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Forensic DNA Research and Development

Date Published
November 17, 2015

Forensic DNA analysis has played a crucial role in the investigation and resolution of crimes and missing persons cases since the late 1980s.

The demand for tools and technologies in all areas of forensic science, including DNA testing, far exceed the current capabilities of the field. To help meet that demand, the NIJ has funded forensic DNA research and development projects for over two decades.

We fund research and development in the following broad categories:

Alternative Genetic Markers 

While short tandem repeat (STR) typing forms the backbone of current national DNA databases and day-to-day forensic casework, additional DNA marker systems are under exploration in the research arena. These new DNA marker systems include single nucleotide polymorphisms (SNPs), Alu-insertion elements, and phenotypic predictors. Alternative genetic markers and assays can potentially provide further information about biological samples under investigation, such as an estimation of ethnic origin, physical characteristics, and skin, hair, or eye color.

Compromised DNA Evidence

Biological samples collected from crime scenes, mass disasters, and missing persons cases may have been exposed to harsh environmental conditions such as heat, direct sunlight, and water that break down the chemical structure of DNA. Environmental exposure damages DNA by randomly breaking the molecules into smaller pieces. Inhibitors of the polymerase chain reaction (PCR), such as some textile dyes, can also interfere with the ability to recover a full DNA profile from biological evidence. New DNA tests are being developed to recover information from smaller regions of DNA, which are more likely to be intact following DNA damage. These new DNA tests include miniSTRs (using PCR primers close to the STR repeat region) and single nucleotide polymorphisms (SNPs). Whole genome amplification and DNA repair methods are also being evaluated to determine the possibility of enriching PCR amplifiable material from limited or damaged DNA templates.

Human DNA  Quantitation

When biological evidence from a crime scene is processed to isolate the DNA present, all sources of DNA are extracted. Thus, non-human DNA such as bacterial, fungal, plant, or animal material may also be present in the total DNA recovered from the sample along with the relevant human DNA of interest. For this reason, the DNA Advisory Board (DAB) Standards that govern forensic DNA testing of forensic casework require human-specific DNA quantitation (standard 9.3). This requirement ensures that appropriate levels of human DNA can be included in the subsequent polymerase chain reaction (PCR) amplification of short tandem repeats (STRs) evaluated in a DNA profile.

Equally important is the fact that multiplex STR typing works best with a fairly narrow range of human DNA. Typically 0.5 to 2.0 ng of input DNA works best with commercial STR kits. Too much DNA results in overblown electropherograms that make interpretation of results more challenging. Too little DNA can result in loss of alleles due to stochastic amplification in a low copy number regime.

In recent years, research in human DNA quantitation has focused on new "real-time" quantitative PCR (qPCR) techniques. Quantitative PCR methods enable automated, precise, and high-throughput measurements. Interlaboratory studies have demonstrated the importance of human DNA quantitation on achieving reliable interpretation of STR typing and obtaining consistent results across laboratories.

General Tools and Information

A number of general tools are being developed to aid State and local forensic DNA laboratories. Studies have been performed or are ongoing to improve the efficiency of casework, to examine population variation with forensic DNA markers, to evaluate different DNA storage media, to assess capabilities of DNA in ascertaining human pigmentation or time since deposition from crime scene samples, and to examine the costs of blind proficiency testing. In addition, valuable information is being made available to aid forensic practitioners, researchers, and officers of the court through Internet resources such as NIST's STRBase.

Miniaturization and Automation

New technologies are being developed to miniaturize DNA testing instruments and to improve automation of the processes involved. Both miniaturization and automation have the potential to improve the speed and to reduce the cost of DNA analysis. In addition, miniaturizing the instrumentation required to perform DNA testing could enable examination of biological samples at the crime scene if desired in the future here in the United States.

Mitochondrial DNA

Mitochondrial DNA (mtDNA) has provided forensic scientists with a valuable tool for determining the source of DNA recovered from damaged, degraded, or very small biological samples. MtDNA is a small circular genome located in the mitochondria, which are located outside of a cell's nucleus. Most human cells contain hundreds of copies of mtDNA genomes, as opposed to two copies of the DNA that is located in the nucleus. This high copy number increases the likelihood of recovering sufficient DNA from compromised DNA samples, and for this reason, mtDNA can play an important role in missing persons investigations, mass disasters, and other forensic investigations involving samples with limited biological material. Additionally, mtDNA is maternally inherited. Therefore, barring a mutation, an individual's mother, siblings, as well as all other maternally-related family members will have identical mtDNA sequences. As a result, forensic comparisons can be made using a reference sample from any maternal relative, even if the unknown and reference sample are separated by many generations.

NIJ has supported research to develop tools to rapidly screen biological evidence to obtain mtDNA information, as well as tools for separating the individual components of mtDNA mixtures and to improve the resolving power of mtDNA information. In addition, a NIST (National Institute of Standards and Technology) standard reference material (SRM 2392-I) has been characterized to aid in certification of mtDNA sequencing procedures

Non-Human DNA

Forensic investigations can be aided by association of biological material from animals, plants, or microbes to a victim or suspect. For example, domestic animals such as cats and dogs live in human habitats and may deposit hair that can be used to associate a suspect with a particular crime scene or victim. Thus, efforts are underway to improve genetic marker systems and assays for cat and dog DNA. Sources of marijuana may also be linked through the power of DNA testing.

Entomological evidence also can be used to investigate crimes. For example, insects found on a homicide victim can help determine time of death.

Sperm Detection and Separation

The detection of sperm and separation of sperm cells from the victim's DNA is crucial to identifying and characterizing the perpetrator's DNA profile. Improved automation of sperm detection and separation will enable more rape kits to be processed in a timely manner to help solve sexual assault crimes more effectively. Traditionally sperm cells are identified visually in evidentiary samples through light microscopy. New techniques are under development to aid improved visualization of sperm heads and tails with fluorescent staining as well as sperm cell isolation through laser capture microdissection.

Y Chromosome

The Y chromosome DNA testing enables examination of the male-specific portion of biological evidence. This capability can be especially important in situations where a small amount of male DNA may be recovered in the presence of excess female DNA, such as in sexual assault evidence. Y chromosome analysis can also benefit missing persons investigations as it extends the range of potential reference samples. Since fathers pass their Y chromosome onto their sons unchanged (except for an occasional mutation), all males in a paternal lineage will possess a common Y chromosome haplotype.

A core set of Y chromosome short tandem repeat (Y-STR) loci have been selected for use in human identification applications. The core Y-STR loci were recommended by the SWGDAM Y chromosome subcommittee in 2003 and include the following: DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS438, DYS439, and the multi-copy locus DYS385 a/b. Commercial kits now exist that can co-amplify all of the core Y-STR loci in a single multiplex reaction. Several groups are also exploring additional Y-STR loci that have the potential to improve the power of discrimination for Y-STR testing.

National Institute of Justice, "Forensic DNA Research and Development," November 17, 2015, nij.ojp.gov:
Date Created: August 13, 2019