Combined DNA Index System Core Research Articles

Expanded CODIS STR allele frequencies - Evidence for the irrelevance of race-based DNA databases.

The US Federal Bureau of Investigation's (FBI) core Combined DNA Index System (CODIS) short tandem repeat (STR) panel is required for the calculations of random match probabilities (RMPs) in forensic DNA analysis. Current practice dictates that RMPs should be generated across appropriate reference STR allele frequency databases, including African American, Asian, Caucasian, Hispanic, and Native American, when the suspect's race is unknown. Should the suspect declare their race, a specific reference database that pertains to that designation is used. This practice is based on the presumption that racial population group is relevant for calculating conservative RMPs that favor the defendant. The core CODIS panel has been expanded to 20 STRs, however, the relationship between RMP and race has not been re-evaluated. Genetic structure analyses and Bayesian-based population assignment of expanded CODIS profiles from one race-neutral and five race-specific reference databases revealed that STR data could not distinguish races as distinct biological clusters. For instance, while the average race-specific RMPs for Hispanic or Caucasian profiles were almost equally-conservative when calculated from either population's reference database, the Hispanic profiles closely affined with the Native American population. Race-neutral RMPs computed with a correction factor (θ) of 0.03 favor the defendant as much as race-specific RMPs based on a θ of 0.01. Insufficient genetic differentiation observed among the US racial populations as well as inconsequential differences between race-specific and race-neutral RMPs undermine the value of using "race" in the context of forensic DNA analysis and support the argument that forensic databases should be race-neutral.

Fast P(RMNE): Fast forensic DNA probability of random man not excluded calculation

High throughput sequencing (HTS) of DNA forensic samples is expanding from the sizing of short tandem repeats (STRs) to massively parallel sequencing (MPS). HTS panels are expanding from the FBI 20 core Combined DNA Index System (CODIS) loci to include SNPs. The calculation of random man not excluded, P(RMNE), is used in DNA mixture analysis to estimate the probability that a person is present in a DNA mixture. This calculation encounters calculation artifacts with expansion to larger panel sizes. Increasing the floating-point precision of the calculations allows for increased panel sizes but with a corresponding increase in computation time. The Taylor series higher precision libraries used fail on some input data sets leading to algorithm unreliability. Herein, a new formula is introduced for calculating P(RMNE) that scales to larger SNP panel sizes while being computationally efficient (patent pending).

Fast P(RMNE): Fast forensic DNA probability of random man not excluded calculation

High throughput sequencing (HTS) of DNA forensic samples is expanding from the sizing of short tandem repeats (STRs) to massively parallel sequencing (MPS). HTS panels are expanding from the FBI 20 core Combined DNA Index System (CODIS) loci to include SNPs. The calculation of random man not excluded, P(RMNE), is used in DNA mixture analysis to estimate the probability that a person is present in a DNA mixture. This calculation encounters calculation artifacts with expansion to larger panel sizes. Increasing the floating-point precision of the calculations allows for increased panel sizes but with a corresponding increase in computation time. The Taylor series higher precision libraries used fail on some input data sets leading to algorithm unreliability. Herein, a new formula is introduced for calculating P(RMNE) that scales to larger SNP panel sizes while being computationally efficient (patent pending).

Population genetic data of the AmpFℓSTR® Identifiler® Plus and PowerPlex® 16 HS STR loci in four Canadian populations

Allele frequencies and forensically relevant population statistics were estimated for the short tandem repeat (STR) loci of the AmpFℓSTR® Identifiler® Plus and PowerPlex® 16 HS amplification kits, including D2S1338, D19S433, Penta D, and Penta E, for three First Nations Aboriginal populations and for Caucasians in Canada. The cumulative power of discrimination was ≥ 0.999999999999984 and the cumulative power of exclusion was ≥ 0.999929363 for both amplification systems in all populations. No significant departure from Hardy-Weinberg equilibrium was detected for D2S1338, D19S433, Penta D, and Penta E or the 13 Combined DNA Index System core STR loci after correction for multiple testing. Significant genetic diversity was observed between these four populations. Comparison with published frequency data for other populations is also presented.

Assessment of application value of 19 autosomal short tandem repeat loci of GoldenEyeTM 20A kit in forensic paternity testing

This study was carried out to assess the application value of 19 autosomal short tandem repeat (STR) loci of GoldenEye 20A kit, in which 13 combined DNA index system core STR loci and PentaE, PentaD, D2S1338, D19S433, D12S391, and D6S1043 of six STR loci could be used in forensic paternity testing in Chinese population. We amplified the genomic DNA from blood samples on FTA paper of 289 paternity testing cases by using the GoldenEye 20A kit. The amplified products were detected by capillary electrophoresis, and then the genotypes of 20 genetic markers including 19 STR loci as well as Amelogenin for sex determination were analyzed by GeneMapper v3.2 and GeneMarker HID Software. The results of genotypes were compared to the three commonly used commercial kits including AmpFℓSTR Identifiler, PowerPlex16, and AmpFℓSTR Sinofiler kits. Compared to the three other common commercial kits, the GoldenEye 20A kit had higher value of combined paternity index in certainty of paternity or non-exclusion paternity cases, and more numbers of STR loci were excluded in exclusionary paternity cases. Our data in this study showed that the GoldenEye 20A kit has a higher application value in forensic paternity testing and will be of help for kinship analysis.

An Updated Validation of Promega’s PowerPlex® 16 System: High Throughput Databasing Under Reduced PCR Volume Conditions on Applied Biosystem’s 96 Capillary 3730xl DNA Analyzer*

The PowerPlex 16 System from Promega Corporation allows single tube multiplex amplification of sixteen short tandem repeat (STR) loci including all 13 core combined DNA index system STRs. This report presents an updated validation of the PowerPlex 16 System on Applied Biosystem's 96 capillary 3730xl DNA Analyzer. The validation protocol developed in our laboratory allows for the analysis of 1536 loci (96 x 16) in c. 50 min. We have further optimized the assay by decreasing the reaction volume to one-quarter that recommended by the manufacturer thereby substantially reducing the total cost per sample without compromising reproducibility or specificity. This reduction in reaction volume has the ancillary benefit of dramatically increasing the sensitivity of the assay allowing for accurate analysis of lower quantities of DNA. Due to its substantially increased throughput capability, this extended validation of the PowerPlex 16 System should be useful in reducing the backlog of unanalyzed DNA samples currently facing public DNA forensic laboratories.