genophiler® and genostat®: tools for objective evaluation of dna testing results forensic...
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Genophiler® and GenoStat®:Tools for objective evaluation of
DNA testing results
Forensic Bioinformatics (www.bioforensics.com)
Jason R. GilderAugust 17, 2007
• Automation of GeneScan and Genotyper• Consistent electronic analysis of all samples• Organizes all output – can be read on any
computer• Summary table of all labeled peaks• Draws your attention to potential issues
Summary Sheet
The * indicates that this peak
may be involved in pullup…
Pullup
Clicking here will show us the GenoTyper annotated
electropherogram…
Simplified table
• Overall view of samples• Single line display• Clicking sample displays electropherogram
Project Screen Shot
Analysis Parameters:
Size Standards:
Standard electropherogram
• Similar to laboratory output
• Limited view
• Hard to evaluate low-level results
Genotyper zoom
• Close view of baseline and potential low-level alleles
• View from 0 to 150 RFU
• Helps expert make an informed decision
Another example of Genophiler zoom
• Genophiler also provides a zoomed graph to 150 RFUs• Shows smaller peaks more clearly• Here, the peaks that were not reported by the lab may
be evidence of an unknown, minor contributor
Sample results window
• All detected peaks
• Size
• Peak height
• Peak area
• Data collection point
Sample information window
• Time and date of analysis
• Analysis instrument
• Machine conditions
• Analysis parameters
Raw data window
• Pre-separated spectral data
Poor raw data
Other Issues: EPT Data
• Shows current, voltage, laser power, and temperature
• For good analysis, should be constant (flat)
Problematic EPT data
Side-by-side interface
Consistency report
• We perform two analyses for every case– GeneScan default RFU threshold (50)– Reproduce the testing lab’s analysis
• Compares analysis results between testing laboratory and ABI defaults
• Highlight peaks that are labeled in one analysis and not the other
Genophiler® LOD/LOQ Table
Sample Run Sample Name Sample
Nickname
Limit of Detection
(LOD)
Limit of Quantitation
(LOQ)
Average baseline signal
Baseline signal
std. dev.
Run 2_17_06C7P16 9947a
6K11_3ul 05-2Pos Control
(2-17)-2 19 49 5.86 4.34
Run 2_17_06C7P16 9947a
6K11_3ulPos Control
(2-17)-1 19 49 5.72 4.34
Run 2_17_06 G7C16 9947a
6K11_3ulPos Control (2-17)-C 18 48 5.82 4.18
Run 2_17_06 D7P16 RBReagent
Blank (2-17)
18 48 5.75 4.20
Notes: - LOD/LOQ derived from the methodology validated in J. Gilder, T. Doom,
K. Inman, and D. Krane. "Run-specific limits of detection and quantitation for STR-based DNA testing." Journal of Forensic Sciences. 2007;52(1):97-101.
- Limit of Detection (LOD) is the average baseline signal (in RFUs) plus three standard deviations (μb + 3σ).
- Limit of Quantitation (LOQ) is the average baseline signal (in RFUs) plus ten standard deviations (μb + 10σ).
- Positive controls not exhibiting the full 9947A profile are not included in the above table.
Removing labels in GenoTyper
Default view (as found in printout)
Genotyper: Show peaks that were manually removed
Genophiler CD
• Full electronic record of the case
• All results in electronic format on CD-ROM
• All data files, analysis parameters, projects, macros, etc.
• Works on any computer with a web browser
• Can make printouts of everything
Potential issues that are flagged
Potential issues that are flagged
• Mixtures• Peak height imbalance• Missing genotype information• High peaks• Low average peak height• Indications of degradation• Pull-up• Inconsistent PP/CO results
Mixture
• Locus or loci containing three or more labeled peaks
Peak height imbalance
• Any heterozygous loci differing by more than 30%
65%
Defendant
Missing genotype information
• At least one locus with no labeled peaks
High peak
• Any peak above the point of saturation (4000 RFUs)• Can lead to pull-up
Defendant
Low average peak height
• An average peak height less than 400 RFUs
Degradation
• Potential breakdown of DNA sample• Slope calculated through best-fit linear regression
Slope = -17
Defendant
Pull-up• Two peaks in two different dyes occurring at
approximately the same data collection point
Evidence Q5
Inconsistent PP/CO results
• Different results in Profiler Plus and COfiler
Defendant
Potential issues that are flagged
• Mixtures• Peak height imbalance• Missing genotype information• High peaks• Low average peak height• Indications of degradation• Pull-up• Inconsistent PP/CO results
Genophiler report
“An expert will be able to explain the significance and implications of these findings in your particular case.”
“All of the statements listed below about the data in your case can be verified by any competent expert who has access to GeneScan and Genotyper software and to the data you provided to us.”
Genophiler does not
• Perform mixture interpretation
• Make allele calls
• Assess the quality of a profile
• Make any judgment calls
GenoStat
• DNA statistics package– Random match probabilities– Related random match probabilities– Mixture statistics (CPI)– 167 population allele frequency
databases
• Mixture resolution– Separate mixtures into contributor
components
• Free
Standard stats mode
Standard stats mode
Random match
probability
Standard stats modeUnrelated
Sibling
Half-Sibling
Parent/Child
Uncle/Nephew
Cousins
Standard stats modeMixture
stats
Standard stats mode
Theta substructure
factor
Standard stats mode
FBI population databases
Standard stats mode
Load any of 167 population
databases
Mixture resolution mode
Mixture resolution mode
One hypothesis = fully resolved
Mixture resolution mode
Set peak height ratio
Mixture resolution mode
Minimum peak height threshold
Mixture resolution mode
Inferred mixture ratio
Partially-resolved mixture
Partially resolved mixture
Partially-resolved mixture
Manually exclude mixture hypotheses
Partially-resolved mixture
Manually exclude loci from statistics
Partially-resolved mixture
Constrained CPI uses only plausible mixture hypotheses
Questions?
www.bioforensics.com