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Using Familias and FamLinkAthens 29 May, 2014
Familias
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Familias
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– Calculate likelihoods in relationship testing– Define “arbitrary” relationships– Different mutation models– Silent alleles– Subpopulation correction– Generate pedigrees– Calculate priors– Easy to use / Userfriendly
Familias – At a glance
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- Define general frequency database- Change mutations
Familias – At a glance
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- Define marker specific database sizes- Define dropout probability- Mutations- Silent allele
Familias – At a glance
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- Case data dialog- Import/Edit DNA data- Compare profiles
Familias – At a glance
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- Compare profiles
Familias – At a glance
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- Random match probability
Familias – At a glance
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- Define pedigrees/hypotheses
Familias – At a glance
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- Defining relations- As Parent-ChildPaternity:
Siblings:
Parent Child
Alleged father Child
Mother Child
Parent Child
Father Sibling1
Mother Sibling1
Father Sibling2
Mother Sibling2
Recent news in Familias 3
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– New mutation model– Simulation interface– DVI module– Blind search feature– Direct matching– Random match calculation– Create database feature– Dropouts
Familias – Simulations
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- Simulation options
Familias – Simulations
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- Simulation results
Familias – Simulations
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- Simulations- Find good thresholds
- False positive/negative rate
- Investigate what we can expect- Include
- Kinship- Mutations- Silent alleles- Multiple pedigrees
- Investigate the number of persons we must genotype
- Investigate the number of markers we must include
Familias – DVI
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- What is a DVI operation?- What is the purpose of developing a DVI module?- “Alternative” softwares- Brief overview- Blind search module
Familias – DVI
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- Add Unidentified persons
Familias – DVI
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- Blind search
Familias – DVI
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- Blind search results
Familias – DVI
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- Add reference data
Familias – DVI
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- Edit reference family
Familias – DVI
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- Matching
Familias – Dropouts
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- What is a dropout?- The model
- Conditional genotype probabilities- Dropout probability
- Low quality profiles- Estimation of dropout probabilities
- Logistic regression- LR for a number of dropout probabilities
Dropout versus silent allele
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L1: 16,17L2: 10,11
L1: 17,18L2: 10,10
L1: 19,19L2: 12,12
Familias – Questions?
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FamLink
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FamLink What can FamLink do?
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–
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User-friendly software
Similar to Familias in many ways
Perform likelihood calculations on a number of pedigrees
Takes linkage between markers into
account Does not implement a good
mutation model Simulation interface
predefined
–
–
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– Implements the Lander-Green
• Different than Familias
• Merlin
algorithm
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FamLink – At a glance
– Define
allele
frequency
database
– Currently restricted to two markers
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FamLink – At a glance
– Define
recombination
rate
– Between 0 and 0.5
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FamLink – At a glance
– Convert
genetic
distance
(cM)to recombination
rate
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FamLink – At a glance
– Select
main
hypothesis
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FamLink – At a glance
– Select
alternative
hypotheses
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FamLink – At a glance
– Define
DNA
data
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FamLink – At a glance
– Calculate
likelihoods
– We display two methods
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FamLink – Familias connection
– Calculate likelihoods for a
Familias
project
– Get likelihoods for all your markers• Linkag
econsidered
for all markers
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FamLink – Questions?
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EXERCISES
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