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Forensic Bioinformatics (www.bioforensics.com)

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1 Forensic Bioinformatics (www.bioforensics.com)
Genophiler® and GenoStat®: Tools for objective evaluation of DNA testing results Jason R. Gilder August 17, 2007 Forensic Bioinformatics (www.bioforensics.com)

2 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

3 The * indicates that this peak may be involved in pullup…
Summary Sheet The * indicates that this peak may be involved in pullup…

4 Clicking here will show us the GenoTyper annotated electropherogram…
Pullup Clicking here will show us the GenoTyper annotated electropherogram…

5 Simplified table Overall view of samples Single line display
Clicking sample displays electropherogram

6

7 Project Screen Shot

8 Analysis Parameters: Size Standards:

9

10 Standard electropherogram
Similar to laboratory output Limited view Hard to evaluate low-level results

11 Genotyper zoom Close view of baseline and potential low-level alleles
View from 0 to 150 RFU Helps expert make an informed decision

12 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

13 Sample results window All detected peaks Size Peak height Peak area
Data collection point

14 Sample information window
Time and date of analysis Analysis instrument Machine conditions Analysis parameters

15 Raw data window Pre-separated spectral data

16 Poor raw data

17 Other Issues: EPT Data Shows current, voltage, laser power, and temperature For good analysis, should be constant (flat)

18 Problematic EPT data

19 Side-by-side interface

20 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

21 Genophiler® LOD/LOQ Table
Sample Run Sample Name Sample Nickname Limit of Detection (LOD) Quantitation (LOQ) Average baseline signal Baseline std. dev. Run 2_17_06 C7P a 6K11_3ul 05-2 Pos Control (2-17)-2 19 49 5.86 4.34 6K11_3ul (2-17)-1 5.72 G7C a (2-17)-C 18 48 5.82 4.18 D7P16 RB Reagent Blank (2-17) 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):    - 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.

22 Removing labels in GenoTyper

23 Default view (as found in printout)
Genotyper: Show peaks that were manually removed

24 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

25 Potential issues that are flagged

26 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

27 Mixture Locus or loci containing three or more labeled peaks

28 Peak height imbalance Any heterozygous loci differing by more than 30%
65% Defendant

29 Missing genotype information
At least one locus with no labeled peaks

30 High peak Any peak above the point of saturation (4000 RFUs)
Can lead to pull-up Defendant

31 Low average peak height
An average peak height less than 400 RFUs

32 Degradation Potential breakdown of DNA sample
Slope calculated through best-fit linear regression Slope = -17 Defendant

33 Pull-up Two peaks in two different dyes occurring at approximately the same data collection point Evidence Q5

34 Inconsistent PP/CO results
Different results in Profiler Plus and COfiler Defendant

35 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

36 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.”

37 Genophiler does not Perform mixture interpretation Make allele calls
Assess the quality of a profile Make any judgment calls

38 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

39 Standard stats mode

40 Random match probability
Standard stats mode Random match probability

41 Standard stats mode Unrelated Sibling Half-Sibling Parent/Child
Uncle/Nephew Cousins Standard stats mode

42 Standard stats mode Mixture stats

43 Theta substructure factor
Standard stats mode Theta substructure factor

44 FBI population databases
Standard stats mode FBI population databases

45 Load any of 167 population databases
Standard stats mode Load any of 167 population databases

46 Mixture resolution mode

47 Mixture resolution mode
One hypothesis = fully resolved

48 Mixture resolution mode
Set peak height ratio

49 Mixture resolution mode
Minimum peak height threshold

50 Mixture resolution mode
Inferred mixture ratio

51 Partially-resolved mixture

52 Partially-resolved mixture
Manually exclude mixture hypotheses

53 Partially-resolved mixture
Manually exclude loci from statistics

54 Partially-resolved mixture
Constrained CPI uses only plausible mixture hypotheses

55 Questions?


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