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

The comparison of the

software program

Bonaparte with the

Missing

Persons/DVI-module of CODIS 7

Dr.Ir. C.P. (Kees) van der Beek MBA Custodian Dutch DNA-database

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Content of the presentation

•Dutch missing persons DNA-database •History of Bonaparte

•Properties of Bonaparte

•Comparison of Bonaparte with CODIS 7 •Conclusions

Dutch missing persons DNA-database

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

chil-dren are possible (low stringency search) but in this way only comparisons with single parents are possible •For more complex pedigrees other programs were used

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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

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.

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

Bayesian networks

X

X

Assume child missing.

Remains of UI found with genotype GUI

Father _f, mother _m have genotype: Gf en Gm

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)

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Bayesian network of a pedigree

W.Wiegerinck, W. Burgers 8

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

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Flight 8U 771 (Tripoli Crash)

W.Wiegerinck, W. Burgers 10

• Crash of Afriqiyah Airways flight 771

• 103 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.

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Pedigree Editor

family member with DNA profile family member without DNA profile

Missing person Stackpanel with all

Individuals in current project.

Probabilities denoting confidence in parent-child relations.

Import of DNA-profiles

• Excel

• XML-files (CODIS / Genemapper)

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Match Results

Global list of matches

Number of mutations in pedigree: Δ Mut = mutations due to UI

Min Mut = mutations inherent in pedigree Mut = Min Mut + Δ Mut

Bonaparte - Report

+ Pedigree picture + LR per locus + Match parameters + total LR

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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

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

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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 DNA-gateway 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

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