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Statistical analyses of genetical data from trios

Statistical analyses of genetical data from trios. Thore.Egeland@medisin.uio.no Dep of Medical Genetics Ullevål University Hospital, Oslo. NAFA 2007 Sep 1, 1230. Contents. Forensics Paternity, wine and disasters Genehunting Genetical causes for cleft lip or palate. Common theme: Trios.

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Statistical analyses of genetical data from trios

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  1. Statistical analyses of genetical data from trios Thore.Egeland@medisin.uio.no Dep of Medical Genetics Ullevål University Hospital, Oslo NAFA 2007 Sep 1, 1230

  2. Contents • Forensics • Paternity, wine and disasters • Genehunting • Genetical causes for cleft lip or palate

  3. Common theme: Trios

  4. Female:AA Man: aa Child: Aa Trios. Data from one locus

  5. Forensics

  6. Female:AA Man: aa Child: Aa Forensic terminology Mendel

  7. Female:AA Man: aa Child: Aa Paternity index (PI) H1: Man father H2: Unknown man father (No doubt about mother)

  8. Freeware: Familias http://www.math.chalmers.se/~mostad/familias/

  9. Several loci • We can multiply PI-s from several markers provided they are unlinked. • If PI-s based on five markers are 10, 5, 2, 10, 20the combined result is PI=10*5*2*10*20=20 000 • Interpretation??

  10. Essen-Möller’s index (1938) • Assume 50% probability of paternity apriori. Then the posterior probability of paternity is W=PI/(1+PI)=0.99995=99.995% • Interpretation easier! But?

  11. Other applications: wine • “Historical Genetics: The Parentage of Chardonnay, Gamay, and Other Wine Grapes of Northeastern France”.Bowers et al. Science 3 September 1999.

  12. Other applications:disasters

  13. Genehunting

  14. Trios: affected child aa Aa aA

  15. Allele A is transmitted from the father aa Aa aA

  16. aa Aa Aa aa Aa Aa Basic idea • Collect a number of trios. Count the number of times A and a is transmitted. Departure from 50-50 transmission indicates that gene is involved. • Parent-of –origin effects can also be explored. ....

  17. Problem formulation • H0: No association gene-disease • HA: Association gene-disease • Equivalently • H0: A is transmitted with probability 50% • HA:A is transmitted with probability not equal 50% • p-value: “Probability of falsely claiming association”.

  18. Cleft lip and palate A transmitted: 0+1+9+16=26 times a transmitted: 0+1+9+7=17 times Lie and Jugessur, 2002

  19. P-value calculation • A transmitted: 26 times • a transmitted: 17 times • TDT-statistic: (17-26)2/(17+26)=1.88 • p-value=0.17 • Interpretation?

  20. Summary • In forensic identification problems, relationships are proved or disproved. • Paternity cases involve trios and is the predominant example. • Genehunting based on trios is practical and robust. Family relations must be confirmed.

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