What Is Probabilistic Genotyping and How Do You Choose the Best PG Software?
Pain Points with Complex DNA Mixtures
All too often crime scene evidence contains complex DNA profiles, which leads labs across the country to experience a key challenge — interpretation, and deconvolution of those complex DNA mixtures. Despite their diligent efforts in processing the evidence and generating these profiles, they regularly hit a dead-end when it comes to reporting meaningful conclusions; often reporting a sample as inconclusive. Probabilistic genotyping software can help alleviate these pain points.
Many crime labs do not yet possess the tools, training, or experience to unravel these complex results. This is because manual mixture interpretation is time-consuming, prone to errors and bias with a large portion of samples deemed as uninterpreted. The trend in the type of samples forensic laboratories are asked to resolve, along with improved extraction methods, amplification chemistries, and improved CE instrumentation have exceeded the ability to adequately resolve mixtures using binary mixture interpretation protocols. When laboratories try to analyze highly complex mixtures, such as “touch” items with more than two contributors and stochastic data, binary methods (CPE, CPI, Modified RMP) fail miserably. With traditional binary methods, there exists no way to factor uncertainty.
Current strategies to evaluate low-level mixtures with dropout using binary methods are insufficient. The existing CPE/CPI methods have no fundamental validity, there exist no unambiguous and rigorous mathematical proofs — it is fundamentally flawed and at best, a “stab” at the weight of the evidence.
PG Software: “Game Changer”
But now, the hours and hours of complex forensic report generation based on near-endless mixture interpretation procedures are a thing of the past. Probabilistic genotyping forensic software greatly streamlines this process with an objective interpretation of otherwise horrendous mixtures. The use of software to evaluate DNA profile evidence is widespread in the forensic biology community. Since the late 1990s software tools have been used to apply statistical evaluation models to observed DNA profile data.
Probabilistic Genotyping software (PGS) cuts through the fog of uncertainty and breathes new life into results previously deemed uninterpretable. Its technology helps link a genetic sample from a crime scene to a person of interest (POI) by facilitating genetic analysis in tricky situations, like when a sample is partially degraded or contains DNA from multiple people.
Genetic samples gathered from the crime scene and POI are separately analyzed using a method that looks at various sections of DNA whose length varies from person to person. A profile is then created. The lab will compare the evidence’s profile with that of the POI using a computer simulation of various scenarios. If the POI were — or were not — a contributor to the sample, PGS provides a likelihood that the evidence collected would have led to the evidence profile that was produced. The relative values of these two probabilities can be used by investigators to determine the strength of the evidence in favor of or against the POI.
Over 100 laboratories in the US are reported to use PGS. PGS analyses are used by law enforcement offices, crime or forensics laboratories, defense attorneys, and law offices at the county, city, state, and federal levels. Some notable PG tools are STRMix, BP Sentry, and EuroForMix. For the remainder of this piece, we’ll focus on BP Sentry.
BP Sentry Spotlight
BP Sentry was developed by a not-for-profit US and international consortium and provides robust probabilistic genotyping methods without the baggage of commercial profit-oriented providers. It interprets and deconvolutes complex samples with little user intervention, streamlining workflows unblocking bottlenecks to free up manpower for other tasks.
BP Sentry provides a Frequentist and Bayesian methodology to resolve complex mixtures and provide mixture deconvolution. BP Sentry is lab agnostic and can process both capillary electrophoreses (CE) and massive parallel sequencing (MPS) data using proprietary probabilistic framework.
Years ago, the ISFG published recommendations for the interpretation of low-level mixtures when dropout is possible (Gill et al. 2012). Probabilistic genotyping tools provide the ability to utilize all data above the laboratory’s empirically determined analytical threshold by accounting for “uncertainty” wherein BP Sentry incorporates a probability of allelic drop-out, drop-in (and if warranted, alternate hypotheses including the ability to account for possible “related suspects”) in the likelihood ratio (LR.) Report wording is generated based on the Probabilistic Genotyping results while carrying over all phenotypes, evidence descriptions, evidence tracking, and serological results.
Other, more expensive probabilistic genotyping software exists but lacks transparency, peer review and poses continuous admissibility challenges due to its black-box mentality. Some software is thought to have overly complex calculations or the inability to adequately testify to the results. To combat this fear, BP Sentry includes a comprehensive step-by-step calculation manual, numerous published papers, and multiple spreadsheet solutions demonstrating the PG algorithm in action — and full concordance.
BP Sentry is also time cognizant. It can provide calculations in seconds and minutes rather than antiquated hours and days.
Most importantly, the data is reproducible. BP Sentry produces consistent results each time the same scenario is calculated.
As Probabilistic Genotyping Software is relatively new to the forensic toolbox, methods are constantly improving and evolving, gaining more traction and usage. It’s already been responsible for the resolution of over 300,000 cases, particularly with violent crime and sexual assaults, as well as the exoneration of innocent individuals who were wrongly accused. It’s a revolutionary tactic for interpreting DNA profiles that allows justice to prevail…exoneration or conviction.
