666.20 - The Lander-Green Algorithm Biostatistics 666...

Info iconThis preview shows pages 1–14. Sign up to view the full content.

View Full Document Right Arrow Icon
The Lander-Green Algorithm Biostatistics 666 Lecture 22
Background image of page 1

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

View Full Document Right Arrow Icon
Last Lecture… Relationship Inferrence z Likelihood of genotype data z Adapt calculation to different relationships Siblings Half-Siblings Unrelated individuals z Importance of modeling error
Background image of page 2
Today … z The Lander-Green Algorithm z Multipoint analysis in general pedigrees z The basis of modern pedigree analysis packages
Background image of page 3

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

View Full Document Right Arrow Icon
Hidden Markov Model 1 X 2 X 3 X M X 2 I 3 I M I 1 I ) | ( 1 2 I I P ) | ( 2 3 I I P (...) P ) | ( 1 1 I X P ) | ( 2 2 I X P ) | ( 3 3 I X P ) | ( M M I X P IBD states form a Hidden Markov Chain along the chromosome …
Background image of page 4
Fundamental Calculations z Enumerate possible IBD states z Transition probability for neighboring IBD states z Probability of genotype data given IBD state
Background image of page 5

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

View Full Document Right Arrow Icon
Lander-Green Algorithm z More general definition for I, the "IBD vector" z Probability of genotypes given “IBD vector” z Transition probabilities for the “IBD vectors” = = = 1 1 2 1 1 ) | ( ) | ( ) ( ... I m i i i I m i i i I X P I I P I P L m
Background image of page 6
Part I “IBD Vectors” Inheritance Vectors Descent Graphs Gene Flow Pattern
Background image of page 7

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

View Full Document Right Arrow Icon
“IBD Vector” Specifications z Specify IBD between all individuals z Must be compact z Must allow calculation of: Conditional probabilities for neighboring markers Probability of observed genotypes
Background image of page 8
“IBD Vector” z Specify the outcome of each meiosis Which of the two parental alleles transmitted? z Implies founder allele carried by each individual z Implies whether a pair of chromosomes is identical-by-descent
Background image of page 9

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

View Full Document Right Arrow Icon
For any pedigree, consider … z What are the meioses? z What are the possible outcomes for the entire set of meioses?
Background image of page 10
Example …
Background image of page 11

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

View Full Document Right Arrow Icon
What we are doing . .. z Listing meioses z Alternating outcomes z The outcomes of all meioses define our “IBD vector” V 1 V 2 V 3 V 4 Meiosis 1 Meiosis 2 Meiosis 2
Background image of page 12
Example … Descent Graph AB CD EF GH This is one representation of inheritance in the pedigree. The 8 founder alleles
Background image of page 13

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

View Full Document Right Arrow Icon
Image of page 14
This is the end of the preview. Sign up to access the rest of the document.

{[ snackBarMessage ]}

Page1 / 40

666.20 - The Lander-Green Algorithm Biostatistics 666...

This preview shows document pages 1 - 14. Sign up to view the full document.

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