GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR.

GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR. Research Abstract Details 

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GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR. Abstract Text:

Mark Kidd,Boaz Nadler,Shrikant Mane,Geeta Eick,Maximillian Malfertheiner,Manish Champaneria,Roswitha Pfragner,Irvin Modlin,

Accurate quantitation of target genes depends on correct normalization. Use of genes with variable tissue transcription (GAPDH) is problematic, particularly in clinical samples, which are derived from different tissue sources. Using a large-scale gene database (Affymetrix U133A) data set of 36 gastrointestinal (GI) tumors and normal tissues, we identified 8 candidate reference genes and established expression levels by real-time RT-PCR in an independent data set (n = 42). A geometric averaging method (geNorm) identified ALG9, TFCP2, and ZNF410 as the most robustly expressed control genes. Examination of raw C(T) values demonstrated that these genes were tightly correlated between themselves (R2 > 0.86, P < 0.0001), with low variability [coefficient of variation (CV) <12.7%] and high interassay reproducibility (r = 0.93, P = 0.001). In comparison, the alternative control gene, GAPDH, exhibited the highest variability (CV = 18.1%), was significantly differently expressed between tissue types (P = 0.05), was poorly correlated with the three reference genes (R2 < 0.4), and was considered the least stable gene. To illustrate the importance of correct normalization, the target gene, MTA1, was significantly overexpressed (P = 0.0006) in primary GI neuroendocrine tumor (NET) samples (vs. normal GI samples) when normalized by geNorm(ATZ) but not when normalized using GAPDH. The geNorm(ATZ) approach was, in addition, applicable to adenocarcinomas; MTA1 was overexpressed (P < 0.04) in malignant colon, pancreas, and breast tumors compared with normal tissues. We provide a robust basis for the establishment of a reference gene set using GeneChip data and provide evidence for the utility of normalizing a malignancy-associated gene (MTA1) using novel reference genes and the geNorm approach in GI NETs as well as in adenocarcinomas and breast tumors.

GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR. Publishing Authors By Initials

M Kidd,B Nadler,S Mane,G Eick,M Malfertheiner,M Champaneria,R Pfragner,I Modlin,

For similar biological factors: biological markers: tumor markers, biological research abstracts see: biological factors: biological markers: tumor markers, biological research

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MEDLINE DATE:

GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR. Journal Published:

PUBLICATION TYPE: Research Support, Non-U.S. Gov

Journal: Physiological genomics

VOLUME: 30

Page Numbers: 363-70

Journal Abbreviation: Physiol. Genomics

ISSN: 1531-2267

DAY: 24

MONTH: 04

YEAR: 2007

GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR. Information

Number of References:

LANGUAGE: eng

NlmUniqueID: 9815683

GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR. Keywords Mesh Terms:

KEYWORDS: Tumor Markers, Biological

MESH TERMS: isolation & purification

Chemical & Substance for Abstract: GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR. Information

Substance Name: Tumor Markers, Biological

Registry Number: 0

Grant and Affiliation Information for GeneChip, geNorm, and gastrointestinal tumors: novel reference genes for real-time PCR.

AFFILIATION: Gastrointestinal Research Group, Yale University School of Medicine, New Haven, Connecticut, USA.

Country: United States

AGENCY: United States NCI

GRANT: R01-CA-115825

ACRONYM: CA

MEDLINETA: Physiol Genomics

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