Besides raw detecon there are a number of problems

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Unformatted text preview: y related species (i.e. humans, chimpanzees and other mammals). 22 Copy Number Variants •  altera/ons of the DNA of a genome that results in the cell having an abnormal number of copies of one or more sec/ons of the DNA 23 •  Eleva/ng the gene copy number of a par/cular gene can up ­regulate that gene. •  CNVs have been associated with suscep/bility or resistance to disease. •  Are associated with au/sm, schizophrenia, learning disabili/es, autoimmune disorders, and cancer. •  Higher copy number of CCL3L1 has been associated with lower suscep/bility to HIV infec/on. •  Most common CNVs have li[le or no role in causing disease. 24 Detec/on of SV’s Using Paired ­ End Short Read Data Paired ­End Data •  The paired ­ends of a clone help iden/fy deformi/es/ structural varia/on in the donor genome. •  Some SVs are copy neutral (inversions), while others are copy number variant (dele/ons/duplica/ons). •  Besides raw detec/on, there are a number of problems that we might want to solve computa/onally. Paired ­end short read data (insert distribu/on known due to fragment size selec/on) 27 Methods for Detec/ng SVs 28 Mate ­pair or paired ­end mapping abnormali/es Read ­depth signals Split read alignments Using BWA or some other alignment tool. 29 Mate ­pair or paired ­end mapping abnormali/es Read ­depth signals Split read alignments 30 Mate ­pair or paired ­end mapping abnormali/es Read ­depth signals Split read alignments 31 Mate ­pair or paired ­end mapping abnormali/es Read ­depth signals Inser/on Split read alignments Dele/on 32 Mate ­pair or paired ­end mapping abnormali/es Read ­depth signals Split read alignments 33 Mate ­p...
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This note was uploaded on 02/10/2014 for the course CS 680 taught by Professor Staff during the Fall '08 term at Colorado State.

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