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Evaluating forensic DNA evidence Forensic Bioinformatics ( Dan E. Krane Biological Sciences, Wright State University,

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Presentation on theme: "Evaluating forensic DNA evidence Forensic Bioinformatics ( Dan E. Krane Biological Sciences, Wright State University,"— Presentation transcript:

1 Evaluating forensic DNA evidence Forensic Bioinformatics ( Dan E. Krane Biological Sciences, Wright State University, Dayton OH 45435

2 Three generations of DNA testing DQ-alpha TEST STRIP Allele = BLUE DOT RFLP AUTORAD Allele = BAND Automated STR ELECTROPHEROGRAM Allele = PEAK

3 DNA in the Cell Target Region for PCR chromosome nucleus Double stranded DNA moleculeAATT TT CC GG AA AA TT cell

4 DNA content of biological samples: Type of sampleAmount of DNA Blood 30,000 ng/mL stain 1 cm in area200 ng stain 1 mm in area2 ng Semen 250,000 ng/mL Postcoital vaginal swab0 - 3,000 ng Hair plucked shed ng/hair ng/hair Saliva Urine 5,000 ng/mL ng/mL 2 2

5 Basic terminology: Genetics DNA Polymorphism (many forms) –Regions of DNA which differ from person to person Locus (plural = loci) –Site or location on a chromosome Allele –Different variants which can exist at a locus DNA Profile –The combination of alleles for an individual

6 Basic terminology: Technology Amplification or PCR (Polymerase Chain Reaction) –A technique for replicating DNA in the laboratory (molecular Xeroxing) –Region to be amplified defined by PRIMERS –Can be color coded Electrophoresis –A technique for separating molecules according to their size

7 STR Short tandem repeat Describes a type of DNA polymorphism in which: –a DNA sequence repeats –over and over again –and has a short (usually 4 base pair) repeat unit A length polymorphism -- alleles differ in their length 5 repeats: AATG AATG AATG AATG AATG 6 repeats: AATG AATG AATG AATG AATG AATG 4 repeats: AATG AATG AATG AATG 3 repeats: AATG AATG AATG

8 Reading an electropherogram Peaks correspond to alleles Electropherogram D3vWAFGA D8D21D18 D5D13D7 BLUE GREEN YELLOW RED Amelogenin XX = female XY = male bps Red = ROX size standard

9 Automated STR Test

10 Crime Scene Samples & Reference Samples Differential extraction in sex assault cases separates out DNA from sperm cells Extract and purify DNA

11 Extract and Purify DNA Add primers and other reagents

12 PCR Amplification Groups of amplified STR products are labeled with different colored dyes (blue, green, yellow) DNA regions flanked by primers are amplified

13 The ABI 310 Genetic Analyzer: SIZE, COLOR & AMOUNT

14 ABI 310 Genetic Analyzer: Capillary Electrophoresis Amplified STR DNA injected onto column Electric current applied DNA separated out by size: –Large STRs travel slower –Small STRs travel faster DNA pulled towards the positive electrode Color of STR detected and recorded as it passes the detector Detector Window

15 Profiler Plus: Raw data

16 D3vWAFGA D8D21D18 D5D13D7 Am RAW DATA PROCESSED DATA GENESCAN divides the raw data into a separate electropherogram for each color: Blue Green Yellow Red GENOTYPER identifies the different loci and makes the allele calls The type of this sample is: –D3: 16, 17 –vWA: 15, 15 –FGA: 21,23 –Amelogenin: X, Y –D8: 16, 16 –D21: 28, 29 –D18: 14, 19 –D5: 8, 12 –D13: 11, 13 –D7: 10 10

17 Statistical estimates: the product rule 0.222x x2 = 0.1

18 Statistical estimates: the product rule = in 79,531,528,960,000,000 1 in 80 quadrillion 1 in 101 in 1111 in 20 1 in 22,200 xx 1 in 1001 in 141 in 81 1 in 113,400 xx 1 in 1161 in 171 in 16 1 in 31,552 xx

19 D3S1358FGAVWA AMELD8S1179D21S11D18S51 D5S818D13S317D7S820 Profiler Plus

20 D3S1358 AMEL D7S820 D16S539 TH01 TPOX CSF1PO Cofiler

21 D3S1358D16S539 VWA AMEL D8S1179 D21S11 D18S51 D19S433 D5S818FGA D2S1338 TPOX TH01D13S317 CSF1POD7S820 Identifiler


23 Components of a DNA report The samples tested –Evidence samples (crime scene) –Reference samples (defendant, suspect) The lab doing the testing The test used: –Profiler Plus, Cofiler, Identifiler, mtDNA The analyst who did the testing Results and conclusions: –Table of alleles –Narrative conclusions

24 Table of alleles Some labs include more information than others Usually includes information about mixed samples May also include: –Indication of low level results –Indication of results not reported –Relative amounts of different alleles (in mixed samples) No standard format

25 Narrative conclusions Indicates which samples match Includes a statistical estimate Identifies samples as mixed May include an identity statement i.e., samples are from the same source to a scientific degree of certainty (FBI) May allude to problems (e.g. interpretative ambiguity, contamination)

26 Looking beneath the report

27 Sources of ambiguity in STR interpretation Degradation Allelic dropout False peaks Mixtures Accounting for relatives Threshold issues -- marginal samples

28 Degradation When biological samples are exposed to adverse environmental conditions, they can become degraded –Warm, moist, sunlight, time Degradation breaks the DNA at random Larger amplified regions are affected first Classic ski-slope electropherogram Peaks on the right lower than peaks on the left LARGELARGE SMALLSMALL

29 Allelic Dropout Peaks in evidence samples all very low –Mostly below 150 rfu Peaks in reference sample much higher –All well above 800 rfu At D13S817: –Reference sample:8, 14 –Evidence sample:8, 8 14 allele has dropped out -- or has it? Tend to see with marginal samples 1500 Evidence sample Reference sample 150 ?

30 False peaks & machine problems False peaks: –Contamination –Dye blob –Electrical spikes –Pull-up Machine problems: –Noise –Baseline instability –Injection failures

31 Mixed DNA samples

32 How many contributors to a mixture if analysts can discard a locus? How many contributors to a mixture? Maximum # of alleles observed in a 3 person mixture # of occurrencesPercent of cases ,498, ,938, ,702, There are 45,139,896 possible different 3-way mixtures of the 648 individuals in the MN BCI database. 8,151 1,526,550 32,078,976 11,526,

33 How many loci must have six or fewer alleles to be confident there were only three contributors? Nine loci are commonly used. No kit tests at more than 16 loci. Approximately 144 loci must be examined for 95% confidence that there were only 3 contributors.

34 Opportunities for subjective interpretation?

35 D3: 12, 17vWA: 15, 17FGA: 22, 26

36 Opportunities for subjective interpretation?




40 Accounting for relatives

41 Likelihood ratios for allele sharing:

42 Automatically runs GeneScan and GenoTyper Presents all output in a web page Performs expert analysis to identify problems Generates a report detailing all testing issues


44 Genophiler output:


46 Genophiler also flags potential problems for further review:

47 Forensic BioInformatics ( Uses Genophiler to generate easily interpreted files Objectively applies analysis parameters to all samples Fast turn around times Efficiently draws attention to problems requiring further review

48 Resources Books –Forensic DNA Typing by John M. Butler (Academic Press) Internet –Applied Biosystems Website: (see human identity and forensics) –Promega Website: (see Genetic Identity) –STR base: (very useful) Scientists –Larry Mueller (UC Irvine) –Simon Ford (Lexigen, Inc. San Francisco, CA) –William C. Thompson (UC Irvine) –William Shields (SUNY, Syracuse, NY) –Marc Taylor (Technical Associates, Ventura, CA) –Carll Ladd (Connecticut State Police) Testing laboratories –Technical Associates (Ventura, CA) –Forensic Analytical (Haywood, CA) Other resources –Forensic BioInformatics (Dayton, OH)

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