Array Comparative Genomic Hybridization: Protocols and by Diponkar Banerjee (auth.), Diponkar Banerjee, Sohrab P. Shah

By Diponkar Banerjee (auth.), Diponkar Banerjee, Sohrab P. Shah (eds.)

The earliest descriptions of human chromosomes initiated the genomics revolution that's now upon us. Array Comparative Genomic Hybridization: Protocols and Applicationsexplores the scope of what's now attainable so far as documenting abnormalities linked to numerous human cancers. whereas the expertise for interrogating the human genome maintains to conform, refinement of comparative genomic hybridization (CGH) utilizing array CGH and similar applied sciences have supplied huge, immense perception into human cancers at a reasonable scale. Written within the profitable Methods in Molecular Biology™ sequence layout, chapters comprise introductions to their respective issues, lists of the required fabrics and reagents, step by step, effortlessly reproducible protocols, and notes on troubleshooting and warding off recognized pitfalls.

Authoritative and simply available, Array Comparative Genomic Hybridization: Protocols and Applicationsprovides researchers with well-honed methodologies to profit those ideas for his or her personal use in study or scientific diagnostic laboratories.

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5. Add 5 μl of Stop Buffer to each tube and place on ice. The reaction can be stored at −20 °C overnight. 6. Purify sample with Microcon Centrifugal Filters Ultracel YM-30 (Millipore #42410); Add 430 μl of TE buffer to each tube, load on a column, and centrifuge in microcentrifuge for 10 min at 10,000 rpm (6000 × g). Proceed with washing and recovery as described by manufacturer. 7. 5 μl with TE buffer. 8. Check the efficiency of labeling and the yield of DNA using NanoDrop. Typical yield is 7–10 μg of DNA and samples contain 50–80 pmol of labeled nucleotides per μg of DNA.

HMM’s probabilistic approach assigns confidence measures or p-value to the estimate of each probe state. However, this algorithm tends to require significant computational time. The CBS algorithm is similar to ADM-like algorithm in that it samples adjacent probes to arrive at a robust estimation of the true range of the aberrant segment. However, unlike ADM, CBS iterates within any given initial segment and measures the difference of log ratio means between two adjacent candidate segments to find a breakpoint.

8. Przybytkowski E, Ferrario C, Basik M (2011) The use of ultra-dense array CGH analysis for the discovery of micro-copy number alterations and gene fusions in the cancer genome. BMC Med Genomics 4:16 9. Pinto D, Darvishi K, Shi X et al (2011) Comprehensive assessment of array-based platforms and calling algorithms for detection of copy number variants. Nat Biotechnol 29:512–520 10. Klopfleisch R, Weiss AT, Gruber AD (2011) Excavation of a buried treasure–DNA, mRNA, miRNA and protein analysis in formalin fixed, paraffin embedded tissues.

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