Ten years ago, most forensics laboratories tested and analyzed a manageable number of samples. Most of those labs also did not anticipate the current surge of evidence and what would be required to keep up with it. A large number of new cases come from law enforcement agencies, and in many instances contain DNA evidence. It is critical that this evidence be tested as quickly as possible to provide real-time investigative support by way of providing matches to known suspects or utilizing investigative leads that are developed through the Combined DNA Index System (CODIS), which contain known DNA profiles of convicted offenders, arrestees, unidentified human remains, missing persons and relatives of missing persons. Because laboratories cannot immediately work on every case they receive, testing must be prioritized.
Strained operating budgets and high staff turnover put further pressure on productivity. Fortunately, many of these challenges can be mitigated by automating those laboratory operations that can be automated and by employing electronic DNA sample management systems. Without these aids, a limited number of samples could be processed. “We would see more errors and more variations in quality,” noted Brian Hoey, laboratory manager and DNA technical leader at the Missouri State Highway Patrol. “We wouldn’t be able to have a high throughput with built-in quality checks, and would probably be at a greater disadvantage to reduce the backlogs.”
Backlogs could be reduced by combining integrated LIMS and DNA sample management solutions and more staffing, according to Jay Henry, past president of the American Society of Crime Lab Directors (ASCLD). “Relevant stakeholders have to realize that we are only pushing the constraint of backlogs from the interface (evidence intake) to the lab (via automation) and now to the analyst, who must evaluate the data and write and review reports,” he said. “The bottom line is that you will need people to evaluate the information that comes from these samples. So, in essence, it’s a combined solution of working smarter (what we are testing), and working more efficiently (using robotics and sample management software).”
Automated DNA sample management
Many automated and electronic systems are available to the laboratory for sample processing. The following is a list of representative hardware and software products and a discussion of how these are being used in various forensics laboratories.
Robotics
- Tecan Freedom EVO robotic liquid handling workstation for processing samples (Tecan, Morrisville, N.C.)
- AutoLys workstation—automates the entire sample lysis and lysate recovery process (Hamilton Robotics, Reno, Nev.)
- Maxell16 (Promega Corp., Madison, Wis.), iPrep (Invitrogen, Life Technologies, Grand Island, N.Y.), QIAamp kits (QIAGEN, Valencia, Calif.) and EZ1 extraction robots (QIAGEN)—designed for nucleic acid and genomic DNA extraction
- JANUS automated DNA extraction and liquid handling workstation (PerkinElmer, Waltham, Mass.).
DNA sample management software
- LIMS-plus DNA is a standalone DNA application for automating forensic sample processing for casework and databanks. It helps automate delivery of DNA profiles to local, state and national databanks; provides integration across all systems in the forensics laboratory, particularly instrument data and LIMS data sharing; and tracks all methods, reagents, batches and instruments at the sample level and for each examiner (JusticeTrax, Mesa, Ariz.)
- STACS-CW Family of Solutions DNA l software tracks DNA samples, users, consumables, instruments, cases, exhibits, profiles and results. Reports can be generated, and users can create and process batches and add or remove a set of samples with controls to/from a batch at any analytical step as the need arises (STACS DNA, Fairfax, Vir.)
- Crime Fighter BEAST (bar-coded evidence analysis statistical tracking) is a DNA module built into the Crime Fighter BEAST LIMS. It interfaces with instruments and robots. Onscreen worksheets are instantly converted to plate setup files exported directly to the laboratory’s instruments for quantitation, amplification and analysis protocols (Porter Lee Corp., Schaumberg, Ill.).
Automated workflow and DNA sample processing
In 2010, in an effort to make the DNA sample management process as efficient as possible, the Louisiana State Police Crime Laboratory (LSPCL, Baton Rouge, La.) engaged in a Lean Six Sigma Training Project, during which experts in the DNA field studied the unit’s workflow. While the processes were deemed efficient, the laboratory was lacking an electronic DNA sample management solution with the ability to modify workflow, customize procedures and protocols and allow sample and reagent tracking.
Because LSPCL has a casework laboratory and a data-banking laboratory, software solutions must be flexible and have the ability to accommodate varying workflows that involve different equipment, chemistries and processes for the two departments. After researching software solutions for DNA sample management, the team selected LIMS-plus DNA software to support such varying workflows. Without this program, the laboratory could only track a sample at the start of the process and then a final report. The new software permits samples to be tracked through the entire process, including serology testing, extraction, quantitation, amplification and genetic analysis. Once fully implemented, lab efficiency should increase and clerical transcription errors should be minimized because the entire process is electronic, with a single point of manual sample information entry.
Sample tracking
As part of an expedited homicide, sexual assault or violent crime investigation, DNA samples must be processed in real time; thus it is essential that all steps in the process be monitored, recorded and stored in a networked environment. LSPCL requests that investigators whose cases must be processed in real time submit them as quickly as possible. On priority work, the laboratory can provide results in approximately 36 hours. LIMS-plus DNA software ensures that the entire DNA process is transparent and visually displayed to both analysts and management so that samples can be efficiently tracked at each step; bottlenecks can be cleared and adjustments can be made if needed.
Analysis time
Efficiencies in short tandem repeat (STR) chemistries and analysis software can help alleviate backlogs when labs are understaffed or overwhelmed. New STR chemistries increase the number of loci amplified via polymerase chain reaction (PCR), which provides a unique genotype or DNA profile for each person and improved power of discrimination (PD). In turn, the PD imparts a greater ability to distinguish between individuals. The use of additional dyes to label the STR fragments can boost the number of loci amplified in one PCR reaction. Expert system analysis software consistently applies rules to determine the genotype of each sample, making the analysis more time-efficient (see Figure 1).
Figure 1 – Expert system software. Color-coded flagging alerts the analyst to any profiles that failed analysis parameter(s). In this example, the flagging includes red in the file name list for each profile that fired analysis rule(s), a red marker label above the electropherogram indicating this positive control is missing allele 9, and quality flags in the report table at right. Linked navigation displays the selected region in the electropherogram and report table, making analysis review more efficient and allowing analysts to focus on the samples that require evaluation.Forensics laboratories need software that is rapid and versatile enough to accept new chemistries, according to John Fosnacht, vice president of SoftGenetics (State College, Penn.), which makes GeneMarker HID human identify software, a CODIS-approved expert system for STR data analysis. Analysis time savings of up to 40% have been achieved. “New chemistries include additional loci and new dyes,” Fosnacht said. Up to six colors can be analyzed. As new chemistries become available, the software is updated to process them. “When labs switch chemistries, the driving force here is great[er] efficiency,” he added. “These labs must ensure that the software they use to validate the entire process can handle the additional dye capacity.”
Sample removal
While laboratory equipment automation and electronic sample management are becoming the foundation for increased efficiency, they do not provide faster DNA processing. “One of the most important aspects is to look at [the] process and determine if non-value-added steps [can be taken out] and what this will do to [the] process, and then begin the customization from there,” said Missouri DNA technical leader Hoey, whose laboratory uses STACS-CW software. The software was customized for the laboratory to allow samples to be removed at certain points in the sampling process to avoid pushing them all the way through. (Note: the original version of the software necessitated that the sample be pushed through the DNA process regardless of whether it would work or not. With the customized software, the sample could be stopped, that is, the sample with no DNA could be removed and replaced with another sample.)
Sample quality
An important consideration when selecting a DNA sample management solution is sample quality. Samples must be barcoded to ensure proper identification. Most LIMS software programs require laboratories to barcode reagents, track instrument maintenance and utilize set protocols. “You can’t use expired reagents, and you can’t use an instrument that hasn’t been calibrated,” Hoey offered. “All of these aspects portend good quality.”
One of the slowest parts of the DNA sample management process is reviewing the casework. Each DNA case must undergo a technical and administrative review. An electronic solution can dramatically reduce the review time by allowing analysts to focus on interpretations and conclusions rather than clerical review.
Figures 2 and 3 show analysts examining evidence at the Kansas City, Missouri, Police Department Crime Laboratory.
Figure 2 – An examiner studies a shirt for the presence of body fluids.
Figure 3 – An analyst examines evidence for biological fluid using UV light technology.Conclusion
DNA sample processing is a high priority in forensics laboratories because cases are very often time-sensitive and results can greatly impact law enforcement and the solving of cases. While sample processing cannot be hurried, it can be expedited using good management processes and automation. The software used for this purpose must be modifiable for a laboratory’s validated procedures, protocols and workflows. Scientists and analysts need the ability to track samples all the way through the sampling process, and move data into different workflows or back it up and reprocess it if need be. It is essential to know exactly where a sample is in the process so that errors can be addressed, and to ensure the sample can be appropriately prioritized.
An electronic DNA sample processing solution that is able to grow with the laboratory will undoubtedly help to reduce DNA sample backlogs and increase quality.
Dr. Joanie Brocato, Ph.D., is DNA manager at the Louisiana State Police Crime Laboratory (LSPCL), 376 E. Airport Dr., Baton Rouge, La. 70806, U.S.A.; tel.: 225- 925-6216; e-mail: [email protected]; www.lsp.org