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Freeware solutions to mixture interpretation and familial analysis

Freeware solutions to mixture interpretation and familial analysis. Thore Egeland Institute of forensic medicine University of Oslo EAFS Workshop, Sept 8, 2009, Glasgow. Background: LR (Paternity index). Essen-Möllers W: Posterior probabilities. Part 1: Unlinked markers: Familias.

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Freeware solutions to mixture interpretation and familial analysis

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  1. Freeware solutions to mixture interpretation and familial analysis Thore Egeland Institute of forensic medicine University of Oslo EAFS Workshop, Sept 8, 2009, Glasgow

  2. Background: LR (Paternity index). Essen-Möllers W: Posterior probabilities. Part 1: Unlinked markers: Familias. Part 2: Linked markers: FEST. Part 3: Mixtures of relatives: R library forensic. Contents

  3. LR (Paternity index ) H1: John Doe father. H2: Unknown man father. A,A B,B John Doe A,B

  4. Essen-Möller’s W (posterior probability) H1: John Doe father. H2: Unknown man father. A,A B,B John Doe Flat prior A,B pB= 0,05

  5. Several unlinked markers • Extends easily since multiplication is allowed.

  6. Part 1: familias • Prior models. • Several potentially complex pedigrees. • Mutation model. • Theta-correction. • Silent alleles.

  7. 1 2 3 5 4 Complex pedigrees . Many hypotheses - 941, 942, 943 and 944 found dead. - Only 943 old enough to be a mother. - DNA-profiles available for 1,2,3,4 and 5. XX 943 XY 941 944 942

  8. Modelling mutations • Mutation rate varies with • Sex of parent and locus.Alleles tend to mutate to close alleles:

  9. Theta - correction General formula available.

  10. If kinship:

  11. Female A Child B Silent alleles. Classical example H1: Female mother H2: unrelated Silent allele S, i.e, Female A,S and Child B,S?

  12. Egeland, T; Mostad, P; Mevåg, B; Stenersen, M: For Sci Int Vol 110, Nr. 1, 2000.

  13. General DNA data Case related DNA Known relations Persons Pedigrees (calculations)

  14. (changed)

  15. Part 2: Linked markers: FEST

  16. Unlinked markers may be insufficient • There are symmetric relations which cannot be resolved using unlinked autosomal markers. • There are distant family relationships that cannot be resolved since there are too few unlinked markers. • Haplotype data (Y, mtDNA) may sometimes help.

  17. B B A A half-sibs grand parent-grand child • Problem (Thompson, 1986): • A and B share no, one or two alleles IBD with probabilities:0.5, 0.5, 0. • Identical likelihoods. B A uncle-niece 18

  18. H1: A and B share a great-grandfather (HS-3-3 relation). H2: A and B unrelated. Distant family relationships

  19. Linked markers needed L2 L1 r: recombination fraction,0: completely linked, 0.5: unlinked. cM 0 r Classical linkage analysis: L1: disease mutation, L2: genetic marker. Objective: determine L1-location We, however, only need null-likelihood 20

  20. Part 3: Related contributors to mixtures • Family relationships must be accounted for when a typed contributor is related to an untyped contributor.

  21. Symmetric cases. Untyped suspect • Assume a stain is available. There is typed victim V.The untyped suspect is a close relative of V: • H1:V+ half-sib • H2:V+uncle • H3:V+grand-father • These hypotheses can not be distinguished based on unlinked autosomal markers

  22. Symmetric cases. Typed suspect • Assume next that the suspect S (half-sib) is typed and matches and that we consider • Hp:V+S, • Hd:V+unknown. • Normally evidence against S will be overwhelming. • Standard calculations, standard softwarelike DNAMIX can be used. • What happens if defence claims the perpetrator is a close relative?

  23. 100 simulations, 10 markers. Caucasian

  24. Implemented by Miriam Marusiakova based on Hu and Fung (2003)

  25. References • Buckleton, Triggs and Walsh (2005). CRC press. • Egeland, Mostad, Mevåg og Stenersen (2000).For Sci Int 110(1), 2000 • Familias: http://www.math.chalmers.se/~mostad/familias/ • Skare, Sheehan and Egeland. Bioinformatics (2009) • FEST: http://folk.uio.no/thoree/ • Hu and Fung (2003). Int J Leg Med 117(4) • R: forensic: http://cran.r-project.org/ (Author: Miriam Marusiakova)

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