Hybridization genomics

D Shalon, SJ Smith, PO Brown. A DNA microairay system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 6 639-645, 1996. MB Eisen, PT Spellman, PO Brown, D Botstem. Cluster analysis and display of genomewide expression patterns. Proc Natl Acad Sci USA 95 14863-14868, 1998. 

F15. Furuta, H., Nishi, S., Le Beau, M. M., Femald, A. A., Yano, H., and Bell, G. I Sequence of human hexokinase HI cDNA and assignment of the human hexokinase m gene (HK3) to chromosome band 5q35.2 by fluorescence in situ hybridization. Genomics 36,206-209 (1996). 

Befort K, Mattei M, Roeckei N, Kieffer B. Chromosomal localization of the delta opioid receptor gene to human lp 34.3-p36.1 and mouse 4D bands by in situ hybridization. Genomics 1994 20 143-145. 

Figure 3.3 Comparison of array CGH among DNA extracted from fresh tissue, FFPE tissue by heating protocol or nonheating protocol for two human tissue samples of metastatic carcinoma in lymph node (a-c), and undifferentiated non-small cell carcinoma (d-f). Array CGH hybridization genomic profiles show ratio values representing relative copy number of single BACs. A good result is scored as 1.0 that indicates a low standard deviation for gains (>0.2), normal (0.0), or losses (<-0.2). In these two cases, fresh samples show best score as 2, both FFPE tissue samples show identical score of 3. Each spot represents the average of three replicates. Clones are ordered by chromosomal position as numbers at the bottom (x axis) of each picture. The y axis is the log2 ratio of test reference intensity. Provided by Sandy DeVries from Dr. Frederic Waldman s Lab at UCSF.

Lovene, M., Savarese, S., Cardi, T, Frusciante, L., Scotti, N., Simon, P. W., Carputo, D. (2007). Nuclear and eytoplasmic genome eomposition of Solanum bulbocastanum (+) Solanum tuberosum somatie hybrids. Genome, 50,443 50. 

D. Shalon, S.J. Smith, P.O. Brown, A DNA Microarray System for Analyzing Complex DNA Samples Using Two-color Fluorescent Probe Hybridization , Genome Res., 6(7), 639-645 (1996). 

Shalon D, Smith SJ, Brown PO. A DNA microarray system for analyzing complex DNA samples using two-color fluorescent probe hybridization. Genome Res 1996 6(7) 639-645. 

Lonvaud-Funel et al. (1989, 1991a) described the identification of LAB during vinification and wine storage by DNA-DNA hybridization. Genomic DNA of the strain to identify was hybridized with total genomic DNA probes extracted from reference strains. They found that this method was particularly efficient when used in colony hybridization to study mixed populations at least five different species can be detected in a mixture with this system (Lonvaud-Funel et al. 1991b). 

Hybridization. Genomic DNA (c. 3 pg)of E. graminis f. sp. horde was digested with the restriction endonucleases Hind III, Sst 1, Pst 1, Xho 1, Sal l, Eco R1 and Bam HI in accordance with the manufacturer s Instructions (BRL), separated by 0.7% agarose gel electrophoresis, and then Southern blotted (45) onto nylon membrane (Hybond-N Amersham International). Prehybridization and hybridization reactions were done at 42°C using 40% deionised formamide, and 5 x SSC and 5 x Denhards solution. 

Okita, C., Meguro, M., Hoshiya, H., Haruta, M., Sakamoto, Y., Oshimura, M. 2003. A new imprinted cluster on the human chromosome 7q21-q31, identified by human-mouse monochromosomal hybrids. Genomics (in press). 

Borneman, A. R., Desany, B. A., Riches, D., Affourtit, J. R, Forgan, A. H., Pretorius, I. S., et al. (2012). The genome sequence of the wine yeast VIN7 reveals an allotriploid hybrid genome with Saccharomyces cerevisiae and Saccharomyces kudriavzevii. FEMS Yeast Research, 12, 88-96. 

Modi, W. S., and Chen, Z. Q. (1998). Localization of the human CXC chemokine subfamily on the long arm of chromosome 4 using radiation hybrids. Genomics 47, 136 139. 

Fig. 4. Construction of a hybrid genome containing genes of SV40, bacteriophage A and E. coli.

For hybridization, genomic DNA is isolated from the tissue to be studied and treated with sodium bisulfite. Subsequently, regions of interest are amplified by PCR. For ensuring an unbiased amphfication of unmethylated and methylated regions, primers without CpG sequence motifs are selected. The amplicons are labeled with a fluorescent dye and hybridized to the microarray. 

Nkongolo, K.K., P. Michael and T. Demers. 2005. Application of ISSR, RAPD, and cytological markers to the certification of Picea mariana, P. glauca, and P. engelmannii trees, and their putative hybrids. Genome 48 302-311. 

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