Factors affecting the analysis of 18O-enriched aqueous samples when using CO2 equilibration in vacutainers™

Increasing use of ¹⁸O-enriched water in biological studies such as those involving doubly labeled water has led to a requirement for a simple cost effective method for analyzing large numbers of ¹⁸O-enriched biological samples. We evaluated the influence of various factors on the precision and accuracy of an equilibration technique in which aqueous samples are equilibrated with CO₂ in evacuated blood collection tubes, Vacutainers^™. Using 10 mL Vacutainers with degassed rubber septa, 1 mL water samples equilibrated in an atmosphere of CO₂ after 16 h on an orbital shaker. δ¹⁸O values became more variable when the sample volume was reduced to 0.25 mL. Varying the evacuation time for the tubes prior to filling with CO₂ between 15 and 75 s had no marked influence on the results. Similarly, sonicating the water samples during this process to remove dissolved gases also had little effect. Bubbling air or CO₂ through the samples prior to analysis led to a reduction in the ¹⁸O content of enriched water samples due to the introduction of ¹⁶O; however, N₂ had no effect on the δ¹⁸O values. Memory effects between samples and instrumental drift were detected with large changes in enrichment (up to 140‰) during mass spectrometric analysis. An analytical procedure and calculations are presented, which in conjunction with two reference waters, may be used to remove these drift effects. This procedure coupled with suggested sample analysis sequences minimizes the influence of memory and allows precision to be optimized. Even in the absence of these precautions, analytical precision on water with δ¹⁸O_V-SMOW content of +30‰ was ca ±0.1‰, and at +175‰ was ±0.37‰, comparable to other ¹⁸O equilibration methods.     

Second-generation sequencing of forensic STRs using the Ion Torrent™ HID STR 10-plex and the Ion PGM™

Second-generation sequencing (SGS) using Roche/454 and Illumina platforms has proved capable of sequencing the majority of the key forensic genetic STR systems. Given that Roche has announced that the 454 platforms will no longer be supported from 2015, focus should now be shifted to competing SGS platforms, such as the MiSeq (Illumina) and the Ion Personal Genome Machine (Ion PGM™; Thermo Fisher). There are currently several challenges faced with amplicon-based SGS STR typing in forensic genetics, including current lengths of amplicons for CE-typing and lack of uniform data analysis between laboratories.Thermo Fisher has designed a human identification (HID) short tandem repeat (STR) 10-plex panel including amelogenin, CSF1PO, D16S539, D3S1358, D5S818, D7S820, D8S1179, TH01, TPOX and vWA, where the primers have been designed specifically for the purpose of SGS and the data analysis is supported by Ion Torrent™ software. Hence, the combination of the STR 10-plex and the Ion PGM™ represents the first fully integrated SGS STR typing solution from PCR to data analysis.In this study, four experiments were performed to evaluate the alpha-version of the STR 10-plex: (1) typing of control samples; (2) analysis of sensitivity; (3) typing of mixtures; and (4) typing of biological crime case samples. Full profiles and concordant results between replicate SGS runs and CE-typing were observed for all control samples. Full profiles were seen with DNA input down to 50 pg, with the exception of a single locus drop-out in one of the 100 pg dilutions. Mixtures were easily deconvoluted down to 20:1, although alleles from the minor contributor had to be identified manually as some signals were not called by the Ion Torrent™ software. Interestingly, full profiles were obtained for all biological samples from real crime and identification cases, in which only partial profiles were obtained with PCR-CE assays. In conclusion, the Ion Torrent™ HID STR 10-plex panel offers an all-in-one solution from amplification of STRs and amelogenin, and sequencing to data analysis.     

Next generation sequencing of SNPs using the HID-Ion AmpliSeq™ Identity Panel on the Ion Torrent PGM™ platform

The HID-Ion AmpliSeq™ Identity Panel (the HID Identity Panel) is designed to detect 124-plex single nucleotide polymorphisms (SNPs) with next generation sequencing (NGS) technology on the Ion Torrent PGM™ platform, including 90 individual identification SNPs (IISNPs) on autosomal chromosomes and 34 lineage informative SNPs (LISNPs) on Y chromosome. In this study, we evaluated performance for the HID Identity Panel to provide a reference for NGS-SNP application, focusing on locus strand balance, locus coverage balance, heterozygote balance, and background signals. Besides, several experiments were carried out to find out improvements and limitations of this panel, including studies of species specificity, repeatability and concordance, sensitivity, mixtures, case-type samples and degraded samples, population genetics and pedigrees following the Scientific Working Group on DNA Analysis Methods (SWGDAM) guidelines. In addition, Southern and Northern Chinese Han were investigated to assess applicability of this panel. Results showed this panel led to cross-reactivity with primates to some extent but rarely with non-primate animals. Repeatable and concordant genotypes could be obtained in triplicate with one exception at rs7520386. Full profiles could be obtained from 100 pg input DNA, but the optimal input DNA would be 1 ng–200 pg with 21 initial PCR cycles. A sample with ≥20% minor contributor could be considered as a mixture by the number of homozygotes, and full profiles belonging to minor contributors could be detected between 9:1 and 1:9 mixtures with known reference profiles. Also, this assay could be used for case-type samples and degraded samples. For autosomal SNPs (A-SNPs), F_ST across all 90 loci was not significantly different between Southern and Northern Chinese Han or between male and female samples. All A-SNP loci were independent in Chinese Han population. Except for 18 loci with H_e <0.4, most of the A-SNPs in the HID Identity Panel presented high polymorphisms. Forensic parameters were calculated as >99.999% for combined discrimination power (CDP), 0.999999724 for combined power of exclusion (CPE), 1.390 × 10¹¹ for combined likelihood ratio (CLR) of trios, and 2.361 × 10⁶ for CLR of motherless duos. For Y-SNPs, a total of 8 haplotypes were observed with the value of 0.684 for haplotype diversity. As a whole, the HID Identity Panel is a well-performed, robust, reliable and high informative NGS-SNP assay and it can fully meet requirements for individual identification and paternity testing in forensic science.     

Dosimetry of the microSelectron-HDR Ir-192 source using PRESAGE™ and optical CT

Optical CT, using a solid polyurethane (PRESAGE™) radiochromic dosimeter, has been used to evaluate dose distributions produced by the microSelectron-HDR Ir-192 source. The anisotropy functions obtained through optical CT are in good agreement with Monte Carlo and previously published results especially at polar angle above 20°. The results indicated an evident potential for using solid polymer dosimetry as an accurate method for 3-D dosimetry, although refinements to the existing methods are necessary before the technique can be used clinically.     

Heterogenous iodination of α-cellulose: Preparation of a radioactive analog of dietary fiber

α-Cellulose has been iodinated by a method which yields a chemically stable iodinated cellulose of high specific activity. The preparation and chemical stability of the derivative are described, together with potential application as a tracer for the study of digestion and as an imaging agent in the digestive tract.     

Direct amplification of casework bloodstains using the Promega PowerPlex® 21 PCR Amplification System

A significant number of evidence items submitted to Forensic Science Service Tasmania (FSST) are blood swabs or bloodstained items. Samples from these items routinely undergo phenol:chloroform:isoamyl alcohol organic extraction and quantitative Polymerase Chain Reaction (qPCR) testing prior to PowerPlex^® 21 amplification. This multi-step process has significant cost and timeframe implications in a fiscal climate of tightening government budgets, pressure towards improved operating efficiencies, and an increasing emphasis on rapid techniques better supporting intelligence-led policing.Direct amplification of blood and buccal cells on cloth and Whatman FTA™ card with PowerPlex^® 21 has already been successfully implemented for reference samples, eliminating the requirement for sample pre-treatment. Scope for expanding this method to include less pristine casework blood swabs and samples from bloodstained items was explored in an endeavour to eliminate lengthy DNA extraction, purification and qPCR steps for a wider subset of samples.Blood was deposited onto a range of substrates including those historically found to inhibit STR amplification. Samples were collected with micro-punch, micro-swab, or both. The potential for further fiscal savings via reduced volume amplifications was assessed by amplifying all samples at full and reduced volume (25 and 13 μL).Overall success rate data showed 80% of samples yielded a complete profile at reduced volume, compared to 78% at full volume. Particularly high success rates were observed for the blood on fabric/textile category with 100% of micro-punch samples yielding complete profiles at reduced volume and 85% at full volume.Following the success of this trial, direct amplification of suitable casework blood samples has been implemented at reduced volume. Significant benefits have been experienced, most noticeably where results from crucial items have been provided to police investigators prior to interview of suspects, and a coronial identification has been successfully completed in a short timeframe to avoid delay in the release of human remains to family members.     

Inter-laboratory evaluation of SNP-based forensic identification by massively parallel sequencing using the Ion PGM™

Next generation sequencing (NGS) offers the opportunity to analyse forensic DNA samples and obtain massively parallel coverage of targeted short sequences with the variants they carry. We evaluated the levels of sequence coverage, genotyping precision, sensitivity and mixed DNA patterns of a prototype version of the first commercial forensic NGS kit: the HID-Ion AmpliSeq™ Identity Panel with 169-markers designed for the Ion PGM™ system. Evaluations were made between three laboratories following closely matched Ion PGM™ protocols and a simple validation framework of shared DNA controls. The sequence coverage obtained was extensive for the bulk of SNPs targeted by the HID-Ion AmpliSeq™ Identity Panel. Sensitivity studies showed 90–95% of SNP genotypes could be obtained from 25 to 100 pg of input DNA. Genotyping concordance tests included Coriell cell-line control DNA analyses checked against whole-genome sequencing data from 1000 Genomes and Complete Genomics, indicating a very high concordance rate of 99.8%. Discordant genotypes detected in rs1979255, rs1004357, rs938283, rs2032597 and rs2399332 indicate these loci should be excluded from the panel. Therefore, the HID-Ion AmpliSeq™ Identity Panel and Ion PGM™ system provide a sensitive and accurate forensic SNP genotyping assay. However, low-level DNA produced much more varied sequence coverage and in forensic use the Ion PGM™ system will require careful calibration of the total samples loaded per chip to preserve the genotyping reliability seen in routine forensic DNA. Furthermore, assessments of mixed DNA indicate the user’s control of sequence analysis parameter settings is necessary to ensure mixtures are detected robustly. Given the sensitivity of Ion PGM™, this aspect of forensic genotyping requires further optimisation before massively parallel sequencing is applied to routine casework.     

Allele frequencies and other forensic parameters of the HID-Ion AmpliSeq™ Identity Panel markers in Basques using the Ion Torrent PGM™ platform

The HID-Ion AmpliSeq™ Identity Panel amplifies 90 autosomal SNPs and 34 Y- SNPs with massively parallel sequencing (MPS) using the Ion Torrent PGM™ platform. In the present study, 105 Basques were analyzed to assess this panel. All loci were in Hardy-Weinberg equilibrium and no association between them was detected. Forensic parameters were calculated as 5.74 × 10⁻³⁶ for combined match probability and 99.99998% for combined power of exclusion. In conclusion, the HID Identity panel and the use of this new MPS technology are very promising tools for paternity testing and human identification in routine casework in the forensic field.     

Effects of using the GlobalFiler™ multiplex system on parent–child analyses of cases with single locus inconsistency

Parent–child analyses sometimes reveal inconsistency of shared alleles at only one locus. This is conventionally called “single locus exclusion”, which results from mutational events and the presence of null alleles. Here, in parent–child analyses of the Japanese population, we detected exclusions by using the GlobalFiler™ system comprising 21 short tandem repeat loci. One- or two-step mutations resulting from strand slippage causing gain or loss were observed in seven of 221 parent–child transmissions. The incidences of single locus inconsistency of alleles were 5.88 × 10⁻² and 8.40 × 10⁻³ for paternal and maternal relationships, respectively. With calculation using a set of 15 loci in the Identifiler® multiplex system, the combined likelihood ratio (CLR) values were limited to less than 100 in all five cases accompanied by single inconsistency. The addition of six loci recovered the CLR values to over 10,000 in three cases. Application of this advanced system may increase the detected occurrence of mutational events, but it should be beneficial for inference in parent–child analyses, particularly in cases accompanied by genetic inconsistency.     

Study of the IsoAid ADVANTAGE™ 125I brachytherapy source dosimetric parameters using Monte Carlo simulation

Monte Carlo calculations have been performed using the MCNP4C code for an iodine seed design. As the ADVANTAGE? I-125, Model IAI-125 source is commercially available for interstitial brachytherapy treatment, dosimetric characteristics (dose rate constant, radial dose function and anisotropy function) of this source were theoretically determined following the updated AAPM task group 43 (TG-43U1) recommendations. The dose distribution around the seed was calculated with Monte Carlo simulation in liquid water. The Monte Carlo calculated dose rate constant of this source in water was found to be 0.986 cGy h^?1 U^?1, with an approximate uncertainty of 0.4%. The obtained result has been compared with the previous study. Comparison of the calculated dose rate constant with the value presented by Meigooni et al. shows a very good agreement. Also the anisotropy function and the radial dose function for this source are graphically compared.     

Determination of 210Pb and 210Po in water using the extractive scintillation cocktail Polex™

Method validation was performed to achieve the accreditation for our determination method of ²¹⁰Pb and ²¹⁰Po in water. A Pb(NO₃)₂ carrier is added to the sample and lead is precipitated with Na₂SxH₂O. ²¹⁰Po is co-precipitated and the extractive scintillation cocktail Polex^™ is used to determine ²¹⁰Po and ²¹⁰Pb. Uranium is also extracted by Polex^™. It can be removed by washing the precipitate with 1% HNO₃. The ingrowth of ²¹⁰Pb from ²²²Rn during transportation time must be calculated. It has to be subtracted from the original ²¹⁰Pb in the sample and taken into account for the calculation of the lower limit of detection.     

Evaluation and comparative analysis of direct amplification of STRs using PowerPlex® 18D and Identifiler® Direct systems

Short tandem repeat (STR) analysis remains the primary forensic tool for DNA identification. Because of the success of forensic DNA typing and the use of database searches to develop investigative leads, there is an increased demand for populating forensic DNA databases. Reference samples tend to be of high quantity and quality and are somewhat standardized in format. Being more predictable in quality than unknown forensic casework samples, reference samples lend themselves to alternate methods of analysis such as direct amplification. Two commercially available direct amplification kits for processing reference samples were evaluated. The kits are PowerPlex^® 18D (Promega Corp., Madison, Wisconsin) and Identifiler^® Direct (Life Technologies, Carlsbad, CA). Both kits offer the core CODIS loci plus amelogenin, and the loci D2S1338, D19S433. The PP18D kit offers two additional loci, Penta E and Penta D. To determine the robustness and reliability of the PP18D and ID Direct amplification systems, buccal cell samples (deposited on FTA paper using the EasiCollect? device (Florham Park, NJ)) from 400 anonymous donors were analyzed under conditions to achieve a high rate of successful typing. First-pass success rates were 96.25%, 96.25%, and 95% for PP18D with a 5 s injection, ID Direct with a 10 s injection, and ID Direct with a 5 s injection, respectively. Profiles that could not be typed were not a result of the kits’ performance but were a result of the inherent variation in the amount of DNA obtained with the collection device and buccal cells. Low signal profiles can be re-analyzed by either re-injecting for a longer time or by re-amplification with an additional PCR cycle. Overloaded profiles can be re-analyzed by re-injecting for a shorter time or by re-amplification with one less cycle. All called typing results, when interpretable, were consistent under the prescribed conditions, different injection times, and 26-28 PCR cycles for both chemistries. Peak height ratios for both kits were well balanced with peaks ranging in height >2000 RFUs to those with one or more peaks with heights <100 RFUs. A change in the ILS morphology sloping downward to the right relative to a normal ILS profile for PP18D and ID Direct was an indication of a poor injection. Re-injection effectively overcame the effect manifested by a sloping ILS phenomenon. A subset of samples were subjected to direct amplification using the reagents in Identifiler^® Plus kit and successful typing results were obtained for the majority of samples. However, the profiles displayed increased amounts of non-adenylated products. The results of this study demonstrate that PP18D and ID Direct are both robust kits for direct amplification. The interpretation guidelines used for this study can form a basis for internal validation studies by databasing laboratories.     

Ultrasound-guided removal of Implanon™ devices

Our study has shown that ultrasound-guided localisation and removal of Implanon™ rods is safe, practical and highly successful. Over a 4-year period, 119 patients had successful, uncomplicated removal of their subdermal devices.The technique is particularly useful for removal of the device when it is not palpable or when an attempt at removal of a palpable device has not been successful.     

Individual identification using the RapidHIT™ ID system for forensic samples

The RapidHIT™ ID system produces GlobalFiler™ analysis results after a short operating time. This device is effective because it automatically extracts DNA from oral mucosal cells or from blood stains and saliva collected at a crime scene, with subsequent polymerase chain reaction performed to produce a DNA profile. Two types of dedicated cartridges are available for RapidHIT™ ID: the RapidHIT™ ID ACE GlobalFiler Express sample cartridge for oral cells and other samples and the RapidINTEL™ sample cartridge for minute samples, such as blood stains. Previously validated specimens include oral mucosa cells and blood stains left at crime scenes. There have been no reports of blood and nail clipping samples collected from the postmortem bodies at the time of death. This report summarizes the results of using the RapidHIT™ ID system by collecting a variety of actual forensic samples from postmortem bodies at different stages of decomposition, which were subsequently analyzed using these cartridges.     

Treatment of glioblastoma using MRIdian® A3i BrainTx™: Imaging and treatment workflow demonstration

For patients with newly diagnosed glioblastoma, the current standard-of-care includes maximal safe resection, followed by concurrent chemoradiotherapy and adjuvant temozolomide, with tumor treating fields. Traditionally, diagnostic imaging is performed pre- and post-resection, without additional dedicated longitudinal imaging to evaluate tumor volumes or other treatment-related changes. However, the recent introduction of MR-guided radiotherapy using the ViewRay MRIdian A3i system includes a dedicated BrainTx package to facilitate the treatment of intracranial tumors and provides daily MR images. We present the first reported case of a glioblastoma imaged and treated using this workflow. In this case, a 67-year-old woman underwent adjuvant chemoradiotherapy after gross total resection of a left frontal glioblastoma. The radiotherapy treatment plan consisted of a traditional two-phase design (46 Gy followed by a sequential boost to a total dose of 60 Gy at 2 Gy/fraction). The treatment planning process, institutional workflow, treatment imaging, treatment timelines, and target volume changes visualized during treatment are presented. This case example using our institutional A3i system workflow successfully allows for imaging and treatment of primary brain tumors and has the potential for margin reduction, detection of early disease progression, or to detect the need for dose adaptation due to interfraction tumor volume changes.     

Amplification volume reduction on DNA database samples using FTA™ Classic Cards

The DNA forensic community always strives towards improvements in aspects such as sensitivity, robustness, and efficacy balanced with cost efficiency. Therefore our laboratory decided to study the feasibility of PCR amplification volume reduction using DNA entrapped in FTA? Classic Card and to bring cost savings to the laboratory. There were a few concerns the laboratory needed to address. First, the kinetics of the amplification reaction could be significantly altered. Second, an increase in sensitivity might affect interpretation due to increased stochastic effects even though they were pristine samples. Third, statics might cause FTA punches to jump out of its allocated well into another thus causing sample-to-sample contamination. Fourth, the size of the punches might be too small for visual inspection. Last, there would be a limit to the extent of volume reduction due to evaporation and the possible need of re-injection of samples for capillary electrophoresis. The laboratory had successfully optimized a reduced amplification volume of 10 μL for FTA samples.     

Competition for DNA binding sites using Promega DNA IQ™ paramagnetic beads

The Promega DNA IQ? system is easily amenable to automation and has been an integral part of standard operating procedures for many forensic laboratories including those of the Royal Canadian Mounted Police (RCMP) since 2004. Due to some failure to extract DNA from samples that should have produced DNA using our validated automated DNA IQ?-based protocol, the competition for binding sites on the DNA IQ? magnetic beads was more closely examined. Heme from heavily blooded samples interfered slightly with DNA binding. Increasing the concentration of Proteinase K during lysis of these samples did not enhance DNA recovery. However, diluting the sample lysate following lysis prior to DNA extraction overcame the reduction in DNA yield and preserved portions of the lysates for subsequent manual or automated extraction. Dye/chemicals from black denim lysates competed for binding sites on the DNA IQ? beads and significantly reduced DNA recovery. Increasing the size or number of black denim cuttings during lysis had a direct adverse effect on DNA yield from various blood volumes. The dilution approach was successful on these samples and permitted the extraction of high DNA yields. Alternatively, shortening the incubation time for cell lysis to 30 min instead of the usual overnight at 56 °C prevented competition from black denim dye/chemicals and increased DNA yields.