title: Stochastic sampling effects in STR typing: Implications for analysis and interpretation.
abstract: The analysis and interpretation of forensic STR typing results can become more complicated when reduced template amounts are used for PCR amplification due to increased stochastic effects. These effects are typically observed as reduced heterozygous peak-height balance and increased frequency of undetected alleles (allelic "dropout"). To investigate the origins of these effects, a study was performed using the AmpFlSTR(®) Identifiler Plus(®) and MiniFiler(®) kits to amplify replicates from a dilution series of NIST Human DNA Quantitation Standard (SRM(®) 2372A). The resulting amplicons were resolved and detected on two different genetic analyzer platforms, the Applied Biosystems 3130xL and 3500 analyzers. Results from our study show that the four different STR/genetic analyzer combinations exhibited very similar peak-height ratio statistics when normalized for the amount of template DNA in the PCR. Peak-height ratio statistics were successfully modeled using the Poisson distribution to simulate pre-PCR stochastic sampling of the alleles, confirming earlier explanations that sampling is the primary source for peak-height imbalance in reduced template dilutions. In addition, template-based pre-PCR sampling simulations also successfully predicted allelic dropout frequencies, as modeled by logistic regression methods, for the low-template DNA dilutions. We discuss the possibility that an accurately quantified DNA template might be used to characterize the linear signal response for data collected using different STR kits or genetic analyzer platforms, so as to provide a standardized approach for comparing results obtained from different STR/CE combinations and to aid in validation studies.
authors.affiliation: State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd., Richmond, CA 94804, USA. Electronic address: mark.timken@doj.ca.gov.
authors.forename: Mark D
authors.initials: MD
authors.lastname: Timken
authors.affiliation: State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd., Richmond, CA 94804, USA. Electronic address: sonja.klein@doj.ca.gov.
authors.forename: Sonja B
authors.initials: SB
authors.lastname: Klein
authors.affiliation: State of California, Department of Justice, Jan Bashinski DNA Laboratory, 1001 W. Cutting Blvd., Richmond, CA 94804, USA. Electronic address: martin.buoncristiani@doj.ca.gov.
authors.forename: Martin R
authors.initials: MR
authors.lastname: Buoncristiani
mesh_terms: D004247:DNA / Q000235:genetics; D006801:Humans; D018895:Microsatellite Repeats / Q000235:genetics*; D016133:Polymerase Chain Reaction; D013269:Stochastic Processes
chemical_list: D004247:DNA
keywords: Heterozygous balance; Logistic regression; Low-template DNA; Poisson; Short tandem repeat; Stochastic