Review Paper: Gene Expression Profiling in Veterinary and Human Medicine: Overview of Applications and Proposed Quality Control Practices

2009 ◽  
Vol 46 (4) ◽  
pp. 598-603 ◽  
Author(s):  
E. J. Kort ◽  
P. Norton ◽  
P. Haak ◽  
B. Berghuis ◽  
S. Ramirez ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
Quality Assurance ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Clinical Care ◽  
Lessons Learned ◽  
Reproducible Research ◽  
Tissue Samples ◽  
Wide Range

High throughput molecular analysis of veterinary tissue samples is being applied to a wide range of research questions aimed at improving survival, development of diagnostic assays, and improving the economics of commercial production of animal products. Many of these efforts also, implicitly or explicitly, have ramifications for the clinical care of humans and, potentially, animals. Here we provide an overview of applications of gene expression profiling in veterinary research and practice. We then focus on the current state of quality control and quality assurance efforts in gene expression profiling studies, underscoring lessons learned from such analysis of human samples. Finally, we propose practices aimed at ensuring the reliability and reproducibility of such assays. The implementation of quality assurance practices by a trained pathologist is an essential link in the chain of events leading ultimately to reliable and reproducible research findings and appropriate clinical care.

scholarly journals Establishment of a New Quality Control and Vaccine Safety Test for Influenza Vaccines and Adjuvants Using Gene Expression Profiling

PLoS ONE ◽  
2015 ◽  
Vol 10 (4) ◽  
pp. e0124392 ◽  
Author(s):  
Haruka Momose ◽  
Takuo Mizukami ◽  
Madoka Kuramitsu ◽  
Kazuya Takizawa ◽  
Atsuko Masumi ◽  
...  
Keyword(s):  
Gene Expression ◽  
Quality Control ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Vaccine Safety ◽  
Influenza Vaccines ◽  
Safety Test

scholarly journals Estrogen and the endometrium: lessons learned from gene expression profiling in rodents and human

2007 ◽  
Vol 13 (4) ◽  
pp. 405-417 ◽  
Author(s):  
P.G. Groothuis ◽  
H.H.N.M. Dassen ◽  
A. Romano ◽  
C. Punyadeera
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Lessons Learned

scholarly journals Differential gene expression profiling in human brain tumors

2001 ◽  
Vol 5 (1) ◽  
pp. 21-33 ◽  
Author(s):  
JAMES M. MARKERT ◽  
CATHERINE M. FULLER ◽  
G. YANCEY GILLESPIE ◽  
JAMES K. BUBIEN ◽  
LEE ANNE McLEAN ◽  
...  
Keyword(s):  
Gene Expression ◽  
Solute Transport ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Cell Biology ◽  
Glutamate Transporter ◽  
Tissue Samples ◽  
Altered Expression ◽  
Primary Glioblastoma ◽  
Normal Tissues

Gene expression profiling of three human temporal lobe brain tissue samples (normal) and four primary glioblastoma multiforme (GBM) tumors using oligonucleotide microarrays was done. Moreover, confirmation of altered expression was performed by whole cell patch clamp, immunohistochemical staining, and RT-PCR. Our results identified several ion and solute transport-related genes, such as N-methyl-d-aspartate (NMDA) receptors, α-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA)-2 receptors, GABAA receptor subunits α3, β1, β2, and β3, the glutamate transporter, the glutamate/aspartate transporter II, the potassium channel KV2.1, hKVβ3, and the sodium/proton exchanger 1 (NHE-1), that are all downregulated in the tumors compared with the normal tissues. In contrast, aquaporin-1, possibly aquaporins-3 and -5, and GLUT-3 message appeared upregulated in the tumors. Our results also confirmed previous work showing that osteopontin, nicotinamide N-methyltransferase, murine double minute 2 (MDM2), and epithelin (granulin) are upregulated in GBMs. We also demonstrate for the first time that the cytokine and p53 binding protein, macrophage migration inhibitory factor (MIF), appears upregulated in GBMs. These results indicate that the modulation of ion and solute transport genes and heretofore unsuspected cytokines (i.e., MIF) may have profound implications for brain tumor cell biology and thus may identify potential useful therapeutic targets in GBMs.

scholarly journals Prognostic gene expression profiling in melanoma: necessary steps to incorporate into clinical practice

2019 ◽  
Vol 6 (4) ◽  
pp. MMT32 ◽  
Author(s):  
Douglas Grossman ◽  
Caroline C Kim ◽  
Rebecca I Hartman ◽  
Elizabeth Berry ◽  
Kelly C Nelson ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Best Practice ◽  
Clinical Care ◽  
Prognostic Gene ◽  
Care Guidelines ◽  
Test Usage ◽  
Current Guidelines

Prognostic gene expression profiling (GEP) tests for cutaneous melanoma (CM) are not recommended in current guidelines outside of a clinical trial. However, their use is becoming more prevalent and some practitioners are using GEP tests to guide patient management. Thus, there is an urgent need to bridge this gap between test usage and clinical guideline recommendations by obtaining high-quality evidence to guide us toward best practice use of GEP testing in CM patients. We focus here on the opportunities and uncertainties associated with prognostic GEP testing in CM, review how GEP testing was incorporated into clinical care guidelines for uveal melanoma and breast cancer and discuss the role of clinical trials to determine best use in patients with CM.

scholarly journals Arrays of Arrays for High-Throughput Gene Expression Profiling

2001 ◽  
Vol 11 (7) ◽  
pp. 1256-1261
Author(s):  
Patrick P. Zarrinkar ◽  
James K. Mainquist ◽  
Matthew Zamora ◽  
David Stern ◽  
John B. Welsh ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Expression Profiles ◽  
Ovarian Tissue ◽  
Disease Diagnosis ◽  
Full Potential ◽  
Ovarian Carcinomas ◽  
Single Experiment ◽  
Tissue Samples

Gene expression profiling using DNA arrays is rapidly becoming an essential tool for research and drug discovery and may soon play a central role in disease diagnosis. Although it is possible to make significant discoveries on the basis of a relatively small number of expression profiles, the full potential of this technology is best realized through more extensive collections of expression measurements. The generation of large numbers of expression profiles can be a time-consuming and labor-intensive process with current one-at-a-time technology. We have developed the ability to obtain expression profiles in a highly parallel yet straightforward format using glass wafers that contain 49 individual high-density oligonucleotide arrays. This arrays of arrays concept is generalizable and can be adapted readily to other types of arrays, including spotted cDNA microarrays. It is also scalable for use with hundreds and even thousands of smaller arrays on a single piece of glass. Using the arrays of arrays approach and parallel preparation of hybridization samples in 96-well plates, we were able to determine the patterns of gene expression in 27 ovarian carcinomas and 4 normal ovarian tissue samples, along with a number of control samples, in a single experiment. This new approach significantly increases the ease, efficiency, and throughput of microarray-based experiments and makes possible new applications of expression profiling that are currently impractical.

scholarly journals Gene expression profiling of human breast tissue samples using SAGE-Seq

2010 ◽  
Vol 20 (12) ◽  
pp. 1730-1739 ◽  
Author(s):  
Z. J. Wu ◽  
C. A. Meyer ◽  
S. Choudhury ◽  
M. Shipitsin ◽  
R. Maruyama ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Breast Tissue ◽  
Human Breast ◽  
Human Breast Tissue ◽  
Tissue Samples

scholarly journals The Utility of Gene Expression Profiling from Tissue Samples to Support Drug Safety Assessments

ILAR Journal ◽  
2017 ◽  
Vol 58 (1) ◽  
pp. 69-79 ◽  
Author(s):  
Daniel P. Stiehl ◽  
Elaine Tritto ◽  
Salah-Dine Chibout ◽  
André Cordier ◽  
Pierre Moulin
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Drug Safety ◽  
Expression Profiling ◽  
Tissue Samples ◽  
Safety Assessments

scholarly journals Whole-Genome Gene Expression Profiling of Formalin-Fixed, Paraffin-Embedded Tissue Samples

PLoS ONE ◽  
2009 ◽  
Vol 4 (12) ◽  
pp. e8162 ◽  
Author(s):  
Craig April ◽  
Brandy Klotzle ◽  
Thomas Royce ◽  
Eliza Wickham-Garcia ◽  
Tanya Boyaniwsky ◽  
...  
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Whole Genome ◽  
Tissue Samples ◽  
Formalin Fixed Paraffin ◽  
Formalin Fixed Paraffin Embedded ◽  
Formalin Fixed

scholarly journals Gene Expression Profiling forIn SilicoMicrodissection of Hodgkin's Lymphoma Microenvironment and Identification of Prognostic Features

2011 ◽  
Vol 2011 ◽  
pp. 1-8 ◽  
Author(s):  
François Bertucci ◽  
Bruno Chetaille ◽  
Luc Xerri
Keyword(s):  
Gene Expression ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Dna Microarrays ◽  
Tissue Sample ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Cancer Tissue ◽  
Tissue Samples ◽  
Prognostic Features

Gene expression profiling studies based on DNA microarrays have demonstrated their ability to define the interaction pathways between neoplastic and nonmalignant stromal cells in cancer tissues. During the past ten years, a number of approaches including microdissection have tried to resolve the variability in DNA microarray measurements stemming from cancer tissue sample heterogeneity. Another approach, designated as virtual orin silicomicrodissection, avoids the laborious and time-consuming step of anatomic microdissection. It consists of confronting the gene expression profiles of complex tissue samples to those of cell lines representative of different cell lineages, different differentiation stages, or different signaling pathways. This strategy has been used in recent studies aiming to analyze microenvironment alterations using gene expression profiling of nonmicrodissected classical Hodgkin lymphoma tissues in order to generate new prognostic factors. These recent contributions are detailed and discussed in the present paper.

Gene expression profiling in human endometrial cancer tissue samples: utility and diagnostic value

2004 ◽  
Vol 93 (2) ◽  
pp. 292-300 ◽  
Author(s):  
E SMIDKOOPMAN ◽  
L BLOK ◽  
T HELMERHORST ◽  
S CHADHAAJWANI ◽  
C BURGER ◽  
...  
Keyword(s):  
Gene Expression ◽  
Endometrial Cancer ◽  
Gene Expression Profiling ◽  
Expression Profiling ◽  
Diagnostic Value ◽  
Cancer Tissue ◽  
Tissue Samples
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