DNA Phenotyping Shows Results

Kathy Marks

One of the benefits of this technology is a significant reduction of the suspect pool which can save time, money and manpower.

Simply stated, DNA phenotyping predicts the physical appearance of an unknown person from their DNA. This technology helps to generate investigative leads; narrows the suspect list or assists when there are no suspects or database hits; and assists with mass casualty situations and identifying unknown remains. Companies committing resources to developing this technology utilize a number of different approaches.


Laurence Rubin, Chief Executive Officer and Director of Identitas, stated that IDentify is a computer algorithm developed to analyze multiple DNA markers and produce phenotypic data. Identify uses both public and proprietary SNP markers which improve the accuracy and utility of the analyses for investigative purposes.

Rubin stressed that the information produced is not evidentiary, but rather investigational. It is a tool for the investigator to refine his focus or consider another direction.

When there are no arrests in the first 24-48 hours, investigators are often stymied, with no additional evidence to advance an investigation. Current DNA profiling depends on reference samples in a database to use for comparison to the collected DNA evidence. When the quality or quantity of the DNA is poor or suboptimal and no “match” is in the system, present technologies are severely limited.

The IDentify process facilitates descriptive (phenotypic) results from limited amounts of crime scene DNA without requiring reference samples. Compare it to scanning a barcode in a grocery store where a reference identifier is stored. If the barcode doesn’t match any of the products stored in that system, then no information regarding the product or its cost can be obtained. The IDentify system doesn’t use a “barcode”; instead, it constructs a “picture” of what the product might look like and creates useful information to ultimately identify the product.

Rubin stated, “We strive to provide information in those cases where investigators are stuck and can’t proceed. IDentify can potentially characterize relevant data, narrowing the pathways going forward, saving time and money.”

Rubin stated that the quantity of DNA needed is very small, optimally five nanograms; although, in many cases, they have been able to generate actionable data with less. The scale required and the ability to perform more than one set of analyses provides advantages for crime labs, particularly when sample quantity is very limited. IDentify can generate data from DNA on gender, hair and eye color, and composite biogeographical ancestry – all in one single analysis.

IDentify can extend relationship testing to a greater degree than current Short Tandem Repeat (STR) markers, using 800,000 Single-Nucleotide Polymorphisms (SNPs) to delineate third- and, in some cases, fourth-degree relatives. This is important for mass disaster and missing persons’ investigations.

Crime scene investigations’ adaptation of new techniques may sometimes be slow due to needed validation and explanation, expensive equipment and the required adaptation of newer scientific skills.When the criminal justice system becomes more comfortable with advanced DNA technologies, these and other approaches will be utilized to improve the quality, efficiency and accuracy of the investigative process. Rubin stated, “Identitas aims to be at the forefront of this new era, as we have partnered with law enforcement on multiple occasions to improve and deliver our product.” Identitas’ goal is to produce a cost efficient, rapid turnaround test, with an all in one process.

Toronto (Canada) Cold Case Homicide Investigator D/Sgt Stacy Gallant submitted 19 cases to Identitas for phenotyping in a real-world study project, using certain criteria to decide what best to submit. DNA had to have been processed at the Centre of Forensic Sciences and identified as coming from the offender, except in cases of found human remains. Other available investigative steps which had, or had not, been taken were considered and samples had to come from serious felony cases (homicide, sexual assault, armed robbery, found human remains).

The IDentify analysis corroborated the offender’s physical description for race/ethnicity in six cases.It provided a physical description which was not previously known in six more and, in two, it significantly changed the direction in the search for the offender due to the physical description provided. Toronto Police reported a high degree of satisfaction in these results.


Cydne Holt, Associate Director, Forensic Genomics, at Illumina, stated, “The MiSeqFGx Forensic Genomics System gives forensic testing the potential to deliver extended capabilities, higher resolution and greater efficiency – leading to more reliable results. The system is the first forensically validated, targeted, ‘massively parallel sequencing (MPS)’ solution, also known as ‘next generation sequencing (NGS)’ for forensic genomics. MPS is the DNA sequencing ‘gold standard’; the MiSeqFGx System brings that integrity to forensic DNA typing, bringing it to the modern age.”  The system consists of three parts: the ForenSeq DNA Signature Prep Kit, the MiSeqFGx sequencer and the ForenSeq Universal Analysis Software.

By combining multiple types of forensic polymorphisms into a single analysis, the MiSeqFGx system provides more actionable information in less time with the least amount of sample (<1ng), and at an attractive price.

Laboratory efficiency is increased by simultaneously reducing the number of “inconclusive” results and compiling all the genetic testing in one result. This makes multiple rounds of expensive, iterative testing a thing of the past. Additionally, unlike conventional methods, the MiSeqFGx system is able to target short, valuable DNA regions, allowing successful testing of old, degraded or inhibited samples.

Visible traits can be estimated by the MiSeqFGx System for use as “investigative leads.”  The system provides information about eye color and hair color, as well as biogeographical ancestry among population groups.It is used for missing persons’ cases, unidentified human remains and when there’s no known suspect and no database “hit.”

These data are visualized and reported using the ForenSeq Universal Analysis Software, built specifically for forensic genomics, with the collaboration of forensic experts around the world. As more and more reliable forensic DNA targets are discovered and verified, Illumina seeks to offer broader and deeper visible trait information, in a highly accurate and responsible way.

David Ballard, Ph.D., a postdoctoral scientist, and Laurence Devesse, a forensic research associate, are members of the Forensic Genetics Group at King’s College, London, led by Denise Syndercombe-Court, Ph.D. The team is at the forefront of forensic genomics and, through establishment of a Knowledge Transfer Partnership (KTP), their work with the MiSeqFGx Forensic Genomics System is leading the way in the maturation of modern forensic identification technologies.

Their research has led to another use for DNA phenotyping. The Group has successfully used the MiSeqFGx System for complex immigration cases. In the UK, individuals can apply for family members from abroad to come live with them. If they are turned down due to doubt of a familial relationship, then the individual can appeal and file a request for genetic testing.

“We’ve had two cases where we’ve seen multiple exclusions with standard forensic STRs,” Dr. Ballard stated. “Normally, labs will determine that two to three exclusions between a parent and a child means that there is no parental relationship. When we ran these cases through the MiSeqFGx System, we were able to prove that they were related as parent and child, thanks to the breadth of markers within the ForenSeq DNA Signature Prep Kit. Without the MiSeqFGx System, proving that would have been very complex, if not impossible.” The ability of the MiSeqFGx System to discern relatedness could also help in resolving paternity and missing persons’ cases and assist in disaster victim identification.

Parabon® NanoLabs Snapshot           

Parabon Snapshot DNA Phenotyping is used when crime scene DNA does not match any others found in databases (or known suspects), and to generate additional information about human remains. The original funding for Parabon Snapshot came from the Department of Defense. Parabon is involved in a separate project with the Armed Forces DNA Identification Laboratory to identify unknown remains using new methods for inferring distant kinship.

The traits which can be determined are those externally visible and those which are highly heritable, such as eye color, hair color, skin color, facial shape, and freckling. Ancestry is determined on two scales, first by region on a global scale, including East Asian, Oceanian, Native American, African, Middle Eastern, European and Central Asian. Ancestors might be from different regions and people with characteristics of two or more regions are called admixtures.

People from intermediate regions will appear as a mixture between two closely related regions (and the subsequent regional ancestry analysis will localize them to a specific region), whereas truly admixed individuals will appear as a mixture between more distant regions and the regional ancestry analysis will still show them as coming from multiple regions.

Because Snapshot cannot determine age or environmental factors, composites are made based on a subject who is 25 years old and of normal weight. Snapshot can also do an age progression based on normal patterns for someone of that ancestry to present a composite of how the subject might appear at a particular age range.

Dr. Ellen McRae Greytak, Parabon NanoLabs’s Director of Bioinformatics, stated that the composite is not intended to be an individual ID, but a portrayal of the summary of the detailed report which accompanies it. The information is presented with confidence levels for each trait. The information can help generate leads, prioritize suspects and contacts and exclude possible suspects.

Only highly heritable traits can be predicted in varying percentages. Eye color is nearly 100% heritable, while freckling is harder to predict because of the environmental factor of sunlight exposure. Percentages are presented as confidence statements. Eye colors are blue, green, hazel, brown, and black, but eyes which are dark blue or green are hard to distinguish and the confidence level may be lower.

The data may allow law enforcement to exclude most of the suspect pool. Greytak stated that, “We exclude phenotypes which are less than ten percent consistent with the prediction, so exclusions can be at anywhere from 90% to 99.99% confidence on excluded phenotypes. We explain it as ‘it’s the same as an eyewitness statement, factual information, such as a white subject with blue eyes.’ It’s a genetic witness.”

The Snapshot procedure uses SNPs which are changes in the DNA sequence, rather than using STR for DNA analysis as is commonly used for CODIS and other databases. Each person has millions of SNPs, compared to the 13-27 used in STR, providing much more data to work from. Greytak stated that “STR treats DNA as a fingerprint and Snapshot treats it as a blueprint, all the information to actually build that person. We are using that to infer that person’s physical appearance.”

Greytak reports that they deal with decades old cold cases with no leads. Snapshot can provide detectives with information which might allow them to exclude 95% of possible suspects.

Snapshot has been successfully utilized, with several arrests, and at least one conviction in a case in which they had participated by providing a composite. Extensive research in developing Snapshot included collecting reference samples and finding each trait’s genetic markers, using already published research and developing markers of their own. Blind evaluations were done in which they prepared composites and then compared them to the actual appearance of the subjects, successfully providing such comparisons to the media, police departments and other groups, such as the University of North Texas.

Departments typically contact Parabon and will need to provide the quality of the DNA, how it has been stored, if it is a mixture, and if there is enough DNA to test. If the DNA is appropriate to test, it may sent be to Parabon at a cost of $3600 per sample.

Galveston (TX) Major Crimes Unit Detective Derek Gaspard stated that his department used Snapshot on the decapitated remains of a female found in 1988, never identified, but believed to be a white female. Snapshot provided eye-opening results in July 2016 when their unidentified victim was found to be an Asian female, geographically from Central East Asia (China).

This was their first use of Snapshot, but they plan to use it to narrow a suspect pool on another case. Gaspard said of the new DNA method, “It is wonderful, especially for our case where we don’t know either the identity of the victim or her killer.”

Aurora (CO) Police Cold Case Squad Detective Stephen Conner used Snapshot on a case involving the triple murders of a family. Their focus on a white male was confirmed and the field of suspects was narrowed down.

Conner spoke to how he uses Snapshot, “The usefulness of Snapshot is as an investigative tool. Since I have no idea of what a suspect may look like in any given case, Snapshot can assist in providing that information.” The composite is what a suspect may look like and other investigative factors are applied, such as whether the suspect was in Colorado at that time. “This technology is a tool, not a magic bullet.”

Kathy Marks is a retired child abuse investigator with 30 years of experience; a writer and researcher; and the author of numerous law enforcement articles. She may be contacted at kathymarks53@aol.com.