Over the course of several decades of forensic DNA research efforts, scientists have defined a group of particular STRs that best serve as a set of standards for identification of individuals. In the case of criminal forensics, 13 different STRs sprinkled throughout the chromosomes are referred to, along with a supporting database, as the Combined Indexing System (CODIS for short). Established in 1998, CODIS is used by U.S. criminal labs and has been popularized by its frequent mention in crime shows and popular media. McMahon makes the important distinction that AFDIL utilizes CODIS STRs for their identification procedures in addition to several other defined STR loci. He also emphasizes that the Armed Forces Medical Examiner System database is completely separate from the CODIS database used in criminal forensics.
Another effective and related tool AFDIL analysts may rely on to help solve a case of identification is Y chromosomal DNA analysis using Y-chromosome specific STRs. All three DNA approaches proved to be necessary in the case of positively identifying Jim Van Bendegom’s remains; a valuable combination when used together, they offer the highest degree of discrimination. The availability of three different forensic DNA technologies has aided analysts in cases whereby testing one or two types of a sample's DNA did not yield a conclusive analysis.
“It’s very important to have many different tools in your tool belt—or different ways to attack a human identification challenge because of the various ages and conditions of samples,” says McMahon.
Once DNA testing has revealed an unidentified sample’s mito-type and/or autosomal and Y chromosome STR profiles, the information can then be compared with reference samples present in the AFDIL database. A final report that includes all these instructive DNA differences is sent back out to the DPAA lab, and based on their review they may recommend that DNA analysts search against a specific database of family reference samples. By the end, these searches “kick out the potential results—no matches, one possible match, or many possible matches.” And, depending on the results, additional analyses may be run as forensic scientists hone in on the information needed to make a conclusive identification.
Critical to AFDIL’s success, yet challenging to its speed, are the standards the agency must uphold. The Defense Science Board, established by the Department of Defense, mandates that all DNA identification procedures be immune to errors, and thus every analysis must be conducted in duplicate. So, per protocol, two separate DNA extractions are obtained from the same sample and the data analysis is done by two independent analysts. Every case goes through multiple levels of review; in order for a report to be sent back out to the DPAA those two results must match exactly.
Major advances in forensic DNA analysis are serving to impact the certainty of identification. As McMahon says, “We’re constantly trying to improve how we do things and evaluating any technologies that are three to five years out.”
One major technological breakthrough, Next Generation Sequencing (NGS), was recently incorporated into AFDIL’s toolbox. So innovative, AFDIL is currently the only forensics lab in the U.S. using this technology. As Lieutenant Colonel Alice Briones, Deputy Chief Medical Examiner and doctor of forensic pathology, explains, NGS is able to sequence the smallest and most degraded forensic samples, typically those that cannot be analyzed through conventional mitochondrial DNA analysis or autosomal DNA STR analysis. Although the process takes longer to run and is extremely labor intensive, the results it can provide are pivotal to the most challenging cases of forensic DNA analysis.
Briones realizes that NGS is more than just a complex DNA technology; it represents a means with which to bring closure to families who may have never received it. “The work we do brings the science, the past, and the present communities all together. We use it to bring our service members home,” she says. “I feel that as a scientist, what more honorable mission can we do?”
CODIS STR Loci with Chromosomal Positions
Location of the 13 CODIS loci and sex chromosome STR loci used for criminal forensic analysis as well as AFDIL's autosomal DNA testing.