A method for high-throughput gene expression signature analysis
Genome biologyPublished 19 July 2006Open access
D. D. Peck, Emily Crawford, Kenneth N. Ross, Kimberly Stegmaier, Todd R. Golub, Justin Lamb
Citations213
SJR quartileQ1
SJR score5.71
SNIP2.21
Generate an AI Snapshot to get a quick, structured summary of this paper.
Study Snapshot
ObjectiveStudy objective
MethodsResearch methodology
PopulationPopulation studied
Sample sizeSample sizes
OutcomesStudy outcomes here
ResultsStudy results comes here
LimitationsResearch study limitations comes here
A concise AI-generated summary of the paper will appear here once you click Generate AI Snapshot.
TL;DR
A solution based on the combination of ligation-mediated amplification with an optically addressed microsphere and flow cytometric detection system for gene expression 'signatures' in large numbers of samples is described.
Abstract
Genome-wide transcriptional profiling has shown that different biologic states (for instance, disease and response to pharmacologic manipulation) can be recognized by the expression pattern of relatively small numbers of genes. However, the lack of a practical and cost-effective technology for detection of these gene expression 'signatures' in large numbers of samples has severely limited their exploitation in important medical and pharmaceutical discovery applications. Here, we describe a solution based on the combination of ligation-mediated amplification with an optically addressed microsphere and flow cytometric detection system.
Keywords
Biochemistry, Genetics and Molecular Biology
New England Journal of MedicineA Gene-Expression Signature as a Predictor of Survival in Breast Cancer
6,520 Citations2002Marc J. van de Vijver, Yudong D. He +19 more
The gene-expression profile studied is a more powerful predictor of the outcome of disease in young patients with breast cancer than standard systems based on clinical and histologic criteria.
ScienceA Ligase-Mediated Gene Detection Technique
832 Citations1988Ulf Landegren, Robert Kaiser +2 more
An assay for the presence of given DNA sequences has been developed, based on the ability of two oligonucleotides to anneal immediately adjacent to each other on a complementary target DNA molecule, which permits the rapid and standardized identification of single-copy gene sequences in genomic DNA.
CellA Mechanism of Cyclin D1 Action Encoded in the Patterns of Gene Expression in Human Cancer
421 Citations2003Justin Lamb, Sridhar Ramaswamy +8 more
Patterns of gene expression in human tumors have been deconvoluted to reveal a mechanism of action for the cyclin D1 oncogene and this work demonstrates that tumor gene expression databases can be used to study the function of a humanoncogene in situ.
Nature GeneticsGene expression–based high-throughput screening(GE-HTS) and application to leukemia differentiation
271 Citations2004Kimberly Stegmaier, Kenneth N. Ross +4 more
In screening 1,739 compounds, it is identified 8 that reliably induced the differentiation signature and, furthermore, yielded functional evidence of bona fide differentiation, indicating that GE-HTS may be a powerful, general approach for chemical screening.
Journal of Molecular DiagnosticsMolecular Classification of Crohn's Disease and Ulcerative Colitis Patients Using Transcriptional Profiles in Peripheral Blood Mononuclear Cells
243 Citations2006Michael E. Burczynski, Ron Peterson +13 more
The results suggest that a peripheral blood mononuclear cell-based gene expression signature can provide a molecular biomarker that can complement the standard diagnosis of UC and CD.
BloodGene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment
222 Citations2004Annuska M. Glas
The FL stratification profile is a more reliable marker of clinical behavior than the currently used histologic grading and clinical criteria and may provide an important alternative to guide the choice of therapy in patients with FL both at presentation and at relapse.
Nature BiotechnologyProfiling alternative splicing on fiber-optic arrays
209 Citations2002Joanne M. Yeakley, Jian‐Bing Fan +6 more
A sensitive and specific assay for parallel analysis of mRNA isoforms on a fiber-optic microarray platform that permits analysis of RNA transcripts without prior RNA purification or cDNA synthesis is described.
Genome ResearchA Versatile Assay for High-Throughput Gene Expression Profiling on Universal Array Matrices
184 Citations2004Jian‐Bing Fan, Joanne M. Yeakley +14 more
A flexible, sensitive, and quantitative gene-expression profiling system for assaying more than 400 genes, with three probes per gene, for 96 samples in parallel, that can cost-effectively profile the expression of hundreds of genes in thousands of samples is reported.
Nature BiotechnologyEnhanced detection and distinction of RNA by enzymatic probe ligation
132 Citations2000Mats Nilsson, Gisela Barbany +3 more
Conditions for efficient ligation of pairs of DNA oligonucleotides hybridizing next to one another on RNA strands are presented, permitting discrimination of any single nucleotide probe–target mismatch by a factor of between 20- and 200-fold.
Genome ResearchBADGE, BeadsArray for the Detection of Gene Expression, a High-Throughput Diagnostic Bioassay
111 Citations2001Liwei Yang, D K Tran +1 more
The study showed that the BADGE assay was capable of profiling expression of multiple genes at affordable cost and rapid speed.
Journal of Clinical MicrobiologyNovel, ligation-dependent PCR assay for detection of hepatitis C in serum
58 Citations1996T. Hsuih, Young Nyun Park +6 more
When serial 10-fold dilutions of synthetic HCV RNA were tested, there was a good correlation between the amount of PCR product and the initial number of RNA molecules, with a sensitivity of 100HCV RNA molecules per reaction.