Forensic ancestry analysis with two capillary electrophoresis ancestry informative marker (AIM) panels: Results of a collaborative EDNAP exercise.

There is increasing interest in forensic ancestry tests, which are part of a growing number of DNA analyses that can enhance routine profiling by obtaining additional genetic information about unidentified DNA donors. Nearly all ancestry tests use single nucleotide polymorphisms (SNPs), but these currently rely on SNaPshot single base extension chemistry that can fail to detect mixed DNA. Insertion-deletion polymorphism (Indel) tests have been developed using dye-labeled primers that allow direct capillary electrophoresis detection of PCR products (PCR-to-CE). PCR-to-CE maintains the direct relationship between input DNA and signal strength as each marker is detected with a single dye, so mixed DNA is more reliably detected. We report the results of a collaborative inter-laboratory exercise of 19 participants (15 from the EDNAP European DNA Profiling group) that assessed a 34-plex SNP test using SNaPshot and a 46-plex Indel test using PCR-to-CE. Laboratories were asked to type five samples with different ancestries and detect an additional mixed DNA sample. Statistical inference of ancestry was made by participants using the Snipper online Bayes analysis portal plus an optional PCA module that analyzes the genotype data alongside calculation of Bayes likelihood ratios. Exercise results indicated consistent genotyping performance from both tests, reaching a particularly high level of reliability for the Indel test. SNP genotyping gave 93.5% concordance (compared to the organizing laboratory's data) that rose to 97.3% excluding one laboratory with a large number of miscalled genotypes. Indel genotyping gave a higher concordance rate of 99.8% and a reduced no-call rate compared to SNP analysis. All participants detected the mixture from their Indel peak height data and successfully assigned the correct ancestry to the other samples using Snipper, with the exception of one laboratory with SNP miscalls that incorrectly assigned ancestry of two samples and did not obtain informative likelihood ratios for a third. Therefore, successful ancestry assignments were achieved by participants in 92 of 95 Snipper analyses. This exercise demonstrates that ancestry inference tests based on binary marker sets can be readily adopted by laboratories that already have well-established CE regimes in place. The Indel test proved to be easy to use and allowed all exercise participants to detect the DNA mixture as well as achieving complete and concordant profiles in nearly all cases. Lastly, two participants successfully ran parallel next-generation sequencing analyses (each using different systems) and achieved high levels of genotyping concordance using the exercise PCR primer mixes unmodified.

RNA/DNA co-analysis from human menstrual blood and vaginal secretion stains: results of a fourth and fifth collaborative EDNAP exercise.

The European DNA Profiling Group (EDNAP) organized a fourth and fifth collaborative exercise on RNA/DNA co-analysis for body fluid identification and STR profiling. The task was to identify dried menstrual blood and vaginal secretion stains using specific RNA biomarkers, and additionally test 3 housekeeping genes for their suitability as reference genes. Six menstrual blood and six vaginal secretion stains, two dilution series (1/4-1/64 pieces of a menstrual blood/vaginal swab) and, optionally, bona fide or mock casework samples of human or non-human origin were analyzed by 24 participating laboratories, using RNA extraction or RNA/DNA co-extraction methods. Two novel menstrual blood mRNA multiplexes were used: MMP triplex (MMP7, MMP10, MMP11) and MB triplex (MSX1, LEFTY2, SFRP4) in conjunction with a housekeeping gene triplex (B2M, UBC, UCE). Two novel mRNA multiplexes and a HBD1 singleplex were used for the identification of vaginal secretion: Vag triplex (MYOZ1, CYP2B7P1 and MUC4) and a Lactobacillus-specific Lacto triplex (Ljen, Lcris, Lgas). The laboratories used different chemistries and instrumentation and all were able to successfully isolate and detect mRNA in dried stains. The simultaneous extraction of RNA and DNA allowed for positive identification of the tissue/fluid source of origin by mRNA profiling as well as a simultaneous identification of the body fluid donor by STR profiling, also from old and compromised casework samples. The results of this and the previous collaborative RNA exercises support RNA profiling as a reliable body fluid identification method that can easily be combined with current STR typing technology.

Home visits by community nurses for cancer patients after discharge from hospital: an evaluation study of the continuity visit.

After discharge from the hospital, patients with cancer can have several problems at home. In this project, patients with cancer, who at time of discharge from the hospital were not indicated for nursing care at home, were offered three home visits by a community nurse. A prospective, descriptive study was undertaken to assess indicators of usefulness of these "continuity visits." It was registered how many and what patients [sex, age, (time of) diagnosis, social support, therapy] wanted to receive the visit. Care needs, as mentioned by the patients during the continuity visits, were reported after the visit by the community nurse. Both patients and community nurses completed an evaluation form after the first visit. A continuity visit was offered to 337 patients; 112 patients received a first, 50 a second, and 24 a third continuity visit. Older patients, patients without social support, and those diagnosed less than half a year before more often agreed to received a first visit. Reasons for patients not receiving a second or third visit were either that patients did not want one or on the contrary they were in need of immediate nursing care or had died before the visit. Two weeks after discharge, 93% of the patients experienced one or more physical, psychological, or social problems; 70% mentioned a need for information; and 47% needed emotional support. Both patients and community nurses evaluate the first visit positively. The findings suggest that continuation of the offer of the first continuity visit could be useful.

Detection of staphylococcal enterotoxin B employing a piezoelectric crystal immunosensor.

This paper reports on a study concerning the development of a biochemical sensor for Staphylococcal Enterotoxin B (SEB), a substance within the bracket of biological warfare. A 20 MHz piezoelectric quartz crystal sensor device was employed in a flow injection system. The assay for SEB is based on a competition scheme using polyclonal antibodies (anti-SEB). Three parameters, i.e. the flow rate in the flow cell, the incubation time and the anti-SEB concentration, were optimized. A detection limit of 0.1 microgram/ml was obtained, whereas at concentrations of SEB of 10 micrograms/ml or higher the sensor response was completely inhibited. The results were compared with a competition enzyme linked immunosorbent assay.

Development of a surface acoustic wave gas sensor for organophosphorus nerve agents employing lanthanide compounds as the chemical interface.

The results of a study dealing with surface acoustic wave gas sensors for organophosphorus compounds such as nerve agents are described. Several lanthanum coordination compounds were applied as the chemical interface. The various sensors prepared were challenged with both the nerve agent sarin and the simulant dimethyl methylphosphonate. Many aspects were studied, such as sensitivity, selectivity, reversibility and response rate as well as the effect of temperature and structural features. Detection limits down to 0.1 ppm were found. Response rates require further improvement. Degradation phenomena were observed which in some cases yielded irreversible responses. The selectivity for organophosphorus compounds was found to be promising.