Using Familias and Fam Link Athens 29 May

Using Familias and Fam. Link Athens 29 May, 2014

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – – – – Calculate likelihoods in relationship testing Define “arbitrary” relationships Different mutation models Silent alleles Subpopulation correction Generate pedigrees Calculate priors Easy to use / Userfriendly 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – At a glance - Define general frequency database - Change mutations 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – At a glance - Define marker specific database sizes Define dropout probability Mutations Silent allele 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – At a glance - Case data dialog - Import/Edit DNA data - Compare profiles 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – At a glance - Compare profiles 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – At a glance - Random match probability 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – At a glance - Define pedigrees/hypotheses 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – At a glance - Defining relations - As Parent-Child Paternity: Parent Child Alleged father Child Mother Child Siblings: 10 Parent Child Father Sibling 1 Mother Sibling 1 Father Sibling 2 Mother Sibling 2 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Recent news in Familias 3 – – – – New mutation model Simulation interface DVI module Blind search feature Direct matching Random match calculation Create database feature Dropouts 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – Simulations - Simulation options 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – Simulations - Simulation results 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – Simulations - Find good thresholds - - Investigate what we can expect - Include - 10 False positive/negative rate Kinship Mutations Silent alleles Multiple pedigrees - Investigate the number of persons we must genotype - Investigate the number of markers we must include www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – DVI - What is a DVI operation? What is the purpose of developing a DVI module? “Alternative” softwares Brief overview Blind search module 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – DVI - Add Unidentified persons 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – DVI - Blind search 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – DVI - Blind search results 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – DVI - Add reference data 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – DVI - Edit reference family 10 www. umb. no

- Matching NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias – DVI 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES 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 10 www. umb. no

Dropout versus silent allele L 1: 19, 19 L 2: 12, 12 23 L 1: 16, 17 L 2: 10, 11 L 1: 17, 18 L 2: 10, 10

– Questions? NORWEGIAN UNIVERSITY OF LIFE SCIENCES Familias 30 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link 10 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link What can Fam. Link do? – User-friendly software – Similar to Familias in many ways – Perform likelihood calculations on a number of predefined pedigrees – Takes linkage between markers into account – Does not implement a good mutation model – Simulation interface – Implements the Lander-Green algorithm 10 • Different than Familias • Merlin www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link – At a glance – Define allele frequency database – Currently restricted to two markers 11 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link – At a glance – Define recombination rate – Between 0 and 0. 5 12 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link – At a glance – Convert genetic distance (c. M) to recombination rate 13 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link – At a glance – Select main hypothesis 14 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link – At a glance – Select alternative hypotheses 15 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link – At a glance – Define DNA data 16 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES 17 Fam. Link – At a glance – Calculate likelihoods – We display two methods www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link – Familias connection – Calculate likelihoods for a Familias project – Get likelihoods for all your markers • Linkage considered for all markers 18 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES Fam. Link – Questions? 30 www. umb. no

NORWEGIAN UNIVERSITY OF LIFE SCIENCES EXERCISES 31 www. umb. no