Evaluating allelic drop-out probabilities using a Monte-Carlo simulation approach
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![Page 1: Evaluating allelic drop-out probabilities using a Monte-Carlo simulation approach](https://reader033.fdocuments.in/reader033/viewer/2022052904/5583bb33d8b42a7a798b4a5b/html5/thumbnails/1.jpg)
25 March 2013
Evaluating Drop-out Probabilities
Hinda Haned
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2 Estimating drop-out probabilities | Avila June 2013
A three-person mixture
sample: epithelial cells recovered from the victim of an assault two suspects are detained by the police
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3 Estimating drop-out probabilities | Avila June 2013
A three-person mixture
Hypotheses Hp: the victim, suspect 1 and one unknown contributed to the sample Hd: the victim and two unknowns contributed to the sample
Evaluation of the two hypotheses using likelihood ratios
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4 Estimating drop-out probabilities | Avila June 2013
Sensitivity analysis - LRmix
LRs range from 103 to 107:103 PrD=0.99107 PrD=0.41
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5 Estimating drop-out probabilities | Avila June 2013
Available methods Experimental mixtures (Perez et al, Coratian Med J, 2011)
the levels of drop-out, based on large sets of DNA mixtures obtained in different conditions
DNA quants Number of contributors Ratio of contribution
Maximum likelihood principle LoComation software (Gill et al 2007)
Drop-out probabilities that maximize the probability of observing the questioned epg
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6 Estimating drop-out probabilities | Avila June 2013
Available methods Experimental mixtures (Perez et al, Coratian Med J, 2011)
the levels of drop-out, based on large sets of DNA mixtures obtained in different conditions
DNA quants Number of contributors Ratio of contribution
Maximum likelihood principle LoComation software (Gill et al 2007)
Drop-out probabilities that maximize the probability of observing the questioned epg
Methods derive estimates from empirical distributions
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7 Estimating drop-out probabilities | Avila June 2013
Qualitative approach to the estimation of PrD
Relies on: the number of alleles observed in the sample the genotypes of the hypothesized contributors under H
What are the probabilities of dropout that could have led to observing the same number of alleles recovered in the sample?
?
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8 Estimating drop-out probabilities | Avila June 2013
Qualitative approach to the estimation of PrD
Relies on: the number of alleles observed in the sample the genotypes of the hypothesized contributors under H
What are the probabilities of dropout that could have led to observing the same number of alleles recovered in the sample?
?
What is the distribution of the number of alleles for the questioned sample, conditioned on PrD?
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9 Estimating drop-out probabilities | Avila June 2013
Qualitative approach to the estimation of PrD
What are the probabilities of dropout that could have led to observing the same number of alleles recovered in the sample?
?
We don’t know the probabilities of drop-out, but we can evaluate the drop-out probabilities that could have led to a mixture similar to the one we are investigating
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10 Estimating drop-out probabilities | Avila June 2013
Qualitative approach to the estimation of PrD
What are the probabilities of dropout that could have led to observing the same number of alleles recovered in the sample?
?
Build the empirical distributions of the numbers of alleles, conditioned on the probabilities of dropout ranging in [0,1] using Monte-Carlo simulations
We don’t know the probabilities of drop-out, but we can evaluate the drop-out probabilities that could have led to a mixture similar to the one we are investigating
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11 Estimating drop-out probabilities | Avila June 2013
Monte Carlo method
Any method which solves a problem by generating suitable random numbers and observing that fraction of the numbers obeying some property or properties.
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12 Estimating drop-out probabilities | Avila June 2013
Monte Carlo method
Any method which solves a problem by generating suitable random numbers and observing that fraction of the numbers obeying some property or properties.
Questioned sample properties:• three-person mixture: SGM+ • 33 alleles observed in the epg• profiles of victim and suspect available
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13 Estimating drop-out probabilities | Avila June 2013
Monte Carlo method
Any method which solves a problem by generating suitable random numbers and observing that fraction of the numbers obeying some property or properties.
Questioned sample properties:• three-person mixture: SGM+ • 33 alleles observed in the epg• profiles of victim and suspect available
Simulate a large number of mixtures that have these properties
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14 Estimating drop-out probabilities | Avila June 2013
Important note!
The hypothesized contributors change under Hp and under Hd: Derive distribution of the numbers of alleles under Hp and under Hd separately
Yields two distributions, one under Hp and one under Hd
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15 Estimating drop-out probabilities | Avila June 2013
Mixture 33 alleles
VictimUnknownUnknwon
HdMixture 33
alleles
VictimSuspectUnknown
Hp
Monte-Carlo simulation procedure
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16 Estimating drop-out probabilities | Avila June 2013
VictimSuspect
Unknown By randomly sampling from the Dutch DNA frequencies
fixed 36 alleles
17 alleles
Step 1: simulate 1000 mixtures Mixture #1 51 distinct
alleles
Mixture #1000 53 distinct
alleles
Mixture #2 50 distinct
alleles
…
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17 Estimating drop-out probabilities | Avila June 2013
drop-outVictimSuspectUnknown
Mixture #1 51 alleles
Pr(D) # surviving alleles
0.01 51
0.02 50
… …
0.50 25
…
0.99 1
Step 2: Apply drop-out
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18 Estimating drop-out probabilities | Avila June 2013
Repeat the procedure 1000 times Simulate 1000 mixtures For each mixture, record the number of alleles obtained after the simulated drop-out procedure
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19 Estimating drop-out probabilities | Avila June 2013
Repeat the procedure 1000 times
PrD sim1 sim2 sim3 sim4 sim5 sim6 sim7 sim8 sim9 sim10 …
0,01 51 50 49 50 53 54 45 47 51 51 …
0,03 50 50 44 44 51 39 47 51 44 50 …
0,05 46 44 44 40 44 41 41 50 41 51 …
0,09 38 48 43 41 42 33 40 41 40 38 …
0,17 38 37 33 44 37 51 46 39 36 44 …
… … … … … … … … … … … …
0,89 7 6 9 6 5 3 7 10 9 7 …
0,91 6 8 9 7 8 5 4 5 3 3 …
0,93 8 4 3 3 7 8 5 2 4 7 …
0,95 5 0 7 4 3 4 2 3 8 4 …
0,97 1 3 0 1 2 2 0 0 2 2 …
0,99 0 1 1 1 0 3 0 0 2 0 …
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20 Estimating drop-out probabilities | Avila June 2013
We look at the distributions of the numbers of alleles obtained in the simulation procedure
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21 Estimating drop-out probabilities | Avila June 2013
We are only interested in those where we obtained 33 alleles (the number observed in the epg).
Distribution of the numbers of alleles among the 1000 mixtures
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22 Estimating drop-out probabilities | Avila June 2013
Now we look at the distribution of the numbers of alleles and the corresponding drop-out probabilities
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23 Estimating drop-out probabilities | Avila June 2013
We are only interested in those where we obtained 33 alleles (the number observed in the epg).
Distribution of the numbers of alleles among the 1000 mixtures
Hp
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24 Estimating drop-out probabilities | Avila June 2013
The same procedure is carried out under Hd
Victim
Unknown 1Unknown 2
By randomly sampling from the Dutch DNA frequencies
fixed 19 alleles
35 alleles
Mixture #1 49 distinct
alleles
Mixture #1000 48 distinct
alleles
Mixture #2 50 distinct
alleles
…
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25 Estimating drop-out probabilities | Avila June 2013
drop-outVictimSuspectUnknown
Mixture #1 49 alleles
Pr(D) # surviving alleles
0.01 48
0.02 47
… …
0.50 25
…
0.99 1
Apply drop-out
The simulation procedure is repeated on a 1000 mixtures
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26 Estimating drop-out probabilities | Avila June 2013
Distribution of the numbers of alleles among the 1000 mixtures
We are only interested in those where we obtained 33 alleles (the number observed in the epg).
Hd
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27 Estimating drop-out probabilities | Avila June 2013
5% - 95% percentiles of the distributions
Under Hp
5% 0.19
95% 0.45
Under Hd
5% 0.09
95% 0.41
The drop-out estimates are given as a range: lowest-highest value
[0.09,0.45]
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28 Estimating drop-out probabilities | Avila June 2013
Sensitivity analysis
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29 Estimating drop-out probabilities | Avila June 2013
Sensitivity analysis vs. plausible ranges for PrD
LR 107
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30 Estimating drop-out probabilities | Avila June 2013
Summary the ranges of the drop-out probability can be evaluated separately under Hp and Hd
avoid reporting values of drop-out that are supported by one hypothesis but not by its alternative
qualitative data only
peaks slightly under threshold not taken into account
Assess the uncertainty the data!
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31 Estimating drop-out probabilities | Avila June 2013
LRmix moduleAvailable in Forensim 4.1
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32 Estimating drop-out probabilities | Avila June 2013