Biology subjects

Hansen, M. H.

Publications and source records attributed to Hansen, M. H..

3 recordsLinked to original sources

bioRxiv2025

Gene expression profiling for forensic age assessment of porcine skin wounds

Determining the age of wounds is of utmost importance in both veterinary and human forensic pathology. The aim of this study was to design and optimize quantitative polymerase chain reaction (qPCR) primers for use on degraded RNA samples obtained in veterinary forensic cases, hereby ensuring assay robustness. Moreover, the aim was to evaluate if an expression signature, based on optimized short-amplicon primers, was able to differentiate porcine experimental granulation tissue according to age and if this could be used for wound age assessment in veterinary forensic cases. Initially, 12 samples of experimental granulation tissue (n=6) and skin (n=6) from two pigs were deliberately exposed to RNA degrading conditions before being stored in RNAlater. A panel of 24 robust primers were selected based on the intentionally degraded samples. Granulation tissue (5, 10, 15, 20, 25, 30, and 35 days of age) (n=94) and control skin (n=47) from 47 experimental pigs was sampled and stored in RNAlater. Furthermore, granulation tissue and fibrous scar tissue were sampled from 14 veterinary forensic cases. Microfluidic qPCR was performed to evaluate the gene expression of 24 genes. An expression signature of 14 genes reflected the age of the experimental wounds. The 5-day old wounds displayed the biggest divergence from the control skin. As the granulation tissue matured, gene expression gradually approached the levels observed in intact skin. The forensic samples clustered somewhat separately from the experimental samples. In conclusion, granulation tissue from the experimental wounds displayed a time-dependent expression profile based on 14 short-amplicon primers suitable for use with low-quality RNA. However, an expression profile of 14 genes cannot be used as the sole method for forensic age assessments of porcine wounds.

genetics↗

bioRxiv2025

A multidisciplinary approach for the study of age-dependent expression patterns in porcine experimental wounds

Determining the age of wounds in both human and veterinary subjects is a critical aspect of forensic pathology. Gross and histopathological evaluations are used for age estimations, however, these evaluations are subjective as they rely on the opinion and experience of the examining pathologist. Therefore, the aim of the study was to create a multidisciplinary approach to discover accurate and objective indicators of wound age in veterinary forensic cases. In the present study we utilized a porcine experimental wound healing model. Granulation tissue from wounds at different ages (5, 10, 15, 20, 25, 30, and 35 days) (n=188) and control skin samples (n=47) from 47 experimental pigs were evaluated macroscopically, histologically, immunohistochemically, combined with digital pathology, and flow cytometry. Granulation tissue thickness peaked on day 10 post wounding. Full epithelialization was observed at the earliest on day 20 and the percentage of wound surface covered by epithelium increased with age. Leukocytes including hemosiderophages, neutrophils and accumulation of macrophages all displayed time-dependent infiltration into the wound bed. CD34 showed no time-dependent expression. CD105 expression peaked on day 15. CD45 showed a time-dependent expression pattern in the superficial part of the granulation tissue, with highest expression on day 5 and a decrease with increasing wound age. The findings of this multidisciplinary approach indicate the potential to achieve accurate and objective wound age estimations in veterinary and human forensic investigations.

cell biology↗

bioRxiv2020

Workstation benchmark of Spark Capable Genome Analysis ToolKit 4 Variant Calling

BackgroundRapid and practical DNA-sequencing processing has become essential for modern biomedical laboratories, especially in the field of cancer, pathology and genetics. While sequencing turn-over time has been, and still is, a bottleneck in research and diagnostics, the field of bioinformatics is moving at a rapid pace - both in terms of hardware and software development. Here, we benchmarked the local performance of three of the most important Spark-enabled Genome analysis toolkit 4 (GATK4) tools in a targeted sequencing workflow: Duplicate marking, base quality score recalibration (BQSR) and variant calling on targeted DNA sequencing using a modest hyperthreading 12-core single CPU and a high-speed PCI express solid-state drive. ResultsCompared to the previous GATK version the performance of Spark-enabled BQSR and HaplotypeCaller is shifted towards a more efficient usage of the available cores on CPU and outperforms the earlier GATK3.8 version with an order of magnitude reduction in processing time to analysis ready variants, whereas MarkDuplicateSpark was found to be thrice as fast. Furthermore, HaploTypeCallerSpark and BQSRPipelineSpark were significantly faster than the equivalent GATK4 standard tools with a combined [~]86% reduction in execution time, reaching a median rate of ten million processed bases per second, and duplicate marking was reduced [~]42%. The called variants were found to be in close agreement between the Spark and non-Spark versions, with an overall concordance of 98%. In this setup, the tools were also highly efficient when compared execution on a small 72 virtual CPU/18-node Google Cloud cluster. ConclusionIn conclusion, GATK4 offers practical parallelization possibilities for DNA sequence processing, and the Spark-enabled tools optimize performance and utilization of local CPUs. Spark utilizing GATK variant calling is several times faster than previous GATK3.8 multithreading with the same multi-core, single CPU, configuration. The improved opportunities for parallel computations not only hold implications for high-performance cluster, but also for modest laboratory or research workstations for targeted sequencing analysis, such as exome, panel or amplicon sequencing.

bioinformatics↗