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 know-how for interrogating the human genome maintains to conform, refinement of comparative genomic hybridization (CGH) utilizing array CGH and comparable applied sciences have supplied huge, immense perception into human cancers at a reasonable scale. Written within the winning Methods in Molecular Biology™ sequence layout, chapters contain introductions to their respective issues, lists of the required fabrics and reagents, step by step, comfortably reproducible protocols, and notes on troubleshooting and fending off identified pitfalls.
Authoritative and simply obtainable, Array Comparative Genomic Hybridization: Protocols and Applicationsprovides researchers with well-honed methodologies to benefit those thoughts for his or her personal use in learn or medical diagnostic laboratories.
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Extra resources for Array Comparative Genomic Hybridization: Protocols and Applications
Several steps can be taken to avoid the “garbage-in” problem and thus vastly improve the likelihood of producing high quality data and corresponding interpretation: (1) Careful assessment of sample quality, (2) Rigorous quality control for each step in sample processing, (3) meticulous experimental procedure, and (4) well informed and statistically accurate data processing and analysis. These steps are reviewed herein and will lead to confidence in the data, results, and interpretation. Clinical cancer samples are either formalin-fixed paraffin embedded (FFPE) specimens or snap-frozen tissues of tumor pieces or tumor biopsies.
The higher this ratio the better the quality of the array. If this ratio is low, there is significant noise in the data. 7). 5. ReproducibilityRed/ReproducibilityGreen (reproducibility): For each channel, this metric calculates the median percent coefficient of variation (% CV) of background-subtracted signal for probes replicated on the chip, called noncontrol probes, after outlier rejection. It is a measure of the reproducibility of features. 2) indicates a problem with the hybridization procedure such as slide leakage.
DNA methylation occurs on the C5 position of cytosines (5mC) that precede guanines (CpG dinucleotides) and at non-CpG cytosines in plants and embryonic stem cells in mammals (17–19). Additional modifications of cytosine, including 5-hydroxymethylation (5hmC) and its oxidized derivatives, 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC), catalyzed by the ten-eleven translocation (TET) (20) family of proteins acting on methylated cytosine, have been shown to exist in mammalian cells(21–29). 5hmC, either directly or through 5caC, is thought to lead to the demethylation of 5mC through both passive and active mechanisms, although direct evidence of an active 5mC to cytosine conversion has remained elusive (21, 29–31).