Stanford University, Palo Alto, CA 94304;"}]},{"given":"Wenzhong","family":"Xiao","sequence":"additional","affiliation":[{"name":"Massachusetts General Hospital, Harvard Medical School, Shriners Hospital for Children, Boston, MA 02114"}]},{"name":"the Inflammation and Host Response to Injury Large-Scale Collaborative Research Program","sequence":"additional","affiliation":[]},{"given":"Mehmet","family":"Toner","sequence":"additional","affiliation":[]},{"given":"Shaw","family":"Warren","sequence":"additional","affiliation":[]},{"given":"David A.","family":"Schoenfeld","sequence":"additional","affiliation":[]},{"given":"Laurence G.","family":"Rahme","sequence":"additional","affiliation":[]},{"given":"Grace P.","family":"McDonald-Smith","sequence":"additional","affiliation":[]},{"given":"Douglas L.","family":"Hayden","sequence":"additional","affiliation":[]},{"given":"Philip H.","family":"Mason","sequence":"additional","affiliation":[]},{"given":"Shawn","family":"Fagan","sequence":"additional","affiliation":[]},{"given":"Yong-Ming","family":"Yu","sequence":"additional","affiliation":[]},{"given":"J. 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