Selection and validation of endogenous reference genes using a high throughput approach.
BACKGROUND
Endogenous reference genes are commonly used to normalize expression levels of other genes with the assumption that the expression of the former is constant in different tissues and in different physiopathological conditions. Whether this assumption is correct it is, however, still matter of debate. In this study, we searched for stably expressed genes in 384 cDNA array hybridization experiments encompassing different tissues and cell lines.


RESULTS
Several genes were identified whose expression was highly stable across all samples studied. The usefulness of 8 genes among them was tested by normalizing the relative gene expression against test genes whose expression pattern was known. The range of accuracy of individual endogenous reference genes was wide whereas consistent information could be obtained when information pooled from different endogenous reference genes was used.


CONCLUSIONS
This study suggests that even when the most stably expressed genes in array experiments are used as endogenous reference, significant variation in test gene expression estimates may occur and the best normalization is achieved when data from several endogenous reference genes are pooled together to minimize minimal but significant variation among samples. We are presently optimizing strategies for the preparation of endogenous reference gene mixtures that could yield information comparable to that of data pooled from individual endogenous reference gene normalizations.
Jin
Ping
P
Immunogenetics Section, Department of Transfusion Medicine, Clinical Center, NIH Bethesda, MD 20892, USA. pjin@mail.cc.nih.gov
Zhao
Yingdong
Y
Ngalame
Yvonne
Y
Panelli
Monica C
MC
Nagorsen
Dirk
D
Monsurró
Vladia
V
Smith
Kina
K
Hu
Nan
N
Su
Hua
H
Taylor
Phil R
PR
Marincola
Francesco M
FM
Wang
Ena
E
D002277:Carcinoma / Q000235:genetics / Q000473:pathology; D002460:Cell Line; D045744:Cell Line, Tumor; D018076:DNA, Complementary / Q000235:genetics; D020869:Gene Expression Profiling / Q000379:methods* / Q000592:standards; D005786:Gene Expression Regulation; D005796:Genes; D006801:Humans; D008544:Melanocytes / Q000378:metabolism; D008545:Melanoma / Q000235:genetics / Q000473:pathology / Q000556:secondary; D009506:Nevus / Q000235:genetics / Q000473:pathology; D009693:Nucleic Acid Hybridization; D020411:Oligonucleotide Array Sequence Analysis; D009928:Organ Specificity; D012333:RNA, Messenger / Q000235:genetics; D012334:RNA, Neoplasm / Q000235:genetics; D012015:Reference Standards; D015203:Reproducibility of Results; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012878:Skin Neoplasms / Q000235:genetics / Q000473:pathology
D018076:DNA, Complementary; D012333:RNA, Messenger; D012334:RNA, Neoplasm