Inter-laboratory evaluation of the EUROFORGEN Global ancestry-informative SNP panel by massively parallel sequencing using the Ion PGM™.

The EUROFORGEN Global ancestry-informative SNP (AIM-SNPs) panel is a forensic multiplex of 128 markers designed to differentiate an individual's ancestry from amongst the five continental population groups of Africa, Europe, East Asia, Native America, and Oceania. A custom multiplex of AmpliSeq™ PCR primers was designed for the Global AIM-SNPs to perform massively parallel sequencing using the Ion PGM™ system. This study assessed individual SNP genotyping precision using the Ion PGM™, the forensic sensitivity of the multiplex using dilution series, degraded DNA plus simple mixtures, and the ancestry differentiation power of the final panel design, which required substitution of three original ancestry-informative SNPs with alternatives. Fourteen populations that had not been previously analyzed were genotyped using the custom multiplex and these studies allowed assessment of genotyping performance by comparison of data across five laboratories. Results indicate a low level of genotyping error can still occur from sequence misalignment caused by homopolymeric tracts close to the target SNP, despite careful scrutiny of candidate SNPs at the design stage. Such sequence misalignment required the exclusion of component SNP rs2080161 from the Global AIM-SNPs panel. However, the overall genotyping precision and sensitivity of this custom multiplex indicates the Ion PGM™ assay for the Global AIM-SNPs is highly suitable for forensic ancestry analysis with massively parallel sequencing.

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 100pg 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.

[Automated breast ultrasound vs. handheld ultrasound: BI-RADS classification, duration of the examination and patient comfort]. / Automatisierter Brustultraschall vs. handgeführter Brustultraschall: BI-RADS-Einstufung, Untersuchungsdauer und Erlebnisqualität der Untersuchung.

PURPOSE: Automated breast ultrasound (ABUS) is a potentially valuable adjunct to mammography in breast cancer screening. The reliability and the inter-observer variability in the BI-RADS classification, compared to handheld ultrasound (US), as well as the duration of the examination and patient comfort have only been investigated in a limited number of papers to date. MATERIALS AND METHODS: In a prospective study, we examined 148 breasts of 76 patients with handheld US and ABUS. The ABUS data were evaluated separately by two investigators. Patient comfort was assessed using a standardized questionnaire. RESULTS: The inter-observer agreement for the BI-RADS classification among the two observers using ABUS was high (κ = 0,750), the agreement with handheld US was moderate. The sensitivity in the detection of breast cancer was 87.5 % for handheld US and 75 % for the ABUS evaluation by observer 1. The sensitivity was 87.5 % for the ABUS evaluation and 83 % for mammography by observer 2. The ABUS examination was rated as completely painless by 64 % of the patients. 25 % of the patients indicated minor pain, and 10 % indicated moderate pain. Handheld US was rated as completely painless by 66 % of the patients. 26 % of the patients indicated minor pain, and 8 % indicated moderate pain. CONCLUSION: ABUS examinations focusing on the BIRADS classification have low inter-observer variability, compared to handheld US. The sensitivity of ABUS did not differ significantly from handheld US.

[Unstable pertrochanteric femur fractures. Failure rate, lag screw sliding and outcome with extra- and intramedullary devices (PCCP, DHS and PFN)]. / Die instabile pertrochantäre Femurfraktur. Komplikationen, Fraktursinterung und Funktion nach extra- und intramedullärer Versorgung (PCCP, DHS und PFN).

AIM OF THE STUDY: The dynamic hip screw (DHS) often shows a high incidence of therapeutic failure and an impared outcome in the treatment of the unstable pertrochanteric femur fracture (31A2). Therefore often an intramedullary device is recommended. In a retrospective clinical study we examined whether the percutaneous compression plate (PCCP, Gotfried) provides advantages following unstable fractures in comparison to DHS and PFN. METHODS: From January 2002 to April 2007 135 patients with unstable pertrochanteric femur fractures underwent internal fixation with the PCCP (n = 46, age 78.3, ASA 2.8), DHS (n = 36, age 75.9, ASA 3.0) or PFN (n = 53, age 77.2, ASA 2.8). Radiological and clinical re-examination of the patients (33 PCCP, 24 DHS, 34 PFN) was performed 17 months later. RESULTS AND DISCUSSION: The PCCP was implanted in less time than the DHS and PFN (59 vs. 80 vs. 79 min, p = 0.004). Radiographic screening time was low (PCCP 143 vs. DHS 146 vs. PFN 280 s, p = 0.001). Re-operations for wound infections and haematomas occurred in 2 % after PCCP, 14 % after DHS and 4 % after PFN (p = 0.058). There was a low re-operation rate for fracture fixation complications in PCCP (9 %), in contrast to DHS (25 %) and PFN (13 %, p = 0.109). Cut-out was seen more in DHS (19 %, PCCP 2 %, PFN 4 %, p = 0.005). Lag screw sliding was high with DHS (PCCP 4 mm vs. DHS 9 mm vs. PFN 6 mm, p = 0.032). There was no correlation between lag screw sliding and outcome. PCCP, DHS and PFN had the same functional results in Merle d'Aubigné and Harris hip scores. CONCLUSIONS: Using the minimally invasive PCCP technique in unstable pertrochanteric femur fractures provides a promising therapy option especially with regard to surgical time, radiographic screening time and failure rate. Lag screw sliding was low. There was no advantage of the intramedullary device PFN.

Evaluating microarray-based classifiers: an overview.

For the last eight years, microarray-based class prediction has been the subject of numerous publications in medicine, bioinformatics and statistics journals. However, in many articles, the assessment of classification accuracy is carried out using suboptimal procedures and is not paid much attention. In this paper, we carefully review various statistical aspects of classifier evaluation and validation from a practical point of view. The main topics addressed are accuracy measures, error rate estimation procedures, variable selection, choice of classifiers and validation strategy.

Aerial measurements of artificial radionuclides in Germany in case of a nuclear accident.

Gamma-ray spectrometric systems carried by helicopters prove to be indispensable for the surveillance of environmental radioactivity. The aerial measurements are an important tool for rapid and large-scale nuclide specific determination of soil contamination after an accidental release of radionuclides from a nuclear facility. Furthermore this technique is also applied for the determination of anomalies of elevated radioactivity of natural radionuclides, the detection of lost radioactive sources and geological mapping. For the measurements the helicopters are equipped with a NaI(Tl)-detector array and a high purity germanium-semiconductor (HPGe) detector. Especially with the HPGe-detector it is possible to clearly identify individual radionuclides. To improve and to guarantee the quality of this method several exercises with different fields of interest have been carried out during the last years. Thereby the main focus is on the improvement of the instrumentation, data handling and data analysis. The results of the airborne radionuclide measurements from the Black Forest which was performed in co-operation with the Swiss National Emergency Operation Centre, are presented here. During this exercise the gamma dose rate, soil contamination due to 137Cs and the specific activities of natural radionuclides in soil were determined.