1. Fundamentals of Forensic DNA Typing
Chapter 15
Additional Loci & Non-Human DNA
Fundamentals of Forensic DNA Typing
Slides prepared by John M. Butler
June 2009

2. Chapter 15 – Additional STR Loci, SNPs, and Non-Human DNA
Chapter Summary
While a common set of core STR markers (e.g., the 13 CODIS STRs) are widely used in human identity testing, additional STR markers and other genetic loci, such as single nucleotide polymorphisms (SNPs), will likely play a role in future applications—particularly when kinship analysis may be needed to resolve potential relatives from one another. In some cases, ancestry informative markers (AIMs) can be useful in estimating the ethnic origin of a sample. As additional information is gleaned from genome studies, genetic markers for physical traits may be discovered to enable phenotypic evaluation. Non-human DNA analysis has benefited from use of STR markers found in cats, dogs, and plants.

3. A 26plex Multiplex PCR Assay Developed at NIST
John M. Butler (2009) Fundamentals of Forensic DNA Typing, Figure 15.1
Figure 15.1 A 26plex assay developed with non-core markers that amplifies 25 STRs and amelogenin in a four-dye, bp size range. Figure courtesy of Becky Hill, NIST.

4. Alu Element Insertion PCR Assay
Two possible alleles
Human Alu Repeat
(~300 bp)
AluI
400 bp
100 bp
“long” (+) allele
“short” (-) allele
John M. Butler (2009) Fundamentals of Forensic DNA Typing, D.N.A. Box 15.2
D.N.A. Box 15.2 (figure) Schematic of the Alu element insertion PCR assay. The Alu sequence, which is approximately 300 bp in size, may either be present or absent at a particular location in the human genome. When the flanking region of the Alu repeat is targeted with primers, PCR amplification will result in products that are 400 bp if the Alu element is inserted or 100 bp if it is absent. A simple ethidium bromide-stained agarose gel may be used to genotype individuals. Individuals that are homozygous for the insertion will amplify a 400 bp DNA fragment. Those who are heterozygous for the insertion will amplify both 400 bp and 100 bp fragments, and individuals that are homozygous for the lack of the Alu insertion element will exhibit only the 100 bp DNA fragment.

5. Status of Genetic Marker Systems Used in Forensic DNA Testing
STRs – widely used in casework and national databases world-wide
miniSTRs – smaller versions of STR loci that can work well on degraded DNA
Y-STRs – permits examination of male-only DNA
mtDNA – used in specialty labs for highly degraded specimens or hair that contains limited amounts of DNA
SNPs – potential for identifying ethnicity of evidence sample; still in research and likely to be limited in use

6. Single Nucleotide Polymorphisms (SNPs)
OTC Statement: “While the future utility of SNPs is uncertain, it seems unlikely that this method will replace the standard set of STRs used for routine DNA analysis due to the limited variation of SNPs and difficulties with mixed sample interpretation.”
Butler, J.M., Coble, M.D., Vallone, P.M. (2007) STRs vs SNPs: thoughts on the future of forensic DNA testing. Forensic Science, Medicine and Pathology 3:

7. More Possible Combinations = Improved Ability to Detect Mixtures
SNPs – few possibilities
STRs – many possibilities
Alleles
Alleles A B A B C D E F
Combinations
Combinations AA AA AB AC AD AE AF BB BC BD BE BF CC CD CE CF DD DE DF EE EF FF AB BB
One contributor or more?
At least two contributors to sample

8. Why SNPs Will Likely Not Replace STRs…
Large databases containing STR information (would need to replace data on existing samples with new DNA markers)
Mixture detection and interpretation benefits from marker systems with many alleles (SNPs only have two alleles and three genotype possibilities)
Degraded DNA can be successfully analyzed in many cases by miniSTRs (thus removing the primary motivation for using SNPs…)

9. Compromised Sample Improvements
miniSTRs improve the success rate and recovery of information from compromised DNA evidence

10. Approaches for “challenging” samples: perspectives for the future
Limited sample material (highly degraded DNA)
mtDNA (in use for this purpose since mid-1990s due to high copy number per cell)
Mixed male-female DNA
Y-chromosome STRs
Degraded DNA
miniSTRs
SNPs (?)
Chapter 10 in Forensic DNA Typing, 2nd Edition

11. A MiniFiler Kit Profile
Commercial miniSTR test from ABI focusing on reducing PCR products length for 8 of the larger Identifiler loci
Data from Becky Hill (NIST)
Applied Biosystems Kit

12. Further work with miniSTRs
NC01
NC02
We are currently developing tests
for 26 additional miniSTR loci
Potential utility for missing persons work, kinship analysis, paternity testing, mutation rates etc
Data from Becky Hill (NIST)

13. Comprised Sample Improvements (CSI) Conclusions
Analysis of shorter regions of DNA benefits recovery of information from degraded specimens
miniSTRs are now viewed as the primary way forward and a commercial kit is under development
SNPs, while theoretically beneficial due to small possible amplicons, are limited due to poor abilities to handle mixtures and the need for large multiplexes to improve powers of discrimination
mtDNA due to higher copy number per cell than nuclear DNA will continue to be used where limited samples are recovered (e.g., hair shafts and bone fragments)

14. Protocol Steps for Allele-Specific Primer Extension SNP Assay
Genomic DNA sample
(Multiplex) PCR
ExoSAP Digestion
Amplification
Add SNP primer(s) and SNaPshot mix
SNP Extension (cycle sequencing)
SAP treatment
Primer Extension
Sample prep for 310/3100
Run on ABI 310/3100
Data Analysis (GeneScan)
Analysis
Steps in allele-specific primer extension SNP detection (e.g., minisequencing or SNaPshot) assay. The boxed portions illustrate additional steps performed in this assay relative to STR typing.
Add GS120 LIZ size standard
Use E5 filter (5-dye) and POP4 standard conditions
Type Sample (Genotyper or GeneMapperID)

15. Biogeographical Ancestry
Shriver, M.D. et al. (2003) Skin pigmentation, biogeographical ancestry and admixture mapping. Hum. Genet. 112(4):387-99
From abstract: Ancestry informative markers (AIMs) are genetic loci showing alleles with large frequency differences between populations. AIMs can be used to estimate biogeographical ancestry at the level of the population, subgroup (e.g. cases and controls) and individual…. This work indicates that it is possible to estimate the individual ancestry of a person based on DNA analysis with a reasonable number of well-defined genetic markers.

16. Biogeographical Ancestry (2)
Mark Shriver’s work on ancestry informative markers has been commercialized through the company DNAPrint Genomics
Used in Derrick Todd Lee (Louisiana serial killer) case to overcome faulty eyewitness testimony of a Caucasian perpetrator…

17. Pigmentation (Skin Color, etc.) Prediction
Lamason, R.L. et al. (2005) SLC24A5, a putative cation exchanger, affects pigmentation in zebrafish and humans. Science 310:
From abstract: Lighter variations of pigmentation in humans are associated with diminished number, size, and density of melanosomes, the pigmented organelles of melanocytes. The variant allele is nearly fixed in European populations, is associated with a substantial reduction in regional heterozygosity, and correlates with lighter skin pigmentation in admixed populations, suggesting a key role for the SLC24A5 gene in human pigmentation.

18. Approximate Age Determination
Alvarez, M. and Ballantyne, J. (2006) The identification of newborns using messenger RNA profiling analysis. Anal. Biochem. 357(1):21-34.
From abstract: In theory, it may be possible to determine patterns of gene expression that are age specific, thereby permitting the distinction among tissue samples originating from individuals of different ages (e.g., newborn, adolescent, middle-age, elderly). We have discovered two novel isoforms of gamma hemoglobin messenger RNA, designated HBG1n and HBG2n, which exhibit an extremely restricted pattern of gene expression, being confined to newborn individuals. Multiplex quantitative reverse transcription PCR (qRT-PCR) assays incorporating these novel mRNAs have been designed, tested, and evaluated for their potential forensic use. The results indicate that the assays provide the ability to determine whether a bloodstain originated from a newborn.

19. Age of Bloodstain Deposition
Anderson, S., Howard, B., Hobbs, G.R., Bishop, C.P. (2005) A method for determining the age of a bloodstain. Forensic Sci. Int. 148(1):37-45
From abstract: If there were independent evidence that the biological sample was deposited at the time of the crime, then its age would reveal when the crime occurred. If the time of the crime were known through another means, then the age of the biological sample could potentially exclude the human source as a suspect. We have used real-time reverse transcriptase PCR to show that the ratio between different types of RNA (mRNA versus rRNA) changes over time in a linear fashion when dried human blood from eight individuals was examined over the course of 150 days.

20. Non-Human DNA Testing Cat DNA Dog DNA Other uses of non-human DNA
Plant DNA – for possible linkage to crime location
Marijuana DNA – tracking drug sources
Animal as
Victim (abuse case)
Perpetrator (dog bite)
Silent witness (crime scene linkage)

21. New DNA Test for Cats Developed at NIST
J. Forensic Sci. 2005; 50(5):
SRY (male) 4 7
Male cat 1 5 2 9 10 3 6 8 11
female 4 7
Female cat 2 5 10 1 6 9 8 3 11
Figure 11.1 DNA profiles produced from male (top panel) and female (bottom panel) cat DNA using a multiplex STR typing assay dubbed the “MeowPlex” (Butler et al. 2002). This test examines 11 autosomal STRs and a region of the SRY gene contained on the Y-chromosome that can be used for sex determination.

22. SRY (male) 4 7
Male cat 1 5 2 9 10 3 6 8 11 4 7
Female cat 2 5 10 1 6 9 8 3 11
Figure 17.7 DNA profiles produced from male (top panel) and female (bottom panel) cat DNA using a multiplex STR typing assay dubbed the “MeowPlex” (Butler et al. 2002). This test examines 11 autosomal STRs and a region of the SRY gene contained on the Y-chromosome that can be used for sex determination.

23. Animal DNA Testing
Most non-human DNA tests are specialty tests that will be rarely used by public labs and thus typically will be performed through outsourcing to a contract lab
QuestGen Forensics
UC Davis Vet Gen Lab

24. Challenges with Presenting Non-Human DNA in Court (or other novel DNA methods)
Sensabaugh and Kaye (1998) Jurimetrics 38: 1-16
Novelty of the application
Validity of the underlying scientific theory
Validity of any statistical interpretations
Relevant scientific community to consult in assessing the application may be limited
New methods may not have undergone the scientific scrutiny of regular forensic human DNA testing techniques

25. Chapter 15 – Points for Discussion
Why are SNPs being considered for use in human identity testing?
What are the advantages and disadvantages of SNPs compared to currently used STR markers?
Will SNPs replace STRs as a primary means of forensic DNA testing? Why or why not?
Are there ethical challenges with using SNPs to predict ethnicity and physical traits? If so, what are they and how should the law enforcement community use this type of information in the future?