The comparison of the software program Bonaparte with the Missing Persons/DVImodule. Dr.Ir. C.P. (Kees) van der Beek MBA Custodian Dutch DNA-database

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1 The comparison of the software program Bonaparte with the Missing Persons/DVImodule of CODIS 7 Dr.Ir. C.P. (Kees) van der Beek MBA Custodian Dutch DNA-database Linköping 24 april 2012

2 Content of the presentation Dutch missing persons DNA-database History of Bonaparte Properties of Bonaparte Comparison of Bonaparte with CODIS 7 Conclusions Use of CODIS 7 and Bonaparte in the Netherlands 2

3 Dutch missing persons DNA-database The Netherlands also uses CODIS as its missing persons DNA-database In CODIS 5.7.X only direct comparisons between missing persons and unidentified persons were possible Also comparisons between possible parents and children are possible (low stringency search) but in this way only comparisons with single parents are possible For more complex pedigrees other programs were used (Familias, DNAview) 3

4 History of Bonaparte (I) In 2008 the Dutch government asked the NFI if it was ready to deal with the DNA-based identification of the victims of a mass disaster The NFI knew that the FBI was developing CODIS 6/7 but did not know when it would be ready and if it would fulfil the requirements of the NFI Because governamental funding was available the NFI decided to develop its own missing persons/dvi program together with the University of Nijmegen To calculate LR s Bonaparte uses Baysian networks 4

5 Bayesian networks A Bayesian network is a probabilistic graphical model that represents a set of random variables and their conditional dependences Advantages of working with Bayesian networks: The analysis tool is transparent and flexible Allows to incorporate other factors that play a role such as the measurement of error probability, missing data, statistics of more advanced genetic markers, uncertain relationships, etc. 5

6 Bayesian networks Father Mother Paternal Father Maternal Father Paternal Mother Maternal Mother Paternal Child Maternal Child Child 6 W.Wiegerinck, W. Burgers 6

7 The Likelihood Ratio (LR) Assume child missing. Remains of UI found with genotype GUI Father f, mother m have genotype: Gf en Gm X X Hypothesis1: UI = child (MP) Hypothesis2: UI = unrelated person LR = P(Gf,Gm,GUI UI=child of f and m) P(Gf,Gm,GUI UI=unrelated person) 7

8 Bayesiannetworkof a pedigree Bonaparte calculates probabilities using automatically generated Bayesian networks 8 W.Wiegerinck, W. Burgers 8

9 History of Bonaparte (II) The program was named Bonaparte because Napoleon Bonaparte made last names obligatory in the Netherlands in 1811 When Bonaparte was ready in 2010, CODIS 6/7 was also ready and both programs proved to have many properties in common Right after the validation of Bonaparte a real case came along 9

10 Flight 8U 771 (Tripoli Crash) Crash of Afriqiyah Airways flight fatalities (67 Dutch nationality) Largest previous case had about 20 victims. The identification process took several days. The Tripoli case has about 100 victims (about 10,000 matches). Bonaparte calculates all matches in several minutes. 10 W.Wiegerinck, W. Burgers 10

11 11 Lay-out Bonaparte

12 Stackpanel with all Individuals in current project. family member without DNA profile Missing person Probabilities denoting confidence in parent-child relations. family member with DNA profile Pedigree Editor 12

13 Import of DNA-profiles Excel XML-files (CODIS / Genemapper) F-alleles and allelic-dropouts are allowed 13

14 LR and 10log(LR) Match Results Global list of matches Number of mutations in pedigree: ΔMut= mutations due to UI Min Mut = mutations inherent in pedigree Mut= Min Mut+ ΔMut 14

15 Bonaparte - Report + Match parameters + total LR + DNA-profiles + Pedigree picture + LR per locus + Information about mutations/exclusions 15

16 CODIS Bonaparte comparison (I) Because the NFI did not want to use two programs for the same purpose it decided to compare both programs A student was trained to use both programs and was given the task to compare the different functionalities of both programs Both programs were provided with the same allele frequencies to be able to compare the Likelihood Ratio s calculated by both programs Overall both programs performed well and gave similar results in simple pedigrees without mutations 16

17 CODIS Bonaparte comparison (II) In spite of this the NFI presently prefers Bonaparte because it has several properties which are of special importance to the NFI: The calculations are transparent,have been validated manually and have been published (Dutch accreditation requirement) Baysian networks can easily and quickly handle complex pedigrees with multiple missing persons The mutation model will also detect unnoticed allelic drop-outs Bonaparte can handle incestuous pedigrees and pedigrees with loops Bonaparte shows Likelihood Ratio s and the presence of mutations per locus 17

18 Intended Dutch Missing Persons Setup CODIS will be used as the primary DNA-database for the safe storage of DNA-profiles of unidentified and missing persons and their family members Direct comparisons of missing persons and unidentified persons will still be done in CODIS using the Identity Searcher module CODIS will be used to generate export files for the DNAgateway of Interpol For pedigree searches DNA-profiles are exported from CODIS and imported in Bonaparte to find possible matches with family members. Pedigrees are generated automatically in Bonaparte based on the information exported from CODIS 18

19 Familial Searching in the Netherlands As of April 1, 2012 is allowed in the Netherlands Both the Missing Persons/DVI-module of CODIS 7 and Bonaparte have been used to find possible parents, children and sibblings in the first Dutch familial searching case The candidates found by both programs are presently analyzed to see if the same candidates have been selected and if their LR-ranking is the same 19