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Record linkage of CODIS profiles with SNP genotypes

Explore the advantages of CODIS and SNP genotyping in record linkage, addressing privacy concerns and backward compatibility. Learn about the implications and benefits of combining SNP and CODIS data for improved accuracy and linkage.

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Record linkage of CODIS profiles with SNP genotypes

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  1. Record linkage of CODIS profiles with SNP genotypes Doc Edge February 20th, 2018 NIJ R&D seminar

  2. Acknowledgments Other Collaborators: Jaehee Kim Jun Li Discussion: ArbelHarpak Rosenberg Lab Funding: National Institute of Justice Stanford Graduate Fellowship Bridget Algee-Hewitt Noah Rosenberg

  3. Overview CODIS

  4. Overview CODIS The rest of the genome

  5. Overview CODIS The rest of the genome

  6. Overview CODIS The rest of the genome

  7. Advantages of CODIS • Highly diverse, so low false match probability.

  8. Advantages of CODIS • Highly diverse, so low false match probability. • Possible to get (nearly) unique identifiers with ‘90s-era technology.

  9. Disadvantages of STR genotyping • Few markers mean that it’s hard to • Resolve mixtures • Resolve familial relationships

  10. Disadvantages of STR genotyping • Few markers mean that it’s hard to • Resolve mixtures • Resolve familial relationships • SNP genotyping is now cheaper and more informative (100s of thousands of markers)

  11. Major obstacle to switching to SNPs • Backward compatibility

  12. Major obstacle to switching to SNPs • Backward compatibility • Record linkage could solve this problem

  13. Another reason to be interested • Privacy / Procedure

  14. Another reason to be interested • Privacy / Procedure • “The CODIS loci…do not reveal the genetic traits of the arrestee.” – Maryland v. King (2013)

  15. Implications of linking

  16. Implications of linking Privacy concerns

  17. Implications of linking Privacy concerns Backward compatibility

  18. Implications of linking Privacy concerns Backward compatibility Phenotype prediction

  19. Recombination and linkage Descendants Ancestors Adapted from Li & Jiang, 2005

  20. Recombination and linkage Descendants Ancestors Adapted from Li & Jiang, 2005

  21. Recombination and linkage Descendants Ancestors Adapted from Li & Jiang, 2005

  22. Recombination and linkage Descendants Ancestors Adapted from Li & Jiang, 2005

  23. Recombination and linkage Descendants Ancestors Adapted from Li & Jiang, 2005

  24. Imputation works for SNPs Adapted from Edge, Goroochurn, & Rosenberg, 2013, Figure 4

  25. Imputation works for SNPs GATTACA GATTACA GATTACA GATTACA GATTACA GATTACA Adapted from Edge, Goroochurn, & Rosenberg, 2013, Figure 4

  26. Imputation works for SNPs GATTACA TAGACAT GATTACA GATTACA TAGACAT GATTACA GATTACA GATTACA TAGACAT TAGACAT Adapted from Edge, Goroochurn, & Rosenberg, 2013, Figure 4

  27. Imputation works for SNPs GATTACA TAGACAT GATTACA GATTACA TAGACAT GATTACA GATTACA GATTACA TAGACAT TAGACAT GATTACA TAGACAT Reference Panel Adapted from Edge, Goroochurn, & Rosenberg, 2013, Figure 4

  28. Imputation works for SNPs GATTACA TAGACAT GATTACA GATTACA TAGACAT GATTACA GATTACA GATTACA TAGACAT TAGACAT ??T???? Study Sample ??T???? ??G???? GATTACA TAGACAT Reference Panel Adapted from Edge, Goroochurn, & Rosenberg, 2013, Figure 4

  29. Imputation works for SNPs GATTACA TAGACAT GATTACA GATTACA TAGACAT GATTACA GATTACA GATTACA TAGACAT TAGACAT GATTACA Study Sample GATTACA TAGACAT GATTACA TAGACAT Reference Panel Adapted from Edge, Goroochurn, & Rosenberg, 2013, Figure 4

  30. Question 1 • Is imputation possible in STRs?

  31. Our Data (N = 978) Human Genome Diversity Project (HGDP) Image: NA Rosenberg, 2011

  32. Imputation for human STRs • Beagle 4.1 imputes multi-allelic markers using nearby SNPs. • Assess imputation accuracy (654 in training set, 218 in test set).

  33. CODIS Imputation Accuracy

  34. Question 2 • Can record linkage be performed by combining imputation information across sites?

  35. A data linkage view of the problem

  36. A data linkage view of the problem SNP Genotypes

  37. A data linkage view of the problem SNP Genotypes CODIS genotypes at each locus

  38. A data linkage view of the problem SNP Genotypes CODIS genotypes at each locus Can we link SNP records with CODIS records?

  39. Record linkage

  40. Fellegi & Sunter (1969) for CODIS

  41. Fellegi & Sunter (1969) for CODIS SNP haplotype

  42. Fellegi & Sunter (1969) for CODIS SNP haplotype CODIS allele

  43. Fellegi & Sunter (1969) for CODIS SNP haplotype CODIS allele Prob. of observing pair given NO MATCH

  44. Fellegi & Sunter (1969) for CODIS SNP haplotype CODIS allele Prob. of observing pair given NO MATCH

  45. Fellegi & Sunter (1969) for CODIS SNP haplotype CODIS allele Prob. of observing pair given NO MATCH

  46. Fellegi & Sunter (1969) for CODIS SNP haplotype CODIS allele Prob. of observing pair given NO MATCH Prob. of observing pair given MATCH:

  47. Fellegi & Sunter (1969) for CODIS SNP haplotype CODIS allele Prob. of observing pair given NO MATCH Prob. of observing pair given MATCH:

  48. Fellegi & Sunter (1969) for CODIS SNP haplotype CODIS allele Prob. of observing pair given NO MATCH Prob. of observing pair given MATCH:

  49. Fellegi & Sunter (1969) for CODIS SNP haplotype CODIS allele Prob. of observing pair given NO MATCH Prob. of observing pair given MATCH:

  50. Match-score matrix

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