Using Familias and FamLink

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Using Familias and FamLink
Athens 29 May, 2014
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NORWEGIAN UNIVERSITY OF LIFE SCIENCES
Familias
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Familias

• Calculate likelihoods in relationship testing
• Define arbitrary relationships
• Different mutation models
• Silent alleles
• Subpopulation correction
• Generate pedigrees
• Calculate priors
• Easy to use / Userfriendly

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Familias At a glance

• Define general frequency database
• Change mutations

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Familias At a glance

• Define marker specific database sizes
• Define dropout probability
• Mutations
• Silent allele

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Familias At a glance

• Case data dialog
• Import/Edit DNA data
• Compare profiles

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Familias At a glance

• Compare profiles

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Familias At a glance

• Random match probability

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Familias At a glance

• Define pedigrees/hypotheses

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Familias At a glance

• Defining relations
• As Parent-Child
• Paternity
• Siblings

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Parent Child
Alleged father Child
Mother Child
Parent Child
Father Sibling1
Mother Sibling1
Father Sibling2
Mother Sibling2
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Recent news in Familias 3

• New mutation model
• Simulation interface
• DVI module
• Blind search feature
• Direct matching
• Random match calculation
• Create database feature
• Dropouts

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Familias Simulations

• Simulation options

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Familias Simulations

• Simulation results

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Familias Simulations

• 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

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Familias DVI

• What is a DVI operation?
• What is the purpose of developing a DVI module?
• Alternative softwares
• Brief overview
• Blind search module

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Familias DVI

• Add Unidentified persons

NORWEGIAN UNIVERSITY OF LIFE SCIENCES
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Familias DVI

• Blind search

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Familias DVI

• Blind search results

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Familias DVI

• Add reference data

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Familias DVI

• Edit reference family

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Familias DVI

• Matching

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Familias Dropouts

• 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

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• Dropout versus silent allele

L1 19,19 L2 12,12
L1 16,17 L2 10,11
L1 17,18 L2 10,10
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Familias

Questions?
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NORWEGIAN UNIVERSITY OF LIFE SCIENCES
FamLink
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FamLink
? What can FamLink do?
NORWEGIAN UNIVERSITY OF LIFE SCIENCES

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

Implements the Lander-Green Different than
Familias Merlin
algorithm
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FamLink At a glance

Define
allele
frequency
database
NORWEGIAN UNIVERSITY OF LIFE SCIENCES

Currently restricted to two markers
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FamLink At a glance

Define
recombination
rate
NORWEGIAN UNIVERSITY OF LIFE SCIENCES

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
NORWEGIAN UNIVERSITY OF LIFE SCIENCES

We display two methods
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FamLink Familias connection

Calculate likelihoods for a
Familias
project
NORWEGIAN UNIVERSITY OF LIFE SCIENCES

Get likelihoods for all your markers

Linkage
considered
for all markers
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FamLink

Questions?
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NORWEGIAN UNIVERSITY OF LIFE SCIENCES
EXERCISES
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