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Using Familias and FamLink

Using Familias and FamLink. Athens 29 May , 201 4. NORWEGIAN U N IVERSI T Y OF LIFE SC I ENCES. Fam ilias. 10. w w w. um b.no. Fam ilias. Calculate likelihoods in relationship testing Define “arbitrary” relationships Different mutation models Silent alleles Subpopulation correction

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Using Familias and FamLink

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  1. UsingFamilias and FamLink Athens 29 May, 2014

  2. NORWEGIAN UNIVERSITYOFLIFESCIENCES Familias 10 www.umb.no

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

  4. Familias – At a glance • Define general frequency database • Change mutations NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  5. Familias – At a glance • Define marker specific database sizes • Define dropout probability • Mutations • Silent allele NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  6. Familias – At a glance • Case data dialog • Import/Edit DNA data • Compare profiles NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  7. Familias – At a glance • Compare profiles NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  8. Familias – At a glance • Random match probability NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  9. Familias – At a glance • Define pedigrees/hypotheses NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  10. Familias – At a glance • Defining relations • As Parent-Child Paternity: Siblings: NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  11. Recentnews in Familias 3 • New mutation model • Simulation interface • DVI module • Blind search feature • Direct matching • Random match calculation • Create database feature • Dropouts NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  12. Familias – Simulations • Simulation options NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  13. Familias – Simulations • Simulation results NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  14. 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 NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  15. Familias – DVI • What is a DVI operation? • What is the purpose of developing a DVI module? • “Alternative” softwares • Brief overview • Blind search module NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  16. Familias – DVI • Add Unidentified persons NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  17. Familias – DVI • Blind search NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  18. Familias – DVI • Blind search results NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  19. Familias – DVI • Add reference data NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  20. Familias – DVI • Edit reference family NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  21. Familias – DVI • Matching NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  22. 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 NORWEGIAN UNIVERSITYOFLIFESCIENCES 10 www.umb.no

  23. Dropout versus silent allele L1: 19,19 L2: 12,12 L1: 16,17 L2: 10,11 L1: 17,18 L2: 10,10

  24. Familias – Questions? NORWEGIAN UNIVERSITYOFLIFESCIENCES 30 www.umb.no

  25. NORWEGIAN UNIVERSITYOFLIFESCIENCES FamLink 10 www.umb.no

  26. FamLink WhatcanFamLinkdo? NORWEGIAN UNIVERSITYOFLIFESCIENCES – – – User-friendlysoftware Similar toFamilias in manyways Performlikelihood calculations on anumberof pedigrees Takeslinkage betweenmarkersinto account Doesnotimplementa goodmutationmodel Simulationinterface predefined – – – – ImplementstheLander-Green •Different thanFamilias •Merlin algorithm 10 www.umb.no

  27. FamLink – At a glance – Define allele frequency database NORWEGIAN UNIVERSITYOFLIFESCIENCES – Currently restricted to two markers 11 www.umb.no

  28. FamLink – At a glance – Define recombination rate NORWEGIAN UNIVERSITYOFLIFESCIENCES – Between0 and0.5 12 www.umb.no

  29. FamLink – At a glance – Convert genetic distance (cM) to recombination rate NORWEGIAN UNIVERSITYOFLIFESCIENCES 13 www.umb.no

  30. FamLink – At a glance – Select main hypothesis NORWEGIAN UNIVERSITYOFLIFESCIENCES 14 www.umb.no

  31. FamLink – At a glance – Select alternative hypotheses NORWEGIAN UNIVERSITYOFLIFESCIENCES 15 www.umb.no

  32. FamLink – At a glance – Define DNA data NORWEGIAN UNIVERSITYOFLIFESCIENCES 16 www.umb.no

  33. FamLink – At a glance – Calculate likelihoods NORWEGIAN UNIVERSITYOFLIFESCIENCES – Wedisplaytwomethods 17 www.umb.no

  34. FamLink – Familias connection – Calculatelikelihoodsfora Familias project NORWEGIAN UNIVERSITYOFLIFESCIENCES – Getlikelihoods for all your markers • Linkage considered forallmarkers 18 www.umb.no

  35. FamLink – Questions? NORWEGIAN UNIVERSITYOFLIFESCIENCES 30 www.umb.no

  36. NORWEGIAN UNIVERSITYOFLIFESCIENCES EXERCISES 31 www.umb.no

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