Genomic hybridizations

Kasamatsu A, Endo Y, Uzawa K, Nakashima D, Koike H, Hashitani S, et al. Identification of candidate genes associated with salivary adenoid cystic carcinomas using combined comparative genomic hybridization and oligonucleotide microarray analyses. Int J Biochem Cell Biol 2005 37 1869-80. 

DNA QUALITY EVALUATED BY ARRAY -BASED COMPARATIVE GENOMIC HYBRIDIZATION... 

Array-based comparative genomic hybridization (a-CGH) is a genomic analysis system that allows identification of alterations in DNA sequence and copy number, with a potential goal of individualized diagnosis and targeted cancer therapy.35,36 A number of reports have described application of a-CGH to DNA extracted from FFPE tissues, with variable results.35,37 38... 

DeVries S, Nyante S, Korkola J, et al. Array-based comparative genomic hybridization from formalin-fixed, paraffin-embedded breast tumors. J. Mol. Diagn. 2005 7 65-71. 

Pinkel D, Albertson DG. Comparative genomic hybridization [Review]. Annual Review of Genomics and Human Genetics 2005 6 331-354. 

Ylstra B, Van den IJssel P, Carvalho B, et al. BAC to the future or oligonucleotides a perspective for micro array comparative genomic hybridization (array CGH). Nucleic Acids Res. 2006 34 445 150. 

Daigo Y, Chin S-F, Gorringe KL, et al. Degenerate oligonucleotide primed-polymerase chain reaction-based array comparative genomic hybridization for extensive Amplicon profiling of breast cancers. A new approach for the molecular analysis of paraffin-embedded cancer tissue. Am. J. Pathol. 2001 158 1623-1631. 

Klein CA, Schmidt-Kittler O, Schardt JA, et al. Comparative genomic hybridization, loss of heterozygosity, and DNA sequence analysis of single cells. Proc. Natl. Acad. Sci. USA 1999 96 4494-4499. 

Hapten-labeled DNA probes for FISH assays can be used for BISH assays and those probes can be purchased from various vendors. If commercial hapten-labeled DNA probes are not available, DNA probes can be labeled with haptens by nick translation or by PCR in a laboratory. Nick translation kit can be utilized for labeling DNAprobes with hapten (10976776001, Roche Applied Science, Germany). New probes must be analyzed for the specificity by FISH or BISH assays using a comparative genomic hybridization metaphase control slide. 

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. 

Kallioniemi A, Kallioniemi OP, Sudar D et al. Comparative genomic hybridization for molecular cytogenetic analysis of solid tumors. Science 1992 258 818-821. 

Pinkel D, Albertson DG. Array comparative genomic hybridization and its applications in cancer. Nat... 

Rodriguez V, Chen Y, Elkahloun A et al. Chromosome 8 BAC array comparative genomic hybridization and expression analysis identify amplification and overexpression of TRMT12 in breast cancer. 

Milunsky JM, Huang XL. Unmasking Kabuki syndrome chromosome 8p22-8p23.1 duplication revealed by comparative genomic hybridization and BAC-FISH. Clin Genet 2003 64(6) 509-516. 

Solinas-Toldo S, Lampel S, Stilgenbauer S, Nickolenko J, Benner A, Dohner H, Cremer T, Lichter P. Matrix-based comparative genomic hybridization biochips to screen for genomic imbalances. Genes Chromosomes Cancer 1997 20(4) 399-407. 

Borneman, A. R., Bartowsky, E. J., McCarthy, J., and Chambers, P. J. (2010). Genotypic diversity in Oenococcus oeni by high-density microarray comparative genome hybridization and whole genome sequencing. Appl. Microbiol. Biotechnol. 86, 681-691. 

Recent times have seen the advent of high throughput assays such as array comparative genomic hybridization and cDNA microarray, which have lead to the rapid discovery of thousands of potential biomarkers. However, these need to be validated in tissue-based studies in large datasets to prove their potential utility. As these datasets are typically present in the form of formalin fixed paraffin-embedded tissue blocks, immunohistochemical (IHC) methods are ideal for validation. However, performing whole-section IHC on hundreds to thousands of blocks requires lot of resources in terms of reagents and time. In addition, an average block will yield less than 300 slides of 5 pm each. The tissue microarray (TMA) technique circumvents some of these problems. 

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