Integration and acceleration of virtual microscopy as the key to successful implementation into the routine diagnostic process

<p>Abstract</p> <p>Background</p> <p>The virtual microscopy is widely accepted in Pathology for educational purposes and teleconsultation but is far from the routine use in surgical pathology due to the technical requirements and some limitations. A technical problem is the limited bandwidth of a usual network and the delayed transmission rate and presentation time on the screen.</p> <p>Methods</p> <p>In this study the process of secondary diagnostic was evaluated using the "T.Konsult Pathologie" service of the Professional Association of German Pathologists within the German breast cancer screening program. The characteristics of the access to the WSI (Whole Slide Images) have been analyzed to explore the possibilities of prefetching and caching to reduce the presentation and transfer time with the goal to increase user acceptance. The log files of the web server were analyzed to reconstruct the movements of the pathologist on the WSI and to create the observation path. Using a specialized tool the observation paths were extracted automatically from the log files. The attributes linearity, 3-point-linearity, changes per request, and number of consecutive requests were calculated to design, develop and evaluate different caching and prefetching strategies.</p> <p>Results</p> <p>The analysis of the observation paths showed that a complete accordance of two image requests is a very rare event. But more frequently a partial covering of two requested image areas can be found. In total 257 diagnostic paths from 131 WSI have been extracted and analysed. On average a diagnostic path consists of 16 image requests and takes 189 seconds between first and last image request. The mean linearity was 0,41 and the mean 3-point-linearity 0,85. Three different caching algorithms have been compared with respect to hit rate and additional image requests on the WSI server. Tests demonstrated that 95% of the diagnostic paths could be loaded without any deletion of entries in the cache (cache size 12,2 Megapixel). If the image parts are stored after JPEG compression this complies with less than 2 MB.</p> <p>Discussion</p> <p>WSI telepathology is a technology which offers the possibility to break the limitations of conventional static telepathology. The complete histological slide may be investigated instead of sets of images of lesions sampled by the presenting pathologist. The benefit is demonstrated by the high diagnostic security of 95% accordance between first and second diagnosis.</p

Computational analysis reveals histotype-dependent molecular profile and actionable mutation effects across cancers

Background: Comprehensive mutational profiling data now available on all major cancers have led to proposals of novel molecular tumor classifications that modify or replace the established organ- and tissue-based tumor typing. The rationale behind such molecular reclassifications is that genetic alterations underlying cancer pathology predict response to therapy and may therefore offer a more precise view on cancer than histology. The use of individual actionable mutations to select cancers for treatment across histotypes is already being tested in the so-called basket trials with variable success rates. Here, we present a computational approach that facilitates the systematic analysis of the histological context dependency of mutational effects by integrating genomic and proteomic tumor profiles across cancers. Methods: To determine effects of oncogenic mutations onprotein profiles, we usedtheenergy distance, which comparesthe Euclidean distancesof protein profiles in tumors with an oncogenic mutation (inner distance) to that in tumors without the mutation (outer distance) and performed Monte Carlo simulations for the significance analysis. Finally, the proteins were ranked by their contribution to profile differences to identify proteins characteristic of oncogenic mutation effects across cancers. Results: We apply our approach to four current proposals of molecular tumor classifications and major therapeutically relevant actionable genes. All 12 actionable genes evaluated show effects on the protein level in the corresponding tumor type and showed additional mutation-related protein profiles in 21 tumor types. Moreover, our analysis identifies consistent cross-cancer effects for 4 genes (FGFR1, ERRB2, IDH1, KRAS/NRAS) in 14 tumor types. We further use cell line drug response data to validate our findings. Conclusions: This computational approach can be used to identify mutational signatures that have protein-level effects and can therefore contribute to preclinical in silico tests of the efficacy of molecular classifications as well as the druggability of individual mutations. It thus supports the identification of novel targeted therapies effective across cancers and guides efficient basket trial designs

Guidelines Digital Pathology for Diagnosis on (and Reports of) Digital Images Version 1.0 Bundesverband deutscher Pathologen e.V. (Federal Association of German Pathologist)

Digitalization is entering the medical fields with increasing velocity and impact on diagnostic and therapeutic actions. In addition, it matures to a mandatory tool of quality assurance, reliable inter-disciplinary communication, and promotion of research. The Professional Association of German Pathologists wants to support their members in their thoughts and potential implementation of virtual microscopy and related issues. It founded a committee of digital pathology. Colleagues experienced in routine surgical pathology, information technology and practice have been asked to investigate prerequisites, actual technology stages and financial considerations, and to formulate their recommendations and guidelines. Herein, the official guidelines of the Professional Association of German Pathologists are presented. The guidelines focus on practical issues, Pathologists as well as IT experts or interested researchers are invited to make use of these guidelines. Our readers are also invited to inquire specific tasks or discuss their ideas and experiences. They might either contact the committee directly, or discuss specific points of view by writing a letter to the editor, or by submission of, and to formulate a corresponding interactive publication

Image standards in Tissue-Based Diagnosis (Diagnostic Surgical Pathology)

© 2008 Kayser et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution Licens

The diagnostic path, a useful visualisation tool in virtual microscopy

BACKGROUND: The Virtual Microscopy based on completely digitalised histological slide. Concerning this digitalisation many new features in mircoscopy can be processed by the computer. New applications are possible or old, well known techniques of image analyses can be adapted for routine use. AIMS: A so called diagnostic path observes in the way of a professional sees through a histological virtual slide combined with the text information of the dictation process. This feature can be used for image retrieval, quality assurance or for educational purpose. MATERIALS AND METHODS: The diagnostic path implements a metadata structure of image information. It stores and processes the different images seen by a pathologist during his "slide viewing" and the obtained image sequence ("observation path"). Contemporary, the structural details of the pathology reports were analysed. The results were transferred into an XML structure. Based on this structure, a report editor and a search function were implemented. The report editor compiles the "diagnostic path", which is the connection from the image viewing sequence ("observation path") and the oral report sequence of the findings ("dictation path"). The time set ups of speech and image viewing serve for the link between the two sequences. The search tool uses the obtained diagnostic path. It allows the user to search for particular histological hallmarks in pathology reports and in the corresponding images. RESULTS: The new algorithm was tested on 50 pathology reports and 74 attached histological images. The creation of a new individual diagnostic path is automatically performed during the routine diagnostic process. The test prototype experienced an insignificant prolongation of the diagnosis procedure (oral case description and stated diagnosis by the pathologist) and a fast and reliable retrieval, especially useful for continuous education and quality control of case description and diagnostic work. DISCUSSION: The Digital Virtual Microscope has been designed to handle 1000 images per day in the daily routine work of a pathology institution. It implies the necessity of an automatic mechanism of image meta dating. The non – deterministic correlation between the oral statements (case report) and image information content guides the image meta dating. The presented software opens up new possibilities for a content oriented search in a virtual slide, and can successfully support medical education and diagnostic quality assurance

Diagnosis of congenital heart malformations -possibilities for the employment of telepathology

Goal: In a study of 10 autopsy cases with congenital cardiac malformations we investigated whether obtaining a second opinion by means of telepathology could satisfy quality standards for the diagnosis of cardiac malformations and what the advantages and disadvantages of such a procedure might be. Material: The investigatory samples were 10 formalinfixed hearts with complex malformations from 9 fetuses and one newborn on which autopsies had been performed at the Pathological Institute of the Charité Hospital. The requests for a second opinion, which included text and image data, were sent in the form of Microsoft PowerPoint presentations to 5 experts in 4 countries. Per case the number of images that were sent was between 3 and 7. The size of the files was between 439 and 942 kb. The time required for preparation of the cases for sending them to the specialists was between 1 and 2 hours: this encompassed the time for putting the notation on the images, compressing them, creating a file that included both the images and the clinical data and then sending the case file. Results: All 10 cardiac malformations were correctly identified. In 8 of the 10 cases at least one expert had questions. After these questions had been answered and further images had been sent final correct diagnoses were made in all cases. All experts said that the quality of the images was very good. Use of a standardized findings questionnaire, which also included the marking of anatomic structures and of pathological findings in the images, proved useful. Standardized findings forms facilitate orientation during interpretation of the cases and should be used generally to avoid misunderstandings in telepathological communication. Conclusions: In general it is possible to obtain an effective and reliable diagnosis of congenital heart malformations by means of telepathology. It is far quicker to get a second opinion by this means than by conventional means

Alpine freshwater fish biodiversity assessment: an inter-calibration test for metabarcoding method set up

The analysis of environmental DNA (eDNA) by high throughput sequencing (HTS) is proving to be a promising tool for freshwater fish biodiversity assessment in Europe within the Water Framework Directive (WFD, 2000/60/EC), especially for large rivers and lakes where current fish monitoring techniques have known shortcomings. These new biomonitoring methods based on eDNA show several advantages compared to classical morphological methods. The sampling procedures are easier and cheaper and eDNA metabarcoding is non-invasive and very sensitive, allowing for the detection of traces of DNA. However, eDNA metabarcoding methods need careful standardization to make the results of different surveys comparable. The aim of the EU project Eco-AlpsWater is to test and validate molecular biodiversity monitoring tools for aquatic ecosystems (i.e., eDNA metabarcoding) to improve the traditional WFD monitoring approaches in Alpine waterbodies. To this end, an inter-calibration test was performed using fish mock community samples containing either tissue-extracted DNA, eDNA collected from aquaculture tanks and eDNA samples collected from Lake Bourget (France). Samples were analysed using a DNA metabarcoding approach, relying on the amplification and HTS of a 12S rDNA marker, in two separate laboratories, to evaluate if different laboratory and bioinformatic protocols can provide a reliable and comparable description of the fish communities in both mock and natural samples. Our results highlight good replicability of the molecular laboratory protocols for HTS and good amplification success of selected primers, providing essential information concerning the taxonomic resolution of the 12S mitochondrial marker in describing the Alpine fish communities. Interestingly, different concentrations of species DNA in the mock samples were well represented by the relative DNA reads abundance. These tests confirm the reproducibility of eDNA metabarcoding analyses for the biomonitoring of freshwater fish inhabiting Alpine and peri-Alpine lakes and river

DNA methylation signatures predicting bevacizumab efficacy in metastatic breast cancer

Background: Biomarkers predicting response to bevacizumab in breast cancer are still missing. Since epigenetic modifications can contribute to an aberrant regulation of angiogenesis and treatment resistance, we investigated the influence of DNA methylation patterns on bevacizumab efficacy. Methods: Genome-wide methylation profiling using the Illumina Infinium HumanMethylation450 BeadChip was performed in archival FFPE specimens of 36 patients with HER2-negative metastatic breast cancer treated with chemotherapy in combination with bevacizumab as first-line therapy (learning set). Based on objective response and progression-free survival (PFS) and considering ER expression, patients were divided in responders (R) and non-responders (NR). Significantly differentially methylated gene loci (CpGs) with a strong change in methylation levels (>0.15 or <-0.15) between R and NR were identified and further investigated in 80 bevacizumab-treated breast cancer patients (optimization set) and in 15 patients treated with chemotherapy alone (control set) using targeted deep amplicon bisulfite sequencing. Methylated gene loci were considered predictive if there was a significant association with outcome (PFS) in the optimization set but not in the control set using Spearman rank correlation, Cox regression, and logrank test. Results: Differentially methylated loci in 48 genes were identified, allowing a good separation between R and NR (odds ratio (OR) 101, p<0.0001). Methylation of at least one cytosine in 26 gene-regions was significantly associated with progression-free survival (PFS) in the optimization set, but not in the control set. Using information from the optimization set, the panel was reduced to a 9-gene signature, which could divide patients from the learning set into 2 clusters, thereby predicting response with an OR of 40 (p<0.001) and an AUC of 0.91 (LOOCV). A further restricted 3-gene methylation model showed a significant association of predicted responders with longer PFS in the learning and optimization set even in multivariate analysis with an excellent and good separation of R and NR with AUC=0.94 and AUC=0.86, respectively. Conclusion: Both a 9-gene and 3-gene methylation signature can discriminate between R and NR to a bevacizumab-based therapy in MBC and could help identify patients deriving greater benefit from bevacizumab.(VLID)251037