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lec6 - C260A Lecture 6 Measuring Evidence for Single...

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C260A Lecture 6: Measuring Evidence for Single Nucleotide Polymorphism Christopher Lee October 15, 2009
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Single Nucleotide Polymorphisms Every person’s genome is unique; on average there is one “letter difference” per 1000 letters in the DNA four-base code. These single-base variations are called Single Nucleotide Polymor- phisms (SNPs). Can be innocuous, or can cause devastating diseases like sickle cell anemia. 1
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Detecting SNPs Individual 1: ATGACTG Individual 2: ATGACTG Individual 3: ATGACTG Individual 4: ATGCCTG . 2
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Sequencing: Technical Problems Affordable sequencing methods produce short, random fragments . They are also highly error prone, especially at the end of the read. How to distinguish SNPs from sequencing errors? 3
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Basic Variant Scoring Model Assume true sequence is either normal ( S ) or mutant ( S ); Assume mutant population frequency Pr ( S ) = φ For each read obs i , assume detector gives p ( obs i | S ) and p ( obs i | S ) based on sequencing error probabilities. 4
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p ( obs i | φ ) ? p ( obs | φ ) ? Posterior scoring calculation? 5
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Problems with the Basic Model Assumed fixed mutant frequency φ . When does this mat- ter? Minimum φ detectable with this scoring method? Assumed obs i independent. When does this matter?
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