David Gangitano

Validation of the AmpFlSTR® MiniFilerTM PCR Amplification Kit for Use in Forensic Casework

Abstract:  The AmpFℓSTR® MiniFilerTM PCR Amplification Kit is designed to genotype degraded and/or inhibited DNA samples when the AmpFℓSTR® IdentifilerTM PCR Amplification Kit is incapable of generating a complete genetic profile. Validation experiments, following the SWGDAM guidelines, were designed to evaluate the performance of MiniFiler. Data obtained demonstrated that MiniFiler, when used in conjunction with Identifiler, provided an increased ability to obtain genetic profiles from challenged samples. The optimum template range was found to be between 0.2 and 0.6 ng, with 0.3 ng yielding the best results. Full concordance was achieved between the MiniFiler kit and Identifiler kit except in a single case of a null allele at locus D21S11. Numerous instances of severe heterozygous peak imbalance (<50%) were observed in single source samples amplified within the optimum range of input DNA suggesting that caution be taken when attempting to deduce component genotypes in a mixture.

Monoamine oxidase A genotype, childhood adversity, and criminal behavior in an incarcerated sample.

Background A number of studies have found a functional variable number tandem repeat polymorphism in the upstream regulatory region of the monoamine oxidase A gene (MAOA-uVNTR) interacts with childhood adversity to increase risk for antisocial behavior. Several studies have also reported null findings. Methods Here, we examine the association between MAOA-uVNTR genotype, childhood adversity, and criminal activity in a sample of 99 male volunteers who were incarcerated in a large city jail in the Southern United States. MAOA-uVNTR genotypes were obtained from DNA extracted from buccal swabs. Criminal activity in the year before incarceration and childhood adversity were measured with self-report surveys. Violent arrest rates and property arrest rates were quantified with official records of arrest and accounted for periods of incarceration in local and state correctional facilities. Results The low expressing allele of the MAOA-uVNTR genotype (MAOAL) interacted with abuse to predict self-reports of less serious criminal and delinquent behavior and had a direct association with serious criminal activity. MAOAL genotype interacted with parental criminality to predict self-reports of serious criminal behavior, property arrest rates, and violent arrest rates. Conclusion The findings suggest that crime prevention efforts may be improved through attention to the neurodevelopmental consequence of gene-by-environment interactions.

STR Data for the PowerPlex ® 16 Loci in Buenos Aires Population (Argentina)

DNA samples from 101 unrelated individuals were extracted by Chelex procedure (1) and then quantified using QuantiBlot® Human DNA Quantitation Kit according to the manufacturers instructions (2). DNA samples (1 ng) were amplified and typed by PowerPlex® 16 System (3). The electrophoresis was carried out on the ABI PRISM® 377 DNA Sequencer using GeneScan® Genotyper® and PowerTyper™ 16 Macro software. Data were analyzed using a program provided by R. Chakraborty (University of Texas School of Biomedical Sciences, Houston, Texas). Interclass correlations yielding p

Typing of the locus DYS19 from DNA derived from fingernail clippings using PCR Concert rapid purification system.

DNA extracted from the fingernails of female victims of a violent or aggressive act may assist in the identification of the male. Sometimes with the current autosomal STR loci, however, the victims profile may mask the perpetrators DNA profile or the perpetrators DNA may be substantially lower in quantity than that of the victims DNA. Thus, under these conditions, no characterization is possible. In this paper, an alternative DNA extraction procedure was employed, and the application of an STR locus residing on the Y chromosome DYS19 was typed to allow for genetic characterization of the perpetrator in such cases.

STRESS, GENES, AND GENERALIZABILITY ACROSS GENDER: EFFECTS OF MAOA AND STRESS SENSITIVITY ON CRIME AND DELINQUENCY*

In the current study, we extend the gene-by-environment interaction (cGxE) literature by examining how a widely studied polymorphism, the MAOA upstream variable number tandem repeat (MAOA-uVNTR) interacts with distal and proximal stressors to explain variation in crime and delinquency. Prior research findings have revealed that MAOA-uVNTR interacts with single indicators of environmental adversity to explain criminal behavior in general-population and incarcerated samples. Nevertheless, the genetically moderated stress sensitivity hypothesis suggests that increased risk for criminal behavior associated with variation in the MAOA-uVNTR can be best understood in the context of both distal stress during childhood and proximal stress in adulthood. Therefore, we employed Tobit regression analyses to examine a gene–distal–proximal environment (CGxExE) interaction across gender in a sample of university students (n = 267) and with data from the National Longitudinal Study of Adolescent to Adult Health (Add Health; n = 1,294). The results across both sets of analyses demonstrate that variation in the MAOA-uVNTR interacts with distal and proximal stress to lead to increased risk for criminal behavior in males. Although proximal life stress is associated with an increase in crime and delinquency, this effect is more pronounced among MAOA-L allele carriers that have experienced distal stress.

Development and evaluation of a rapid PCR method for the PowerPlex®S5 system for forensic DNA profiling

Forensic DNA profiling is a multi-step process taking approximately 10h to complete. A reduction in the amount of time required for the amplification step would allow for faster human identification and increase laboratory throughput. The goal of this work was to optimize and evaluate a rapid PCR method for the PowerPlex®S5 system for forensic DNA profiling. By pairing fast chemistries with a fast thermal cycler, we were able to reduce the amplification time by 70% (1 h). Sensitivity and heterozygous peak height ratios were comparable between the fast and standard protocols. However, there was a notable decrease (5%) in peak height ratio at the D18S51 locus with the fast cycling method. An increase in average mean stutter for combined loci of 2.6% was observed in profiles amplified using the fast protocol compared to the standard system. Our results suggest that with further optimization and validation the fast protocol can be used to replace the standard amplification conditions.

Developmental and internal validation of a novel 13 loci STR multiplex method for Cannabis sativa DNA profiling

Marijuana (Cannabis sativa L.) is a plant cultivated and trafficked worldwide as a source of fiber (hemp), medicine, and intoxicant. The development of a validated method using molecular techniques such as short tandem repeats (STRs) could serve as an intelligence tool to link multiple cases by means of genetic individualization or association of cannabis samples. For this purpose, a 13 loci STR multiplex method was developed, optimized, and validated according to relevant ISFG and SWGDAM guidelines. The STR multiplex consists of 13 previously described C. sativa STR loci: ANUCS501, 9269, 4910, 5159, ANUCS305, 9043, B05, 1528, 3735, CS1, D02, C11, and H06. A sequenced allelic ladder consisting of 56 alleles was designed to accurately genotype 101 C. sativa samples from three seizures provided by a U.S. Customs and Border Protection crime lab. Using an optimal range of DNA (0.5-1.0ng), validation studies revealed well-balanced electropherograms (inter-locus balance range: 0.500-1.296), relatively balanced heterozygous peaks (mean peak height ratio of 0.83 across all loci) with minimal artifacts and stutter ratio (mean stutter of 0.021 across all loci). This multi-locus system is relatively sensitive (0.13ng of template DNA) with a combined power of discrimination of 1 in 55 million. The 13 STR panel was found to be species specific for C. sativa; however, non-specific peaks were produced with Humulus lupulus. The results of this research demonstrate the robustness and applicability of this 13 loci STR system for forensic DNA profiling of marijuana samples.

Necrophagous caterpillars provide human mtDNA evidence.

Abstract:  Decomposition of large mammalian carcasses is greatly accelerated through the action of insects. Specialized feeders capable of digesting keratin and collagen found in skin, hair, and tendons and ligaments are attracted to corpses in late stages of dry decomposition and include Tinea pellionella, the casemaking clothes moth, and Tineola bisselliella, the webbing clothes moth (Lepidoptera; Tineidae). Until now, details of the caterpillar behavior as necrophagous insects were vague. Here, we detail the behavior of each species and document the incorporation of human hair into the portable larval shelters constructed by the caterpillars of T. pellionella. Hair of the decedent used as building material for caterpillar shelters provided enough starting template to amplify and sequence the HVI and HVII sections of the control region (mtDNA) of the decedent.

Evaluation of four commercial quantitative real-time PCR kits with inhibited and degraded samples

DNA quantification is a vital step in forensic DNA analysis to determine the optimal input amount for DNA typing. A quantitative real-time polymerase chain reaction (qPCR) assay that can predict DNA degradation or inhibitors present in the sample prior to DNA amplification could aid forensic laboratories in creating a more streamlined and efficient workflow. This study compares the results from four commercial qPCR kits: (1) Investigator® Quantiplex® Pro Kit, (2) Quantifiler® Trio DNA Quantification Kit, (3) PowerQuant® System, and (4) InnoQuant® HY with high molecular weight DNA, low template samples, degraded samples, and DNA spiked with various inhibitors.The results of this study indicate that all kits were comparable in accurately predicting quantities of high quality DNA down to the sub-picogram level. However, the InnoQuant(R) HY kit showed the highest precision across the DNA concentration range tested in this study. In addition, all kits performed similarly with low concentrations of forensically relevant PCR inhibitors. However, in general, the Investigator® Quantiplex® Pro Kit was the most tolerant kit to inhibitors and provided the most accurate quantification results with higher concentrations of inhibitors (except with salt). PowerQuant® and InnoQuant® HY were the most sensitive to inhibitors, but they did indicate significant levels of PCR inhibition. When quantifying degraded samples, each kit provided different degradation indices (DI), with Investigator® Quantiplex® Pro indicating the largest DI and Quantifiler® Trio indicating the smallest DI. When the qPCR kits were paired with their respective STR kit to genotype highly degraded samples, the Investigator® 24plex QS and GlobalFiler® kits generated more complete profiles when the small target concentrations were used for calculating input amount.

Comparison of DNA yield and STR success rates from different tissues in embalmed bodies

Formalin fixation is commonly used to preserve tissue sections for pathological testing and embalming cadavers for medical dissection or burial. DNA extracted from formalin-fixed tissues may also provide an alternative source of genetic material for medical diagnosis and forensic casework, such as identifying unknown embalmed human remains. Formaldehyde causes DNA damage, chemical modifications, and degradation, thereby reducing the quantity and quality of DNA available for downstream genetic analyses. By comparing the DNA yield, level of DNA degradation, and short tandem repeat (STR) success of various tissue types, this study is the first of its kind to provide some guidance on which samples from embalmed bodies are likely to generate more complete STR profiles. Tissue samples were dissected from three male embalmed cadavers and included bone, cartilage, hair, muscle, internal organs, skin, teeth, and nail clippings. DNA was purified from all samples using the QIAamp® FFPE Tissue Kit (Qiagen), quantified using the QuantiFiler® Trio DNA Quantification kit (Life Technologies), and genotyped using the GlobalFiler® PCR Amplification Kit (Life Technologies). Results of this study showed variation in DNA quantity and STR success between different types of tissues and some variation between cadavers. Overall, bone marrow samples resulted in the highest DNA yields, the least DNA degradation, and greatest STR success. However, several muscle, hair, and nail samples generated higher STR success rates than traditionally harvested bone and tooth samples. A key advantage to preferentially using these tissue samples over bone (and marrow) and teeth is their comparative ease and speed of collection from the cadaver and processing during DNA extraction. Results also indicate that soft tissues affected by lividity (blood pooling) may experience greater exposure to formalin, resulting in more DNA damage and reduced downstream STR success than tissues under compression. Overall, we recommend harvesting from selected muscles (gastrocnemius, rectus femoris, flexor digitorum brevis, masseter, brachioradialis) or fingernails for human identification purposes.