mcb104 handout week 14 - G ene Duplication - Multiple...

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Gene Duplication- Multiple copies of a gene in a genome. It is likely that after the duplication the functions of the genes have diverged somewhat (paralogs). Hemoglobin Hox clusters Pseudogene- Open Reading Frame (ORF) or partial ORF that is nonfunctional or inactive due to mutation. Whole Genome Duplication- When an entire genome duplicates (every chromosome) due to ancestral polyploidy. Saccharomyces sensu stricto lineage in yeast. Copy Number Variant- A 1kb or larger segment that is present in variable copy number in the genome. Segmental Duplication- A segment of DNA greater than 1 kb in size that is present in more than one copy in the haploid genome with greater than 90% sequence identity. A segmental duplication CAN BE a type of copy number variant. Techniques: Arrayed Comparative Genomic Hybridization- Label two different samples of genomic DNA (for example, a normal tissue sample and a tumor tissue sample), one with green fluorescence, the other with red fluorescence. Hybridize to a chip that has arrays of Bacterial Artificial Chromosomes (BACs) covering the entire genome. If there is equal hybridization, that spot on the chip (corresponding to a region in the genome) is present in equal copy numbers in both samples. If the spot is green, then that means that there are more copies of that part of the genome in the green-labeled sample. If you observe red, then vice versa. This technique can tell you if there are regions of one sample that has more copies of that genomic region than the other sample. Fluorescence In Situ Hybridization- Make a Fluorescently labeled DNA probe and hybridize it to a fixed tissue sample. The probe will bind to that region of the genomic DNA, revealing the number of copies that region is present in the genome. How many fluorescent spots would you expect to see for a diploid
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This note was uploaded on 01/28/2010 for the course MCB 104 taught by Professor Urnov during the Fall '09 term at University of California, Berkeley.

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mcb104 handout week 14 - G ene Duplication - Multiple...

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