introduction to lrmix studio
TRANSCRIPT
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
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