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Peak Height Ratios in Peak Height Ratios in Forensic STR Analyses:Forensic STR Analyses:
Pattern of Occurrence & Effects of Pattern of Occurrence & Effects of ConcentrationConcentration
Data from:Data from: Illinois State Police Laboratory Illinois State Police Laboratory Broward County Sheriff’s Lab & Broward County Sheriff’s Lab &
Forensic BioinformaticsForensic Bioinformatics
69%
ValidationValidation
Size Ladders are Used to Make Allele Calls
Locus N Mean%ABI
SD 99%CI N Mean%FBI
SD 99%CI
D3S1358 68 93 4 81 167193
9389
5.29.4
7762
VWA 74 93 5 78 180 92 5.6 75
D16S539 70 92 6 74 220 88 9.4 60
FGA 80 93 5 78 269 92 5.7 75
THO1 70 92 6 74 318 91 8.0 67
TPOX 78 92 6 74 298 88 8.6 63
CSF1PO 84 92 6 74 234 88 9.1 61
D8S1179 93 92 6 74 180 93 4.8 79
D21S11 95 91 7 70 230 92 5.5 76
D18S51 100 91 6 73 271 89 6.7 69
D5S818 65 92 5 77 122 93 4.9 78
D13S317 73 93 5 78 173 93 5.6 76
D7S820 79 93 6 75 159261
9288
5.99.4
7460
Figure from: STR ANALYSIS BY CAPILLARY ELECTROPHORESIS: DEVELOPMENT OF INTERPRETATION GUIDELINES FOR THE PROFILER PLUS™ AND COFILER™ SYSTEMSFOR USE IN FORENSIC SCIENCE by Deborah Hobson, Jill Smerick, and Jenifer Smith DNAU I, FBI Laboratory, Washington, D.C.
Scatterplot (Spreadsheet in phril.stw 9v*962c)
-1000 0 1000 2000 3000 4000 5000 6000 7000 8000
RFU2
40
50
60
70
80
90
100
110
PH
R
RFU values for smaller allele in each heterozygote
Frequency table: PHR: =(V4/V3)*100 (PHRATIO.STA in phril.stw)K-S d=.10275, p<.01 ; Lilliefors p<.01
CategoryCountCumulative
CountPercentof Valid
Cumul %of Valid
% of allCases
Cumulative %of All
40.00000<x<=50.0000050.00000<x<=60.0000060.00000<x<=70.0000070.00000<x<=80.0000080.00000<x<=90.0000090.00000<x<=100.0000Missing
2 2 0.23838 0.23840.23838 0.238410 12 1.19190 1.43031.19190 1.430327 39 3.21812 4.64843.21812 4.648479 118 9.4159714.06449.41597 14.0644
275 39332.7771246.841532.77712 46.8415446 83953.15852100.000053.15852 100.0000
0 839 0.00000 0.00000 100.0000
Frequency of Occurrence of Heterozygote Peak Height Ratios in Percentages in All Loci in the Illinois State Police Validation Studies
Histogram: PHR: =(V4/V3)*100K-S d=.10275, p<.01 ; Lilliefors p<.01
Expected Normal
40 50 60 70 80 90 100
X <= Category Boundary
0
50
100
150
200
250
300
350
400
450
500
No. of obs.
Plot of Means and Conf. Intervals (95.00%)Validation Samples
D3 vWA FGA AMEL D8 D21 D18 D5 D13 D7 D16 THO1 TPOX CSF
LOCUS
78
80
82
84
86
88
90
92
94
96
Values in P
ercent
Mean PHR with 95% CI for Each CODIS Locus
D7 CSF D3 D16 TPOX D8 D21 D13 vWA D18 D5 FGA THO1
Locus
0.86
0.87
0.88
0.89
0.90
0.91
0.92
0.93
PH
R
Reference Sample Peak Height Ratios
Median & Range PHR/Locus
D7 CSF D3 D16 TPOX D8 D21 D13 vWA D18 D5 FGA THO1
Locus
0.2
0.3
0.4
0.5
0.6
0.7
0.8
0.9
1.0
1.1
PH
R
2-Way Tables of Descriptive Statistics (PHRATIO.STA in phril.stw)N=839 (No missing data in dep. var. list)
RFUClassPHR
MeansPHRN
PHRStd.Dev.
PHRMinimum
PHRMaximum
< 500rfu500<rfu<10001000-2000rfu2000-4000rfu> 4000rfuAll Grps
85.0742516711.6051146.80233100.000089.30670164 7.4422662.65244 99.627689.56659189 8.6625457.27371 99.843889.94837164 7.1586858.04441 99.907489.40954155 8.2854857.15089 99.906288.66722839 8.9514646.80233100.0000
Analysis of Variance (PHRATIO.STA in phril.stw)Marked effects are significant at p < .05000
VariableSS
Effectdf
EffectMS
EffectSS
Errordf
ErrorMSError
F p
PHR 2730.409 4 682.602464417.4183477.239108.8375230.000001
Scheffe Test; Variable: PHR (PHRATIO.STA in phril.stw)Marked differences are significant at p < .05000
RFUClass{1}
M=85.074{2}
M=89.307{3}
M=89.567{4}
M=89.948{5}
M=89.410< 500rfu {1}500<rfu<1000 {2}1000-2000rfu {3}2000-4000rfu {4}> 4000rfu {5}
0.0007880.0001340.0000480.0006680.000788 0.9992800.9792900.9999850.0001340.999280 0.9967450.9999080.0000480.9792900.996745 0.9898240.0006680.9999850.9999080.989824
The mean Peak Height Ratio is significantly smaller and the variance larger for smaller DNA samples as reflected by the mean RFU of a sample. Above that threshold the mean PHR & Variance does not differ significantly among peak height classes.
Relationship Between DNA Amount and Allele Imbalance
< 500rfu500<rfu<1000
1000-2000rfu2000-4000rfu
> 4000rfu
Mean RFU per Sample
83
84
85
86
87
88
89
90
91
92
Mea
n P
eak
Hei
ght R
atio
Mean ±SE ±1.96*SE
Summary Frequency Table (PHRATIO.STA in phril.stw)Marked cells have counts > 10(Marginal summaries are not marked)
RFUClass 70%Yes
70%No
RowTotals
CountColumn PercentRow PercentTotal PercentCountColumn PercentRow PercentTotal PercentCountColumn PercentRow PercentTotal PercentCountColumn PercentRow PercentTotal PercentCountColumn PercentRow PercentTotal PercentCountTotal Percent
< 500rfu 150 17 16718.63%50.00%89.82%10.18%17.88%2.03%19.90%
500<rfu<1000 162 2 16420.12%5.88%98.78%1.22%19.31%0.24%19.55%
1000-2000rfu 184 5 18922.86%14.71%97.35%2.65%21.93%0.60%22.53%
2000-4000rfu 160 4 16419.88%11.76%97.56%2.44%19.07%0.48%19.55%
> 4000rfu 149 6 15518.51%17.65%96.13%3.87%17.76%0.72%18.47%
All Grps 805 34 83995.95%4.05%
Relationship between RFU & thepercent of profiles with PHR’sabove (Yes) and below (NO) 70%.
Chi-Squared = 21.58, 4df, p = 0.00024
Percent of Samples with PHR Less Than 70% as a Function of the Mean RFU of the Sample in the Illinois State Police Crime Lab Validation
Studies
0
2
4
6
8
10
12
<500 500<Y<1000 1-2000 2-4000 >4000
Mean RFU Values per Sample
Perc
ent o
f PH
R <
70%
Peak Height Ratios for Validation Samples
0 1 2 3 4 5 6 7 8 9
Concentration Class
66
68
70
72
74
76
78
80
82
84
86
88
90
92
94
PH
R as P
ercent
Mean
Mean±SE
Mean±1.96*SE
Reference Samples
0 1 2 3 4 5 6 7
Concentration Class
0.86
0.87
0.88
0.89
0.90
0.91
0.92
0.93
PH
R as P
ercent
Mean Mean±SE Mean±1.96*SE
Amplifications from same dilution tube (~30 pg). (2-012802 10.19 AM)
Allelic imbalance present. Allele dropout @ D18.“Different DNA profiles” @ D3, D21, D18 and D13.
The bottom line is simple; Peak Height Ratios (PHR’s) have a higher probability of being imbalanced and show significantly greater imbalances in small and/or degraded samples of DNA when using Profiler Plus and Cofiler to type STR DNA in crime scene type samples. A significant number of samples at all RFU classes show peak height ratios below 70%. This is especially true of small and/or degraded samples like those collected at many crime scenes. The Illinois State Police DNA lab’s use of a 70% rule to infer single source samples and in interpreting the relative contributions to mixtures is not justified by the data in their own “validation” studies. I have seen similar data from the validation studies of many other crime labs (e.g., Minnesota BCA, Broward County Sheriffs Lab, Bode Technology, West Palm Beach Sheriffs Office, Connecticut State Police CrimeLab, FBI Laboratory, and studies done by the kit’s manufacturers.