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

Info iconThis preview shows pages 1–8. Sign up to view the full content.

View Full Document Right Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon

Info iconThis preview has intentionally blurred sections. Sign up to view the full version.

View Full DocumentRight Arrow Icon
This is the end of the preview. Sign up to access the rest of the document.

Unformatted text preview: C260A Lecture 6: Measuring Evidence for Single Nucleotide Polymorphism Christopher Lee October 15, 2009 Single Nucleotide Polymorphisms Every persons 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 Detecting SNPs Individual 1: ATGACTG Individual 2: ATGACTG Individual 3: ATGACTG Individual 4: ATGCCTG . 2 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 Basic Variant Scoring Model Assume true sequence is either normal ( S ) or mutant ( S ); Assume mutant population frequency Pr ( S ) = For each read obs i , assume detector gives p ( obs i | S ) and p ( obs i | S ) based on sequencing error probabilities. 4 p ( obs i | ) ? p ( obs | ) ? Posterior scoring calculation? 5 Problems with the Basic Model Assumed fixed mutant frequency . When does this mat- ter? Minimum detectable with this scoring method? Assumed obs i independent. When does this matter?...
View Full Document

Page1 / 31

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

This preview shows document pages 1 - 8. Sign up to view the full document.

View Full Document Right Arrow Icon
Ask a homework question - tutors are online