Jan Bashinski DNA Laboratory

Richmond, CA, United States

Jan Bashinski DNA Laboratory

Richmond, CA, United States
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Klein S.B.,Jan Bashinski DNA Laboratory | Buoncristiani M.R.,Jan Bashinski DNA Laboratory
Forensic Science International: Genetics | Year: 2017

Analysis of sexual assault evidence, often a mixture of spermatozoa and victim epithelial cells, represents a significant portion of a forensic DNA laboratory's case load. Successful genotyping of sperm DNA from these mixed cell samples, particularly with low amounts of sperm, depends on maximizing sperm DNA recovery and minimizing non-sperm DNA carryover. For evaluating the efficacy of the differential extraction, we present a method which uses a Separation Potential Ratio (SPRED) to consider both sperm DNA recovery and non-sperm DNA removal as variables for determining separation efficiency. In addition, we describe how the ratio of male-to-female DNA in the sperm fraction may be estimated by using the SPRED of the differential extraction method in conjunction with the estimated ratio of male-to-female DNA initially present on the mixed swab. This approach may be useful for evaluating or modifying differential extraction methods, as we demonstrate by comparing experimental results obtained from the traditional differential extraction and the Erase Sperm Isolation Kit (PTC©) procedures. © 2017 Elsevier B.V.

Tom B.K.,Scientific Investigation Division | Koskinen M.T.,Finnzymes Diagnostics | Dayton M.,Jan Bashinski DNA Laboratory | Mattila A.-M.,Finnzymes Diagnostics | And 8 more authors.
Journal of Forensic Sciences | Year: 2010

Despite the popularity of dogs in US households, canine DNA evidence remains largely untapped in forensic investigations partially because of the absence of well-defined forensic short tandem repeats (STRs), lack of standardized and validated PCR protocols, STR reagent kits, and poorly developed nomenclature. A nomenclature system was established based on internationally recognized recommendations for human forensic STRs for a recently developed canine STR reagent kit. Representative alleles were sequenced from each of the 18 STRs and the sex-typing marker included in the kit. This study also reflects on the impact of point mutations, insertions, and deletions within and outside the STR core repeat structures. An understanding of the STRs' sequence and repeat structures will enable development of a robust and reliable allele nomenclature and improve the accuracy and precision of allele fragment sizing in canine forensic profiling. The expected allele sizes have been calculated, and their repeat stuctures defined based on sequence information. © 2010 American Academy of Forensic Sciences.

PubMed | University of Washington, Forensic Science South Australia, Principal Forensic Services Ltd, ESR Ltd and 3 more.
Type: Journal Article | Journal: Journal of forensic sciences | Year: 2016

The interpretation of complex DNA profiles is facilitated by a Bayesian approach. This approach requires the development of a pair of propositions: one aligned to the prosecution case and one to the defense case. This note explores the issue of proposition setting in an adversarial environment by a series of examples. A set of guidelines generalize how to formulate propositions when there is a single person of interest and when there are multiple individuals of interest. Additional explanations cover how to handle multiple defense propositions, relatives, and the transition from subsource level to activity level propositions. The propositions depend on case information and the allegations of each of the parties. The prosecution proposition is usually known. The authors suggest that a sensible proposition is selected for the defense that is consistent with their stance, if available, and consistent with a realistic defense if their position is not known.

Faber K.L.,Fresno Regional Laboratory | Person E.C.,California State University, Fresno | Hudlow W.R.,Jan Bashinski DNA Laboratory
Forensic Science International: Genetics | Year: 2013

Forensic evidence samples are collected from an unlimited variety of substrates, which may contain compounds known to inhibit the polymerase chain reaction (PCR). These PCR inhibitors are co-extracted with the DNA sample and can negatively affect the DNA typing results, which can range from partial to complete inhibition of the short tandem repeat (STR) PCR. One potential solution is to remove the PCR inhibitors from the extracts prior to the STR PCR with the NucleoSpin® DNA Clean-Up XS kit. The kit contains a NucleoSpin® XS silica column that has a special funnel design of thrust rings along with a very small silica membrane, which allows for sample elution in a small volume that is appropriate for use with current STR typing kits. The NucleoSpin® DNA Clean-Up XS kit was optimized for the best possible DNA recovery and then evaluated for its ability to remove eight commonly encountered PCR inhibitors including: bile salt, collagen, hematin, humic acid, indigo, melanin, tannic acid and urea. Each of these PCR inhibitors was effectively removed by the NucleoSpin® DNA Clean-Up XS kit as demonstrated by generating more complete STR profiles from the cleaned up inhibitor samples than from the raw inhibitor samples. © 2012 Elsevier Ireland Ltd.

Date-Chong M.,Jan Bashinski DNA Laboratory | Hudlow W.R.,Jan Bashinski DNA Laboratory | Buoncristiani M.R.,Jan Bashinski DNA Laboratory
Forensic Science International: Genetics | Year: 2016

The RapidHIT™ 200 Human Identification System and RapidHIT GlobalFiler® Express kit were evaluated and validated for use with single-source reference samples. It was of primary interest to evaluate the system for its efficacy as an expert system and to estimate a first pass success rate, as well as to identify the technical variables impacting that result. While results indicated that this instrument/kit combination can be used to accurately type single-source buccal samples, substantial variability in sensitivity and intra-color balance were observed, as were multiple artifacts, requiring extensive manual editing of the profiles. Artifacts included dye "blobs" and spectral overlap (pull-up) peaks that often originated from relatively low intensity allele peaks. Reduced intra-color balance, in combination with low sensitivity, occasionally resulted in instances of allelic dropout. Overall, 50% of the buccal samples analyzed in this study would have been successfully typed to give full GlobalFiler® profiles without the need for manual review and editing. © 2016 Elsevier Ireland Ltd. All rights reserved.

Buckleton J.,ESR Ltd. | Myers S.,Jan Bashinski DNA Laboratory
Forensic Science International: Genetics | Year: 2014

Walsh et al. [1] outlined a method for adjusting autosomal coancestry values, θA, to take account of the existence of a Y chromosome match, θA|Y. The framework established by Walsh et al. is flexible and allows an investigation of some real world effects such as family structure. It also allows the effect of a Y chromosome match to be placed within the construct of existing casework practice. Most notable is the ability to deal with an assigned value for the autosomal coancestry coefficient and the fact that most casework statistics report a value for unrelated individuals unless case circumstances suggest differently. The values of θA|Y are not much larger than θA and a coherent argument could be made that any adjustment is unnecessary. © 2014 Elsevier Ireland Ltd. All rights reserved.

Hudlow W.R.,Jan Bashinski DNA Laboratory | Buoncristiani M.R.,Jan Bashinski DNA Laboratory
Forensic Science International: Genetics | Year: 2012

We present a rapid alkaline lysis procedure for the extraction of DNA from sexual assault evidence that generates purified sperm fraction extracts that yield STR typing results similar to those obtained from the traditional organic/dithiothreitol differential extraction. Specifically, a sodium hydroxide based differential extraction method has been developed in a single-tube format and further optimized in a 96-well format. The method yields purified extracts from a small sample set (∼2-6 swabs) in approximately 2 h and from a larger sample set (up to 96 swabs) in approximately 4 h. While conventional differential extraction methods require vigorous sample manipulation to remove the spermatozoa from the substrate, the method described here exploits the propensity of sperm to adhere to a substrate and does not require any manipulation of the substrate after it is sampled. For swabs, sample handling is minimized by employing a process where the tip of the swab, including the shaft, is transferred to the appropriate vessel eliminating the need for potentially hazardous scalpels to separate the swab material from the shaft. The absence of multiple handling steps allows the process to be semi-automated, however the procedure as described here does not require use of a robotic system. This method may provide forensic laboratories a cost-effective tool for the eradication of backlogs of sexual assault evidence, and more timely service to their client agencies. In addition, we have demonstrated that a modification of the procedure can be used to retrieve residual sperm-cell DNA from previously extracted swabs. © 2011 Elsevier Ireland Ltd. All rights reserved.

Date-Chong M.,Jan Bashinski DNA Laboratory | Buoncristiani M.R.,Jan Bashinski DNA Laboratory | Aceves M.,Jan Bashinski DNA Laboratory | Orrego C.,University of California at Berkeley
Forensic Science International: Genetics | Year: 2013

The goal of this study was to compare two commonly used methods for the surface decontamination of human hair shafts, and to evaluate the use of a duplex real-time qPCR assay to assess decontamination effectiveness for the purpose of mitochondrial DNA typing. Hair shafts of known mitochondrial DNA haplotype were coated with undiluted saliva, semen or blood, each of known mitochondrial haplotype distinct from the test hair. Surface decontamination was conducted by enzymatic treatment with Terg-a-zyme™ and by chemical treatment with dilutions of sodium hypochlorite (NaClO, bleach). Following DNA extraction, a duplex (nuclear and mitochondrial DNA) real-time qPCR assay was used to quantify mitochondrial DNA and to test for surface contamination by quantifying the exogenous nuclear DNA not removed from the hair shaft. The NaClO treatment was found to be more effective for removing surface contamination than the Terg-a-zyme™ treatment, and it was procedurally simpler to implement, resulting in a significant savings of sample processing time. Exposure to 3% NaClO for up to two minutes had no detrimental effect on quantity or typing of the mitochondrial DNA belonging to the hair. In addition, we demonstrated that the duplex real-time PCR assay is a convenient early-warning diagnostic method for the detection of the presence of external DNA contamination, providing an assessment of the purity of the sample prior to embarking on further analysis by more laborious mitochondrial DNA typing methods. © 2012 Elsevier Ireland Ltd.

Timken M.D.,Jan Bashinski DNA Laboratory | Klein S.B.,Jan Bashinski DNA Laboratory | Buoncristiani M.R.,Jan Bashinski DNA Laboratory
Forensic Science International: Genetics | Year: 2014

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. © 2014 Elsevier Ireland Ltd. All rights reserved.

PubMed | Jan Bashinski DNA Laboratory
Type: | Journal: Methods in molecular biology (Clifton, N.J.) | Year: 2016

The phenol-chloroform (organic) extraction method continues to be a preferred method for extraction of DNA from forensic evidence samples that may contain low quantities of DNA and polymerase chain reaction (PCR) inhibitors. The aqueous extracts from the organic extraction of DNA require subsequent concentration and cleanup, which has traditionally been performed with microdialysis filter units, including the Centricon() and Microcon() centrifugal filter devices. Here, we describe the use of the NucleoSpin() XS silica columns as an alternative for the concentration and purification of the aqueous extracts from the organic extraction and for the removal of PCR inhibitors from existing DNA extracts.

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