by Anna Bennett, PhD, Science Writer, Promega
The backlog of sexual assault evidence kits (SAEKs) in crime laboratories gained national attention when a group of journalists uncovered the issue in a search of crime lab records in 2015. Reasons for the massive kit backlog include funding, time and decision not to prosecute the case. As a result, survivors are left without answers for years.
Serological and autosomal single-tandem repeat (STR) testing is the conventional process for testing sexual assault samples in forensic science. However, both methods are time-consuming, laborious and offer limited sensitivity. Y-Screening, in contrast, is a process that is faster, cheaper and more sensitive than autosomal screening. This method can help labs process their SAEK backlog more efficiently and solve more cases.
The backlog problem
The SAEK backlog exists in two places: 1) in evidence storage facilities where a SAEK is booked into evidence, but DNA analysis has not yet been requested and 2) in crime labs where tests await DNA analysis. Lack of resources is cited as one of the major reasons behind the SAEK backlog. On average, testing a kit costs between $1,000–1,500 (US). Lack of funding combined with increased workload has strained laboratory budgets and contributed to the increased backlog. Similarly, police departments lack the personnel needed for shipping untested kits to labs, tracking submitted kits and following up on leads that result from the SAEK testing.
RAINN (the Rape, Abuse, & Incest National Network) has dedicated several initiatives in the form of grants toward decreasing the backlog of sexual assault samples in public labs. But an article published on the RAINN website addressing this problem states, “It remains imperative to ensure that public crime labs have the necessary capacity to keep up with testing demands.” While the backlog is steadily dwindling, improving efficiency and efficacy of kit testing is still in high need in public forensic labs.
Limitations of current testing methods
Serological screening is the examination of bodily fluids lifted from a SAEK. The goal is to determine if there is any evidence of bodily fluids or contact and to identify potential sources of DNA for further analysis. Traditional serology screening methods may involve microscopic examination, acid phosphatase testing, microscopic sperm detection or other techniques that detect bodily fluids. Serological screening alone was commonly used before the advent of DNA analysis and has several limitations.
Serological tests are limited in both sensitivity and specificity. They fail to detect small amounts of a substance, which results in an indefinable sample. Furthermore, serological screening methods – microscopic examination, for example – can provide information about the presence of specific bodily fluids. However, they may not offer detailed information about individual characteristics within those fluids, such as DNA profiles or specific antigens. Additionally, some bodily fluids, such as semen, saliva, or certain types of blood stains, may degrade over time, making it more challenging to detect and analyze them accurately. The longer the sample has been exposed to environmental conditions, the higher the likelihood of degradation, which can affect the reliability of serological screening results and produce false negatives.
Given these limitations, serology alone cannot be used in identification of genetic contributions to bodily fluids in a SAEK sample. Therefore, DNA based approaches following serology have been the benchmark for forensic analysis of SAEK. Specifically, single-tandem repeat (STR) testing is the gold standard for testing samples containing human DNA. In 1997, the Federal Bureau of Investigation (FBI) identified 13 autosomal STR loci to establish the core of the Combined DNA Index System (CODIS). This database includes profiles contributed by federal, state and local forensic laboratories. The core set of CODIS STR loci are widely used today in both forensic identification in property crimes and sexual assault cases.
During standard STR testing, specific regions of the autosomal DNA are amplified and analyzed. The number of repeats at each STR locus varies between individuals, making them useful for genetic profiling and individual identification. However, this process is labor intensive (extraction, quantification, amplification, capillary electrophoresis, data analysis, and profile interpretation of large amounts of DNA on low-concentration samples) and often ineffective when samples are aged or improperly stored due to breakdown of enzymes used in initial serological screening. Given the large backlog of samples that span decades, autosomal testing is insufficient to solve the backlog problem.
Y-Screening is more efficient
Y-Screening refers to the analysis and examination of the Y-chromosome, or the male sex chromosome, in DNA samples. Y-screening is primarily used in cases where the DNA sample is limited, degraded or mixed with DNA from multiple individuals – which is the case for most of the SAEK backlog. By targeting specific regions of the Y-chromosome, forensic scientists can amplify and analyze the Y-STR profile. Additionally, conventional screening results offer analysts little predictive power as to what DNA profile may result. Recognizing the limitations and challenges associated with traditional serology methods, new SWGDAM recommendations are now instructing the use of a “Direct to DNA” approach where DNA analysis – particularly Y-screening – performed before serology to maximize the chances of obtaining CODIS eligible profiles, which is even more efficient than pervious pipelines.
Y-screening in forensic science has alleviated the limitations of serology and traditional STR screening by targeting the male Y chromosome directly from sample, eliminating the need for time-consuming serological testing combined with autosomal screening. Y-Screening is a process that amplifies STR regions on the Y chromosome directly from sample (“direct-to-DNA") and the resulting Y-STR profile is unmasked in the presence of female DNA. Furthermore, Y-STR testing is more sensitive: Y-STR profiles have been recovered in cases where bodily fluids were first undetected by autosomal STR or other serology means. Thus, Y-STR analysis can reinvigorate the investigation of kit backlogs that have screened negative or produced only the victim's DNA.