University of Central Florida
Biological Evidence Mission Statement
Current Research Projects
Recent Publications
Comprehensive annotated STR physical map of the human Y chromosome
Jack Ballantyne
Associate Professor, Chemistry
Associate Director, National Center for Forensic Science
e-mail: jballant@mail.ucf.edu
Biography:
Jack Ballantyne is an Associate Professor of Chemistry at the University of Central Florida (UCF) and the Associate Director for Research at the National Center for Forensic Science in Orlando, Florida. He possesses a B.Sc. (with Honors) in Biochemistry from the University of Glasgow, Scotland, a M.Sc. in Forensic Science from the University of Strathclyde, Scotland and a PhD in Genetics from the State University of New York at Stony Brook, NY. His current duties include teaching and conducting research in forensic molecular genetics. He teaches a variety of forensic biology courses to baccalaureate and Masters level students in the Forensic Science Program and nucleic acid biochemistry to PhD students in the Biomolecular Sciences Program.
Prior to entering academia, he was a casework forensic scientist in Scotland, Hong Kong and New York where he proffered expert testimony in the criminal courts of these jurisdictions. He was the full time DNA technical leader in Suffolk County, New York and since then has served as a part-time consultant DNA technical leader for the States of Mississippi and Delaware, the City of Dallas and Sedgwick County, Kansas. Inter alia, he is the Chair of the New York State DNA Sub-committee, a regular visiting guest at the Scientific Working Group on DNA Analysis Methods (SWGDAM), a member of the DoD Quality Assurance Oversight Committee and a member of the World Trade Center Kinship and Data Analysis Panel (KADAP).
Biological Evidence Mission Statement
Our goals are to assist the national and international forensic science community by (1) conducting pure and applied research in forensic molecular genetics/biochemistry in order to contribute to the body of forensic science knowledge; (2) validating methods and technologies to facilitate technology transfer, and (3) providing operational support by supporting on-line databases of Y-STR markers and mass fatality initiatives (4) providing rigorous educational programs such as BS, MS in Forensic Science and PhD in Bimolecular Science.
Forensic Biology
What is Forensic Biology?
Forensic Biology is the application of Biology (Genetics, Biochemistry and Molecular Biology) applied to the solution of certain problems that arise in connection with the administration of justice. It is science exercised in the service of the law. More practically it is the study of blood and other physiological material as it relates to establishing a fact that may be at issue in a medical legal investigation.
Situations in which forensic biological evidence may be important
(1) Crimes against a person
- homicide
- assault
- rape/ or other sexual assaults
- criminal paternity
- terrorism
(2) Crimes against property
- burglary
(3) Mass Fatality Incidents
(4) Motor Vehicle Incidents
(5) Paternity/Kinship
Biological Evidence Transfer
Every crime takes place at a certain time at a certain place or places (the scene(s)) and involves a victim and the person or persons committing the crime (perpetrator(s)). The perpetrator may or may not use a weapon. Depending upon the case circumstances, biological material is transferred between the scene, the victim, the perpetrator and the weapon. Evidence transfer is illustrated below with the most common direction of transfer indicated by the arrows.
Types of Biological Evidence
(1) Blood
(2) Semen
(3) Saliva (e.g. Cigarettes)
(4) Vaginal Secretions
(5) Fecal Material
(6) Hair
(7) Urine
(8) Bone
Meaning of a DNA Match
The basic theory behind DNA testing is that no two individuals would be expected to posses the same so-called nuclear DNA type (except identical twins). Typically, a ‘nuclear’ DNA match between a crime scene sample and an individual would be an exceedingly rare event if the individual was not the true source of the crime scene sample. This high degree of individual specificity is often indicated in scientific reports by a statistical evaluation of the rarity of the observed genetic profile. An example of conclusions provided to the Courts when a DNA match is observed would be as follows:
Approximately 1 person in every 5 trillion chosen at random from the population would be expected to possess the same DNA genotype as that found in the questioned sample'. Since 5 trillion is much less than the population of the World (and so one couldn’t have 5 trillion people to compare) an alternative conclusion (based upon the same data) may be adduced. 'The DNA results are 5 trillion times more likely if the questioned sample originated from the suspect than if it had originated from a randomly chosen unrelated individual from the population'.
Y Chromosome Analysis
Males commit 79% of violent crimes and 98% of all sexual assaults. In some cases a failure to obtain the male donor profile by standard DNA techniques is due to the presence of large quantities of female derived DNA. In such cases probative investigative information may still be obtainable by the judicious use of Y chromosome markers. Such markers are essentially blind to the contaminating female derived DNA in male/female DNA admixtures. We continue to develop and refine a number of Y chromosome analysis techniques for forensic casework use.
Development and Validation of Novel Y-STR Markers for Forensic Use
Due to the availability of commercial kits and a broader understanding of the usefulness of Y chromosome markers in certain cases, an increasing number of laboratories in the US have the capability of performing Y-STR analysis in casework. Although commercial Y-STR kits perform well in casework, the match probability of a Y-STR match is modest due to the limited number of loci used. We have developed and validated 10 multiplex analytical systems containing > 100 novel Y-STR loci. The most forensically useful loci have been combined into an Ultra High Discrimination system that we believe has the highest discriminatory power of any multiplex.
DNA Profiling of the Semen Donor in Extended Interval Post-Coital Samples
For a variety of reasons, some victims of sexual assault provide vaginal samples more than 24-36 hours after the incident. The ability to obtain an autosomal STR profile of the semen donor from the living victim diminishes rapidly as the post coital interval is extended. We have used a number of carefully selected Y-STR loci in a variety of multiplex formats to extend the post coital interval (up to 5 days) from which a genetic profile of the semen donor can be obtained. We attribute our success to a number of factors that significantly improve the sensitivity and specificity of the analysis. This work is likely to have a significant impact on the investigation of rape cases.
Compilation and Management of a Comprehensive US Y -STR Reference Database
The significance of a Y-STR match in casework is estimated by reference to a reliable and relevant database of Y-STR profiles. The National Center for Forensic Science (NCFS), in conjunction with the Y-STR Consortium, has created a comprehensive, online Y-STR reference database of more than 13,000 haplotypes.
The U.S. Y-STR Database, a searchable listing of 11- to 17-locus Y-STR haplotypes located on the web at www.usystrdatabase.org, was developed by combining data from NCFS with databases from government, commercial, and academic resources throughout the United States. The database provides tools for laboratories to obtain Y-STR haplotype frequencies needed to calculate matching or paternity probabilities with confidence intervals. Other features include the ability to simultaneously upload multiple haplotypes for searches directly from Genotyper® and GeneMapper® text files, the ability to include or exclude sampled populations, and a report-style printout of the results. Samples are divided into five forensically relevant ancestries: African-American, Asian, Caucasian, Hispanic and Native American.
All forensic laboratories and institutions are invited to contribute to the U.S. Y-STR Database. The resulting increase in the database size and the inclusion of geographically and ethnically varied population groups will increase the scientific and forensic efficacy of the database.
Note: This database does not function like the more commonly used CODIS database. This is a population database only and is intended for use in estimating Y-STR haplotype population frequencies for forensic case work purposes. It cannot be used to identify a particular individual whose sample is in the database. All donors are anonymous, haplotypes cannot be traced back to specific individuals, and original electropherograms do not exist in a curated fashion.
NCFS also maintains, and is still expanding, its own Y-STR database that comprises >100 loci and >2000 samples.
Strategies for Low Copy Number (LCN) Analysis
This project is concerned with the investigation of potential strategies for analyzing samples containing low copy number (LCN) DNA templates. Biological evidence is often encountered with an extremely low number of starting templates (1-15 cells) and requires the development of novel strategies for its collection, analysis and interpretation. We are investigating different strategies by which samples containing low copy numbers of starting DNA template could be DNA profiled, including whole genome amplification and single cell methods. For single cells we capture cells using a laser capture microscope in order to perform what we term ‘smart single cell DNA profiling’
Body Fluid Identification by mRNA Expression Profiling
Conventional methods of body fluid identification use labor-intensive, technologically diverse techniques that are costly in terms of time and sample. For some frequently encountered body fluids (e.g. saliva, vaginal secretions and menstrual blood) no definitive identification technique exists. A pattern of gene expression is produced in body fluid secretions and tissues that uniquely defines each cell type present. This is evidenced by the presence and relative abundance of specific mRNA species. We have developed a number of highly specific mRNA profiling assays for body fluid and tissue identification and transferred them to a variety of commonly used analytical platforms.
Quantitation of Human Specific mRNA
The use of mRNA technology in forensic genetics offers the ability to obtain probative information not readily achievable using other methods. Many of the stains recovered from crime scenes are contaminated with non-human DNA from a variety of organisms including microbial species. The RNA assays developed require the input of a certain quantity of human RNA. In this project we are developing an assay for the accurate and reliable quantitation of human specific RNA in the presence of RNA from other organisms.
Assessment and In Vitro Repair of Damaged DNA Templates in Biological Stains
One of the limiting factors with DNA typing technology is that sometimes DNA isolated from physiological stains recovered from the crime scene is so damaged as to be intractable to analysis. However, current knowledge of the biochemical nature and extent of the DNA damage in biological stains of forensic importance is rudimentary. We are characterizing the molecular lesions that prevent the ability to obtain a standard DNA profile in damaged DNA recovered from crime scene physiological stains with a view to determining possible DNA repair strategies.
Biochemistry of the Dried State
The objective of this study is to investigate the basic chemistry of the dried state, specifically that of the most common expected type of chemical reactions, namely hydrolysis and oxidation. Specifically we are performing kinetic analysis of dry state DNA degradation by determine the rates of such reactions under different environmental conditions. We have concentrated our early efforts on hydrolytic damage to the relatively labile glycosidic bond and deamination of the nitrogenous bases. The general approach is to allow reactions to occur over a period of time at predetermined set temperatures and perform quantitative measurements to determine rate constants and activation energies.
Double Strand Break Repair
Double strand breaks, which arise as a result of microbial action or terrestrial UV irradiation, are the cause of most DNA degradation in forensic samples. We are developing methods for the in vitro repair of double strand DNA breaks using a variety of different approaches, which include one or more of the following: recombination substrate-mediated gap repair, homologous recombination and non-homologous end-joining. The goal is human identification from degraded DNA, indicated by the recovery of a genetic profile from otherwise non-typeable samples. DNA repair success is initially evaluated using SNPs with the ultimate goal the recovery of STR profiles.A Genetic Eye witness: The Determination of Individual Physical Characteristics of the Donor of a Body Fluid Stain
The donor of a body fluid recovered from the crime scene is identified by comparing the crime scene DNA profile to profiles obtained from reference samples obtained from known individuals. However, in the absence of appropriate comparison reference samples, the DNA profile per se presently provides no meaningful information to investigators, with the notable exception of gender determination. A number of other physically recognizable characteristics of an individual may be amenable to molecular genetic analysis and these include skin-, hair- and eye- color, stature (height and weight), age and facial morphology.
Ethnogeographic Ancestry Prediction
We are investigating whether determination of ethnogeographic origin is feasible by the analysis of Y-SNP markers in body fluid stains. As a result of mutation and geographic-specific genetic bottlenecks throughout human history, modern Y chromosome lineages, called haplogroups, exhibit the genetic signatures of their bio-geographical past. We are discovering novel Y-SNP markers that better resolve some of the common haplogroups and to develop hierarchical typing assays for biogeographic ancestry prediction. Maternal lineage and pigmentation markers are being incorporated into the analysis to help resolve haplogroups with a high proportion of ethnically admixed individuals.Ethnoancestry from Bones
Forensic anthropologists can sometimes predict the ethnic identity of a bone using bone morphology. It becomes increasingly difficult or impossible with bone fragments. We are investigating the possibility of obtaining the ethnogeographic ancestry of male bone by Y-SNP typing using both modern and ancient bones. This work could have significant implications for both forensic and archaeological studies.
Determining the Age of an Individual by Messenger RNA Profiling
As humans proceed through developmental from birth to adulthood, sub-sets of the estimated 20-25 thousand human genes will be differentially expressed. Theoretically, a comparison of the gene expression profile from individuals of different ages should reveal constellations of genes whose expression is correlated with a specific age. We discovered novel newborn-specific isoforms of HBG mRNA from which we developed assays that determine whether a bloodstain originated from a newborn baby. We are in the process of identifying other age predictor genes that are expressed at other ages.
Determination of the Age (Time since Deposition) of a Biological Stain
The ability to determine the time since deposition (TSD) of a biological stain found at a crime scene could prove invaluable to investigators, defining the time frame in which the individual depositing the evidence was present. No reliable TSD methods are available at present. The fundamental assumption of this project is that biochemical reactions still occur in the dried state and as dried stains age, damage and degradation to macromolecules such as DNA, RNA and protein occur. We are investigating whether macromolecular degradation intermediates and/or specific nucleic acid base damage can serve as molecular clocks for time since deposition (TSD) estimation.
Microbial Genetic Signatures: A Novel Trace Evidentiary Method
The field of microbial forensics is conventionally confined to the analysis and characterization of evidence from a bio terrorism act. However we are investigating whether certain microbes are sufficiently restricted in their growth potential within different body fluids, or within different individuals, to be of broader use in forensic science. We are characterizing the bacteria that normally grow in human body fluids (e.g. saliva and vaginal secretions) by means of species/strain determination and determining their persistence and stability. Our initial observations indicate that some microbes are likely to be the source of useful biomarkers for certain body fluids.
A Forensic DNA Sourcebook
Casework forensic biologists often need to access information from previously published material such as journal articles, monographs, books and the internet. A useful tool would be a convenient web-accessible Forensic DNA Sourcebook that provides, in a ‘one-stop shopping’ mode, a comprehensive compilation of all relevant resources, and a survey of the published literature. A prototype master DNA Sourcebook document has been created. Each reference in the master document has a link to its abstract/publisher site/full article, depending on the source and availability of the reference. More than 11,000 references have been collected, categorized and hyper-linked to their abstracts.
Optimization, Testing and Validation of Novel DNA Technologies
The National Institute of Justice funds a wide variety of R&D projects whose express aim is the development of novel DNA technologies to make DNA analysis quicker, better or cheaper. NCFS is assisting NIJ in transferring selected novel technologies to the crime lab community by providing assistance to principal investigators (PI), particularly those who are not forensic scientists. Such assistance includes, in consultation with the PI, optimization of the technology for the analysis of forensic specimens of limited quantity and quality, testing of the methodology and, if warranted, a full-scale developmental validation of the refined technology.
mtDNA Analysis of Coding Region SNPs by Pyrosequencing
The use of mitochondrial DNA in forensic analysis has traditionally relied on genetic variation within the two hyper variable (HV) regions of the non-coding Control region to differentiate individuals. However common HV haplotypes exist that may comprise a up to 7% of the Caucasian population. We have investigated the mitochondrial coding region for single nucleotide (SNP) polymorphisms that could differentiate between samples with identical control region haplotypes. The result was the development of a set of multiplex pyrosequencing-based SNP assays (mtSNPlex) that interrogate 10 coding region SNPs. These are particularly useful for differentiating Caucasian individuals.
1. Mass Disaster Genetics. Ballantyne, J. Nature Genetics 15: 329-331 (1997)
2. Immunogloculins: Polyclonal and Monoclonal Antibodies. Ballantyne J., Mandle R. and Bing D. In Hematology: Basic Principles and Practice, Churchill Livingstone, Pennsylvania. 640-651 (2000)
3. Serology Overview. Ballantyne J. In Encyclopedia of Forensic Sciences, Elsevier, Oxford. 1322-1331 (2000)
4. Messenger RNA Profiling: A Prototype Method to Supplant Conventional Methods for Body Fluid Identification. Juusola, J. and Ballantyne J. For. Sci. Int. 135: 85-96 (2003)
5. The Development of an 18 Loci Y-STR system for Forensic Casework. Hall, A. and Ballantyne, J. Anal Bioanal Chem 376 1234-1246 (2003)
6. Novel Y-STR Typing Strategies Reveal the Genetic Profile of the Semen Donor in Extended Interval Post Coital Cervicovaginal Samples. Hall, A. and Ballantyne, J. For Sci Int 136: 58-72 (2003)
7. Strategies for the Design and Assessment of Y-STR Multiplexes for Forensic Use. Hall, A. and Ballantyne, J. For Sci Rev 15(2) 137-149 (2003)
8. The Design and Characterization of a Highly Discriminating 21 Locus Y-STR System for Forensic Casework. Hanson, E. and Ballantyne, J. J Forensic Sci 49(1) 1-12 (2004)
9. SWGDAM Developmental Validation of a 19 locus Y-STR System for Forensic Casework. Daniels, D., Hall, A. and Ballantyne, J. J Forensic Sci 49 (4) 668-683 (2004)
10. Characterization of UVC-Induced DNA Damage in Physiological Stains: Forensic Implications. Hall, A. and Ballantyne, J. Anal Bioanal Chem 380: 72-83 (2004)
11. An mRNA and DNA Co-Isolation Method for Forensic Casework Samples. Alvarez, M, Juusola, J and Ballantyne, J. Anal Biochem
335: 289-298 (2004)
12. Inference of Human Geographic Origins Using Alu Insertion Polymorphisms. Ray D., Walker JA., Hall A., Llewellyn B., Ballantyne J., Christian A., Turteltaub, K. and Batzer, M. For Sci Int 153: 117-124 (2005)
13. Serology Overview. Ballantyne J. In Encyclopedia of Forensic and Legal Medicine, Elsevier, Oxford. Payne James, J., Byard, R., Corey, T. and Henderson, C. (Eds). 53-63 (2005)
14. Multiplex mRNA Profiling for the Identification of Body Fluids. Juusola, J., Ballantyne, J. For Sci Int 152: 1-12 (2005)
15. Whole Genome Amplification Strategy for Forensic Genetic Analysis Using Single or Few Cell Equivalents of Genomic DNA. Hanson, E., Ballantyne, J. Anal Biochem 346: 246-257 (2005)
16. DNA Identifications After the 9/11 World Trade Center Attack., Biessecker, L., Bailey-Wilson, J., Ballantyne, J., Baum, H., Bieber, F., et al. Science 310: 1122-1123 (2005)
17. Comprehensive Annotated STR Physical Map of the Human Y Chromosome: Forensic Implications. Hanson, E., Ballantyne, J. Legal Medicine 8: 110-120 (2006)
18. Novel Thermostable Y-family Polymerases: Applications for the PCR Amplification of Damaged or Ancient DNAs. McDonald, J., Hall, A., Gasparutto, D., Cadet, J., Ballantyne, J., Woodgate, R. Nucleic Acids Research 34(4) (2006)
19. Laser Microdissection Separation of Pure Spermatozoa from Epithelial Cells for Short Tandem Repeat Analysis. Sanders, C. Sanchez, N., Ballantyne, J., Peterson, D. J Forensic Sci 51(4): 748-757 (2006)
20. The Identification of Newborns Using Messenger RNA Profiling Analysis. Alvarez, M., Ballantyne, J. Anal Biochem 357: 21-34 (2006)
21. Creating and Manager Effective Y-STR Databases. Ballantyne, J., Fatolitis, L., Roewer, L. Profiles in DNA 9(2) (2006)
22. Testing and Evaluation of 43 ‘Non-Core’ Y Chromosome Markers for Forensic Casework Applications. Hanson, E., Berdos, P. and Ballantyne, J. J. Forensic Sci 51(6) 1298-1314 (2006)
23. Y-STR Concordance Study Between Y-Plex™5, Y- Plex™6, Y-Plex™12, Powerplex®, Y-Filer™, MPI, and MPII. Gross, A.M., Berdos, P. and Ballantyne, J. J. Forensic Sci 51(6) 1423-28 (2006)
24. Sub-Populations within the Major European and African Derived Haplogroups R1b3 and E3a are Differentiated by Previously Phylogenetically Undefined Y-SNPs. Sims, L.M., Garvey, D. and Ballantyne J. Human Mut 28(1) 97 (2007)
25. Population Data for a Novel, Highly Discriminating Tetra-local Y-STR: DYS503. Hanson, E. and Ballantyne, J. J. Forensic Sci 52 (2) 498-499 (2007)
26. Validity of Messenger RNA Expression Analyses of Human Saliva. Ballantyne J. Letter to Editor. Clin Cancer Res 13 (4) 1350 (2007)
27. Simplified Low Copy Number (LCN) DNA Analysis by Post PCR Purification. Smith, P.J. and Ballantyne, J. J. Forensic Sci 52 (4) 820-829 (2007)
28. Performance Characteristics of Commercial Y-STR Multiplex Systems. Mayntz-Press, K.A and Ballantyne J. J. Forensic Sci 52 (5) 1025-1034 (2007)
29. Population Data for 48 ‘Non-Core” Y Chromosome Loci. Hanson, E. and Ballantyne, J. Legal Medicine 9 221-231 (2007)
30. mRNA Profiling for Body Fluid Identification by Multiplex Quantitative RT-PCR. Juusola, J. and Ballantyne J. J. Forensic Sci 52 (6) 1252-1262 (2007)
31. An Ultra-High Discrimination Y Chromosome Short Tandem Repeat Multiplex DNA Typing System. Hanson, E.K. and Ballantyne, J. PLoS ONE 2(8) e688 1-14 (2007)
32. The Golden Gene (SLC24A5) Differentiates US Sub-Populations within the Ethnically Admixed Y-SNP Haplogroups. Sims, L.M. and Ballantyne, J. Legal Medicine 10 72-77 (2008)
33. A Rare Y Chromosome Missense Mutation in Exon 25 of Human USP9Y Revealed by Pyrosequencing. Sims, L.M. and Ballantyne, J. Biochem Genet (in press) doi:10.1007/s10528-007-9139-1 (2008)
34. Recovery and Stability of RNA in Vaginal Swabs and Blood, Semen, and Saliva Stains. Setzer,M., Juusola, J. and Ballantyne, J. J. Forensic Sci (in press) doi:10.1111/j.1556-4029.2007.00652.x (2008)
35. Y-STR Profiling in Extended Interval (> 3 days) Post Coital Cervicovaginal Samples. Mayntz-Press, K.A., Sims, L.M., Hall, A. and Ballantyne J. J. Forensic Sci (in press) (2008
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Last update: May 29, 2008