Gene copy number

The stable RN A species are represented by repetitive genes. Indeed some species are known to duplicate these genes into extra-chromosomal copies during periods of development. Thus the amphibian, Xempus sp. contains 500 copies of the sequence coding for ribosomal RNA and several thousand copies of the genes for5SRNA.  

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Morlino, G.B., Tizzani, L., Fleer, R. et al. (1999) Inducible amplification of gene copy number and heterologous protein production in the yeast Kluyveromyces lactis. Applied and Environmental Microbiology, 65 (11), 4808 1813. 

The performance of a biotreatment system ultimately depends on optimization of the activity of microbes and the ability to control the process parameters of the treatment system [157]. In this respect, the ability to monitor gene copy numbers and gene expression is highly useful for real time optimization of the efficiency of a biotreatment system. Advanced molecular techniques as well as low cost methods (e.g., antibody detection of enzymes based on color reaction strips fluorescence i.e., GFP marked organisms with UV light detection) can also be applied to monitor the microbial community structure, persistence of the added bacteria, and their interactions with indigenous populations. 

Davies, J. and Reff, M., Chromosome localization and gene-copy-number quantification of three random integrations in Chinese-hamster ovary cells and their amplified cell lines using fluorescence in situ hybridization, Biotechnol. Appl. Biochem., 33, 99-105, 2001. 

Application of Genomic Internal Standard for Quantifying Gene Copy Number. 356... 

Finally, as we show in the last section of the chapter, the method is generally applicable to quantitating nucleic acids rather than just mRNAs. For example, establishment of gene copy number in engineered cell... 

Gene copy number — Tumors are known to contain variable numbers of genes relative to normal tissue. Comparison of the normal and tumor gene populations is useful in identifying tumors and their differentiated states. 

Stasik Cl, Nitta H, Zhang W et al (2010) Increased MTC gene copy number correlates with increased mRNA levels in diffuse large B-cell lymphoma. Haematologica 95 597-603... 

Orntoff TF, Thykjaer T, Waldman FM, WolfH, Cells JE. (2002) Genome-wide study of gene copy numbers, transcripts, and protein levels in pairs of non-invasive and invasive human transitional ceU carcinomas. Mol CellProteomics 1, 37-45. 

Alterations in the gene copy number of miRNAs are detected in a variety of human cancers (41,42,43). Zhang et al. (41) showed that miRNAs exhibited high-frequency genomic alterations in human ovarian, breast cancer, and melanoma using high-resolution array-based comparative genomic hybridization. 

Use of Single-Nucleotide Polymorphism Array for Tumor Aberrations in Gene Copy Numbers... 

Yang SH, Seo MY, Jeong HJ et al. Gene copy number change events at chromosome 20 and their association with recurrence in gastric cancer patients. Clin Cancer Res 2005 11 612-620. 

One of the major problems with using tissue from formalin-fixed or paraffin-embedded samples is the presence of normal tissue in the sample. Contamination from normal cells can be up to 95% (13). This can lead to difficulties with analyzing subsequent assays. For example, detecting loss of heterozygosity can be highly dependant on the amount of normal cell contamination in the sample (14), and gene copy number differences between tumor and germline may be impossible to accurately determine. 

McLeod HL, Keith WN. Variation in topoisomerase 1 gene copy number as a mechanism for intrinsic drug sensitivity. Br J Cancer 1996 74 508-512. 

Hirsch FR, Varella-Garcia M, Bunn PA, Jr. et al. Epidermal growth factor receptor in non-small-cell lung carcinomas correlation between gene copy number and protein expression and impact on prognosis. J Clin Oncol 2003 21 3798-3807. 

Gene Clone Size Gene copy number Enzyme/function/location Expression characteristics Organ specificity... 

Moch, H., Sauter, G., Gasser, T., Bubendorf, L., Presti, J., Mihatsch, M. J., and Waldman, F. M. 1998. EGF-r gene copy number gains detected by fluorescence in situ hybridization in renal cell carcinoma.. /. Pathol. 7 544—548. 

Lee, J.A. and Lupski, J.R., Genomic rearrangements and gene copy-number alterations as a cause of nervous system disorders, Neuron, 52(1), 103, 2006. 

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