Introduction to LRmix Studio

Oskar Hansson

Statistical methods in forensic genetics 20-23 April 2015, Copenhagen

EUROFORGEN-NoE is funded by the European Commission

within the 7th Framework Programme

What is LRmix Studio?

• Expert system dedicated to the interpretation of (complex) forensic DNA mixtures

• Programmed after the likelihood ratio model:

What is LRmix Studio?

• Accommodates for drop-out and drop-in:

• Estimates the drop-out rate from the available data and use this to generate LRs

• Free of charge and open-source (Java)

• Download: http://lrmixstudio.org/download/

LRmix Studio – Features

• Computes likelihood ratios for DNA profiles characterised with autosomal STR kits

• Tested for propositions with up to 4 unknowns and a total of 5 contributors

• Compares any number of replicates to any number of reference profiles (tested with up to 3 reference profiles and 5 replicates)

LRmix Studio – Limitations

• The hypothesized contributors under Hp and Hd are assumed to be unrelated to each other and to the unknowns

• Uncommon and/or untested scenarios may lead to unreliable results

• Cannot handle missing data in reference profiles

• Does not deconvolute mixtures

• Cannot analyse propositions that involve unprofiled related individuals

LRmix Studio graphical user interface

Getting help

Links to a local copy of the manual

Opens up the ‘About’ tab

LRmix Studio user manual

1. What is LRmix Studio? 2. Features 3. Tutorial

3.1 Import sample profiles 3.2 Import or add reference profiles 3.3 Profile summary 3.4 Analysis 3.5 Sensitivity analysis 3.6 Non-contributor tests 3.7 Automatic report generation

4. How to report bugs References

About LRmix Studio

Contact: help@lrmixstudio.org

License agreement

Software version

Import sample profiles

Load the evidence profile(s)

Clear data and start fresh

Load a previously analysed case

Tabs are inactivated to enforce the workflow

The sample file

Notepad++ - Advanced non-destructive text editor

LibreOffice Calc (alternatively: OpenOffice Calc) - Free open-source MS Excel clone

Accepts both: SampleName|Marker|Allele1|Allele2 and: Sample Name|Marker|Allele 1|Allele 2

Samples and/or replicates are

stacked

Important to use identical marker names in all files (sample/ref/db)

Not case-sensitive:

Pentad=PentaD=PenTaD=PENTAD

Is sensitive to spaces: Penta D≠PentaD

The sample file

Sample File Sample Name D10S1248 Height vWA Height D16S539 Height

frag_013_G01.fsa rep.1 12, 13, 14, , , , 220, 203, 66, , , , , 16, 19, , , , , 223, 387, , , , , , 8, 9, 10, 11, 14, , 242, 73, 55, 342, 52, , ,

frag_014_G02.fsa rep.2 12, 13, , , , , 339, 357, , , , , , 16, 19, , , , , 139, 352, , , , , , 8, 11, 14, , , , 169, 175, 64, , , , ,

frag_013_G03.fsa rep.3 12, 13, , , , , 353, 175, , , , , , 16, 19, , , , , 247, 327, , , , , , 8, 11, , , , , 218, 193, , , , , ,

Alternative GeneMapper sample file format

Import sample profiles

The folder from which the file was loaded

A List of all loaded samples/replicates

Next tab activated

Profiles for each sample/replicate

List of markers

Import reference profiles

Add a profile manually

Load reference profile(s)

The list of loci seem to be hard-coded and not derived from the allele

frequency table

Homozygotes

The reference can be saved as a csv file

Contributors and non-contributors

LRmix Studio manual – “Only profiles relevant to the LR analysis should be uploaded. If some of the reference profiles are uploaded but later not used in the analysis tab, they will be considered as non-contributors. Non-contributor profiles can influence the likelihood ratio calculations if the Fst (θ) correction is not nil.”

Profile Summary Customisable highlighting

Possible spurious alleles or additional

contributors

Detects allele drop-out

Detects e.g. parent child relations

The filters can be printed

Determine the number of

contributors

Analysis Dropout

probability per contributor

Number of unknown

contributors

Drop-in probability

Theta correction (Fst or θ)

Allele frequency file

Threads (performance)

Final likelihood ratio LR per locus

Sensitivity Analysis

Drop-out range

Drop-in probability

Theta correction (Fst or θ)

Vary dropout for contributors

Delete selected curve

Drop-out Estimation

Drop-out range

Drop-in probability

Number of iterations

Vary dropout for contributors

Estimated dropout range is shaded in

the plot

Non-contributor Test

Number of random persons

to test

Check the person that will be replaced by a

random person

Difference between the

person of interest and the ‘best’

random person

NB! Drop-out and drop-in values must be > 0

Reports

Other References