Mitochondrial DNA error prophylaxis: assessing the causes of errors in the GEP'02-03 proficiency testing trial

A qualitative and quantitative analytical method was developed and validated for the determination of 49 licit and illicit drugs in oral fluid. Small oral fluid samples, volume 1mL, were collected from volunteers using a modified Omni-Sal device and the analytes were extracted from an oral fluid/buffer mixture using a single Bond Elut Certify solid phase extraction cartridge. Liquid chromatography-tandem mass spectrometry (LC-MS-MS) and gas chromatography-repetitive full scan mass spectrometry (GC-MS) were used in parallel to analyze the extracts for the targeted drugs. Extracts were analyzed by GC-MS in their underivatized form and as their pentafluoropropionyl derivatives. Deuterated internal standards were used for quantification of drugs of abuse by LC-MS-MS to minimize matrix effects. Methadone-d(9) and tumoxetine were used as the internal standards for quantification of non-derivatized and derivatized analytes respectively by GC-MS. Linearity was demonstrated over the range 5-200 ng/mL and limits of detection were less than 4 ng/mL for each drug analyzed. The method demonstrated acceptable recoveries for most of the analytes and good intra- and inter-day precision. Acquisition of data by repetitive full scan GC-MS allows the addition of further analytes to the target menu.     

Trace analysis of peroxide explosives by high performance liquid chromatography-atmospheric pressure chemical ionization-tandem mass spectrometry (HPLC-APCI-MS/MS) for forensic applications

An HPLC-APCI-MS(/MS) method for the (trace) analysis of the most commonly encountered peroxide explosives, hexamethylenetriperoxidediamine (HMTD) and triacetonetriperoxide (TATP), has been developed. With this method, HMTD and TATP have been analyzed in the same run. (Pseudo-)molecular ions of these peroxides have been obtained as base peak under the same condition. A series of product ions was produced from these pseudo-molecular ions ([HMTD - 1]+ and [TATP + NH4]+) in the MS/MS analysis. We also pioneered in showing that a TATP molecular ion [TATP + H]+ can be observed with HPLC-MS/MS. The limit of detection for HMTD and TATP was 0.26 and 3.3 ng, respectively, on column by HPLC-MS in the Full Scan mode and 0.08 and 0.8, respectively, by HPLC-APCI-MS/MS in Selected Reaction Monitoring (single mass unit) mode. The method presented has been applied successfully for the identification of peroxides in the bulk solid state (powder sample), as well as in post-blast extracts originating from a forensic case. For the post-blast extracts, the use of tandem MS has been shown clearly to be of crucial importance for the identification and detection of the peroxide explosives.     

Enhanced kinship analysis and STR-based DNA typing for human identification in mass fatality incidents: the Swissair flight 111 disaster

A bioinformatic tool was developed to assist with the victim identification initiative that followed the Swissair Flight 111 disaster. Making use of short tandem repeat (STR) DNA typing data generated with AmpFlSTR Profiler Plus (PP) and AmpFlSTR COfiler(CO) kits, the software systematically compared each available STR genotype with every other genotype. The matching algorithm was based on the search for: (i) direct matches to genotypes derived from personal effects; and (ii) potential kinship associations between victims and next-of-kin, as measured by allele sharing at individual loci. The software greatly assisted parentage analysis by enabling kinship evaluation in situations where complete parentage trios were unavailable and, in some situations, with distantly related relatives. Exclusion of fortuitous kinship associations (FKA) was made possible through the recovery at the disaster site of at least one remains for every sought-after victim, and was incorporated into the kinship software. The data from the 13 combined STR loci produced 6 and 23 times fewer FKAs when compared with PP alone and AmpFlSTR Profiler (PR) alone, respectively. Identification leads or confirmations of identification were obtained for 218 victims for which DNA reference samples (personal effects and kin) had been submitted. Confirmation of an inferred kinship association was sought through frequency and likelihood calculations, as well as corroborative data from other identification modalities. The use of a simple, yet powerful, automated genotype comparison approach and the use of megaplexes with high power of discrimination (PD) values extended considerably the identification capabilities in the case of the Swissair disaster. The DNA typing identification modality proved to be a valuable component of the large arsenal of identification tools deployed in the aftermath of this disaster.     

Systematic analysis of stutter percentages and allele peak height and peak area ratios at heterozygous STR loci for forensic casework and database samples

To assist the interpretation of STR DNA typing results from forensic casework samples containing mixtures, the range of heterozygous allele peak height and peak area ratios (HR) and stutter percentages (stutter %) for the loci comprised in the AmpFlSTR Profiler Plus (PP) kit were assessed on 468 database and 275 casework single source samples. Stutter % medians were similar for database and casework samples, ranging from 2% to 7%. The upper limit of the stutter value range was 16%, calculated as median +3 SD, although lower locus-specific values could be used. HR medians were 93 +/- 6.5% for database samples, 88 +/- 12% for casework samples. For casework samples, the maximum signal imbalance noted was 52%, calculated as median -3 SD. No significant difference was observed between peak height and peak area calculated values. This study shows the importance of selecting the proper reference database for the establishment of HR threshold values.     

Allele frequencies data and statistic parameters for 16 STR loci-D19S433, D2S1338, CSF1PO, D16S539, D7S820, D21S11, D18S51, D13S317, D5S818, FGA, Penta E, TH01, vWA, D8S1179, TPOX, D3S1358-in the Rio de Janeiro population, Brazil

Allele frequencies for 16 short tandem repeats (STR) loci were determined with a sample of 230-300 unrelated individuals from the population of Rio de Janeiro, Brazil. The loci are the most commonly used in forensic and paternity testing, being analysed by the Identifiler (Applied Biosystems) and PowerPlex 2.1 (Promega) commercial kits. It was proved that Penta E and D18S51 are the most polymorphic loci.     

What Patent Data Reveal about Universities: The Case of Belgium

In recent years, there has been a surge in patenting by Belgian universities. It appears that this increase can be attributed to growth of biotechnology, where there is a greater propensity to patent, to a desire on the part of universities to enhance commercialization through technology transfer offices (TTOs), and to effective collaboration between universities and government-sponsored research centers. Our qualitative analysis reveals that patent statistics could be a misleading indicator of an individual university's technological productivity, since many inventions are developed at universities, yet applied by other institutions.     

STR DNA typing: increased sensitivity and efficient sample consumption using reduced PCR reaction volumes

Improvements in detection limits/sensitivity and lower sample consumption are potential benefits of reducing PCR reaction volumes used in forensic DNA typing of crime scene samples. This premise was studied first with experimental mixtures and a nine-loci megaplex, which demonstrated stochiometric amplification and accurate detection. Next, adjudicated casework samples were subjected to amplification under 15 different template DNA to PCR reaction volume ratios. Reduction of PCR reaction volume and DNA down to 10 microL and 0.500 ng, respectively, produced identical profiles with the same signal intensity and heterozygous allele peak height ratio (HR). Reduction to 5 microL and 0.063 ng yielded HR values that were slightly affected in one to three STR loci. PCR reaction volume reduction can enhance detection and sensitivity while reducing the consumption of irreplaceable crime scene samples.