1 Aspects of Forensic DNA Typing using John M Butler’s slides http://www.cstl.nist.gov/biotech/strbase/FDT2e.htm Statistic 246 Week 2, Lecture 2 Spring 2006 Copyright symbols have been placed at the bottom of figures used directly from the book. The publisher requests that these copyright symbols are retained by slide users in their presentations. This has been retained, but material has been added or removed to suit the purposes of the class. Please check the originals to see exactly what changes has been made. Most other slides are from John Butler’s collection too.
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1
Aspects of Forensic DNA Typingusing John M Butler’s slides
Copyright symbols have been placed at the bottom of figures used directly fromthe book. The publisher requests that these copyright symbols are retained byslide users in their presentations.This has been retained, but material has been added or removed to suit thepurposes of the class. Please check the originals to see exactly what changeshas been made. Most other slides are from John Butler’s collection too.
2
Some generalities
3http://www.ojp.usdoj.gov/nij/pubs-sum/183697.htm
•Report published in Nov 2000
•Asked to estimate where DNAtesting would be 2, 5, and 10 yearsinto the future
ConclusionsSTR typing is here tostay for a few yearsbecause of DNAdatabases that havegrown to containmillions of profiles
The Future of Forensic DNA Testing
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Forensic DNA Typing, 2nd Edition:Biology, Technology, and Genetics of STR Markers
Chapter 1 Overview & History of DNA TypingChapter 2 DNA Biology Review Chapter 3 Sample Collection, Extraction, QuantitationChapter 4 PCR AmplificationChapter 5 Common STRs and Commercial KitsChapter 6 Biology of STRsChapter 7 Forensic IssuesChapter 8 Single Nucleotide PolymorphismsChapter 9 Y-Chromosome DNA TestsChapter 10 Mitochondrial DNA AnalysisChapter 11 Non-Human DNA and Microbial ForensicsChapter 12 DNA Separation MethodsChapter 13 DNA Detection Methods Chapter 14 Instrumentation for STR Typing: ABI 310, ABI 3100, FMBIO Chapter 15 STR Genotyping IssuesChapter 16 Lab ValidationChapter 17 New Technologies, Automation, and Expert SystemsChapter 18 CODIS and DNA DatabasesChapter 19 Basic Genetic Principles and StatisticsChapter 20 STR Database AnalysesChapter 21 Profile Frequency EstimatesChapter 22 Statistical Analysis of Mixtures and Degraded DNAChapter 23 Kinship and Paternity TestingChapter 24 Mass Disaster DNA Victim IdentificationAppendix I Reported STR AllelesAppendix II U.S. Population Data-STR Allele FrequenciesAppendix III Suppliers of DNA Analysis EquipmentAppendix IV DAB QA StandardsAppendix V DAB Recommendations on StatisticsAppendix VI Application of NRC II to STR TypingAppendix VII Example DNA Cases
John Butler
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Human Identity Testing
• Forensic cases -- matching suspect withevidence
• Paternity testing -- identifying father• Mass disasters -- putting pieces back together• Historical investigations• Missing persons investigations• Military DNA “dog tag”• Convicted felon DNA databases
Involves generation of DNA profiles usually withthe same core STR (short tandem repeat) markers
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Basis of DNA Profiling The genome of each individual is unique (with theexception of identical twins) and is inherited from parents
Probe subsets of genetic variation in order to differentiatebetween individuals (statistical probabilities of a randommatch are used)
DNA typing must be performed efficiently andreproducibly (information must hold up in court)
Current standard DNA tests DO NOT look at genes –little/no information about race, predisposal to disease, orphenotypical information (eye color, height, hair color) isobtained
Created by John M. Butler and Dennis J. Reeder (NIST Biotechnology Division), with invaluable helpfrom Jan Redman, Christian Ruitberg and Michael Tung
*Partial support for the design and maintenance of this website is being provided by The NationalInstitute of Justice through the NIST Office of Law Enforcement Standards.*
STRs101: Brief Introduction to STRsSTR Fact Sheets (observed alleles and PCR product sizes)Sequence Information (annotated)Multiplex STR setsSTR Training MaterialsNon-published Variant Allele ReportsThree-Banded PatternsFBI CODIS Core STR LociDNA Advisory Board Quality Assurance StandardsNIST Standard Reference Material for PCR-Based Testing
Chromosomal LocationsMutation Rates for Common LociPublished PCR primersValidation studiesPopulation dataY-chromosome STRsSex-typing markersTechnology for resolving STR allelesReference List Now 2059 referencesAddresses for scientists working with STRs
Links to other web sitesGlossary of commonly used terms
Publications and Presentations from NIST Human Identity Project Team
These data are intended to benefit research and application of short tandem repeat DNA markers tohuman identity testing. The authors are solely responsible for the information herein.
• Generate data with set(s) of samples from desiredpopulation group(s)– Generally only 100-150 samples are needed to obtain
reliable allele frequency estimates
• Determine allele frequencies at each locus– Count number of each allele seen
• Allele frequency information is used to estimate therarity of a particular DNA profile– Homozygotes (p2), Heterozygotes (2pq)– Product rule used (multiply locus frequency estimates)
For more information, see Chapters 20 and 21 in Forensic DNA Typing, 2nd Edition
Allele frequencies denoted withan asterisk (*) are below the5/2N minimum allele thresholdrecommended by the NationalResearch Council report (NRCII)The Evaluation of Forensic DNAEvidence published in 1996.
Mostcommonallele
CaucasianN= 7,636
0.0009
0.12400.2690
--
0.24300.20000.14600.0125
Einum et al. (2004)JFS 49(6)
Allele
11
131415
15.216171819
12 0.0017* --0.0007
0.0031
AfricanAmericanN= 7,602
0.0003*
0.00770.09050.2920
0.00100.33000.20700.06300.0048
0.0045
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Allele
11
131415
15.216171819
12
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Illustrative calculations
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DNA Profile Frequency with all 13 CODIS STR loci
21.283.50
18.6213.8
31.8530.69
9.2526.1811.31
16.29
12.35
8.87
9.171 in
8.37 x 10140.216910CSF1PO
3.94 x 10130.53488TPOX
1.13 x 10130.23186THO1
6.05 x 10110.3212110.11269D16S539
4.38 x 10100.17729D7S820
1.38 x 1090.0480140.339411D13S317
44,818,2590.1407130.384112D5S818
4,845,2170.1391160.137414D18S51
185,0730.2782300.158928D21S11
16,3640.1656140.185412D8S1179
10050.2185220.185421FGA
810.2003180.281517VWA
9.170.2152170.253316D3S1358
Combined value allele value alleleLocus
The Random Match Probability for this profile in the U.S. Caucasian populationis 1 in 837 trillion (1012)
The Same 13 Locus STR Profilein Different Populations
1 in 0.84 quadrillion (1015) in U.S. Caucasian population (NIST)1 in 2.46 quadrillion (1015) in U.S. Caucasian population (FBI)*1 in 1.86 quadrillion (1015) in Canadian Caucasian population*
1 in 16.6 quadrillion (1015) in African American population (NIST)1 in 17.6 quadrillion (1015) in African American population (FBI)*
1 in 18.0 quadrillion (1015) in U.S. Hispanic population (NIST)
*http://www.csfs.ca/pplus/profiler.htm
1 in 837 trillion
These values are for unrelated individualsassuming no population substructure (using only p2 and 2 pq)
NIST study: Butler, J.M., et al. (2003) Allele frequencies for 15 autosomal STR loci on U.S.Caucasian, African American, and Hispanic populations. J. Forensic Sci. 48(4):908-911.(http://www.cstl.nist.gov/biotech/strbase/NISTpop.htm)
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STR Cumulative Profile Frequency with Multiple Population Databases