Malignant rhabdoid tumor of the orbit in an infant.

We present the case of an infant with rapidly progressing orbital tumor that had initial radiological and clinical features of both rhabdomyosarcoma and capillary hemangioma. The patient was eventually diagnosed with malignant rhabdoid tumor of the orbit. We discuss the salient histological and radiological features of our case and review the literature on orbital malignant rhabdoid tumors.

QuPath Algorithm Accurately Identifies MLH1-Deficient Inflammatory Bowel Disease-Associated Colorectal Cancers in a Tissue Microarray.

Current methods for analysing immunohistochemistry are labour-intensive and often confounded by inter-observer variability. Analysis is time consuming when identifying small clinically important cohorts within larger samples. This study trained QuPath, an open-source image analysis program, to accurately identify MLH1-deficient inflammatory bowel disease-associated colorectal cancers (IBD-CRC) from a tissue microarray containing normal colon and IBD-CRC.

Gorham-Stout case report: a multi-omic analysis reveals recurrent fusions as new potential drivers of the disease.

Background: Gorham-Stout disease is a rare condition characterized by vascular proliferation and the massive destruction of bone tissue. With less than 400 cases in the literature of Gorham-Stout syndrome, we performed a unique study combining whole-genome sequencing and RNA-Seq to probe the genomic features and differentially expressed pathways of a presented case, revealing new possible drivers and biomarkers of the disease.

Case Presentation: We present a case report of a white 45-year-old female patient with marked bone loss of the left humerus associated with vascular proliferation, diagnosed with Gorham-Stout disease.

The differential expression of micro-RNAs 21, 200c, 204, 205, and 211 in benign, dysplastic and malignant melanocytic lesions and critical evaluation of their role as diagnostic biomarkers.

Overlapping histological features between benign and malignant lesions and a lack of firm diagnostic criteria for malignancy result in high rates of inter-observer variation in the diagnosis of melanocytic lesions. We aimed to investigate the differential expression of five miRNAs (21, 200c, 204, 205, and 211) in benign naevi (n = 42), dysplastic naevi (n = 41), melanoma in situ (n = 42), and melanoma (n = 42) and evaluate their potential as diagnostic biomarkers of melanocytic lesions. Real-time PCR showed differential miRNA expression profiles between benign naevi; dysplastic naevi and melanoma in situ; and invasive melanoma.

A novel next generation sequencing approach to improve sarcoma diagnosis.

Sarcoma is a rare disease affecting both bone and connective tissue and with over 100 pathologic entities, differential diagnosis can be difficult. Complementing immune-histological diagnosis with current ancillary diagnostic techniques, including FISH and RT-PCR, can lead to inconclusive results in a significant number of cases. We describe here the design and validation of a novel sequencing tool to improve sarcoma diagnosis.

Sequencing-based microsatellite instability testing using as few as six markers for high-throughput clinical diagnostics.

Microsatellite instability (MSI) testing of colorectal cancers (CRCs) is used to screen for Lynch syndrome (LS), a hereditary cancer-predisposition, and can be used to predict response to immunotherapy. Here, we present a single-molecule molecular inversion probe and sequencing-based MSI assay and demonstrate its clinical validity according to existing guidelines. We amplified 24 microsatellites in multiplex and trained a classifier using 98 CRCs, which accommodates marker specific sensitivities to MSI.

Neoplastic cell percentage estimation in tissue samples for molecular oncology: recommendations from a modified Delphi study.

Aims: Results from external quality assessment revealed considerable variation in neoplastic cell percentages (NCP) estimation in samples for biomarker testing. As molecular biology tests require a minimal NCP, overestimations may lead to false negative test results. We aimed to develop recommendations to improve the NCP determination in a prototypical entity - colorectal carcinoma - that can be adapted for other cancer types.

A novel panel of short mononucleotide repeats linked to informative polymorphisms enabling effective high volume low cost discrimination between mismatch repair deficient and proficient tumours.

Somatic mutations in mononucleotide repeats are commonly used to assess the mismatch repair status of tumours. Current tests focus on repeats with a length above 15bp, which tend to be somatically more unstable than shorter ones. These longer repeats also have a substantially higher PCR error rate, and tests that use capillary electrophoresis for fragment size analysis often require expert interpretation.

Validation of the Oncomine focus panel for next-generation sequencing of clinical tumour samples.

The clinical utility of next-generation sequencing (NGS) for a diverse range of targets is expanding, increasing the need for multiplexed analysis of both DNA and RNA. However, translation into daily use requires a rigorous and comprehensive validation strategy. The aim of this clinical validation was to assess the performance of the Ion Torrent Personal Genome Machine (IonPGM) and validate the Oncomine Focus DNA and RNA Fusion panels for clinical application in solid tumour testing of formalin-fixed, paraffin-embedded (FFPE) tissue.

Mutational Analysis Identifies Therapeutic Biomarkers in Inflammatory Bowel Disease-Associated Colorectal Cancers.

Inflammatory bowel disease-associated colorectal cancers (IBD-CRC) are associated with a higher mortality than sporadic colorectal cancers. The poorly defined molecular pathogenesis of IBD-CRCs limits development of effective prevention, detection, and treatment strategies. We aimed to identify biomarkers using whole-exome sequencing of IBD-CRCs to guide individualized management.

N_LyST: a simple and rapid screening test for Lynch syndrome.

Aims: We sought to use PCR followed by high-resolution melting analysis to develop a single closed-tube screening panel to screen for Lynch syndrome. This comprises tests for microsatellite instability (MSI), MLH1 methylation promoter and mutation.

Methods: For MSI testing, five mononucleotide markers (BAT25, BAT26, BCAT25, , ) were developed.

A33 shows similar sensitivity to but is more specific than CDX2 as an immunomarker of colorectal carcinoma.

Aims: CDX2 is widely used as a sensitive and specific immunomarker for colorectal carcinoma (CRC), but neither its sensitivity nor its specificity is absolute. The aim of this study was to compare CDX1 and A33 with CDX2 as immunomarkers for CRC.

Methods And Results: As a pilot study, whole sections of 51 cases of liver metastatic carcinoma with different origins-colorectum (n = 32), breast (n = 3), oesophagogastric tract (n = 4), lung (n = 3), pancreas (n = 8), and prostate (n = 1)-were immunostained with CDX1, CDX2, and A33.

Could molecular pathology testing in lung cancer be more cost-effective?

Aims: EGFR and ALK analysis is routinely undertaken prior to targeted treatment of non-squamous non-small cell lung carcinoma (NSCLC). Increasingly, limited resources require molecular pathology services to be cost-effective without detriment to patient care.

Methods: Data from an audit of molecular pathology testing in the South East Scotland Cancer Network (SCAN) network have been used to explore different testing strategies with the aim of reducing costs; including investigation of thyroid transcription factor 1 (TTF1) expression as a negative predictor for EGFR mutations.

Novel histopathologic feature identified through image analysis augments stage II colorectal cancer clinical reporting.

A number of candidate histopathologic factors show promise in identifying stage II colorectal cancer (CRC) patients at a high risk of disease-specific death, however they can suffer from low reproducibility and none have replaced classical pathologic staging. We developed an image analysis algorithm which standardized the quantification of specific histopathologic features and exported a multi-parametric feature-set captured without bias. The image analysis algorithm was executed across a training set (n = 50) and the resultant big data was distilled through decision tree modelling to identify the most informative parameters to sub-categorize stage II CRC patients.

Quantification of tumour budding, lymphatic vessel density and invasion through image analysis in colorectal cancer.

Background: Tumour budding (TB), lymphatic vessel density (LVD) and lymphatic vessel invasion (LVI) have shown promise as prognostic factors in colorectal cancer (CRC) but reproducibility using conventional histopathology is challenging. We demonstrate image analysis methodology to quantify the histopathological features which could permit standardisation across institutes and aid risk stratification of Dukes B patients.

Methods: Multiplexed immunofluorescence of pan-cytokeratin, D2-40 and DAPI identified epithelium, lymphatic vessels and all nuclei respectively in tissue sections from 50 patients diagnosed with Dukes A (n = 13), Dukes B (n = 29) and Dukes C (n = 8) CRC.

Human tissue in systems medicine.

Histopathology, the examination of an architecturally artefactual, two-dimensional and static image remains a potent tool allowing diagnosis and empirical expectation of prognosis. Considerable optimism exists that the advent of molecular genetic testing and other biomarker strategies will improve or even replace this ancient technology. A number of biomarkers already add considerable value for prediction of whether a treatment will work.

Ex vivo water diffusion tensor properties of the fibroid uterus at 7 T and their relation to tissue morphology.

Purpose: To investigate the water diffusion tensor properties of ex vivo tissue in the fibroid uterus, including the influence of degeneration, and the relevance of the principal eigenvector orientation to the underlying tissue structure.

Materials And Methods: Following hysterectomy, high-resolution structural T(2) -weighted and diffusion tensor magnetic resonance imaging (DT-MRI) were performed on nine uteri at 7 T. Mean diffusivity (MD), fractional anisotropy (FA), and principal eigenvector orientation were measured in myometrium and in myxoid and dense tissue in fibroids.

Hepatic resection for metastatic endometrioid carcinoma.

Background: The role of hepatic resection for gynaecological tumours is not well defined as evidence on the subject is lacking. This article describes a tertiary hepatopancreatobiliary unit's experience with hepatic resection for liver metastases from endometrioid primaries.

Methods: Five women in whom liver metastases developed at 11 months to 10 years post-primary resection are presented.

Post-surgical Pancreatitis Masquerading as Recurrent Neuroendocrine Cancer.

Neuroendocrine tumours of the pancreas can have a spectrum of behaviour from relatively benign to aggressive. Resection can result in cure although metastatic disease is described. We present an unusual case of an apparent local recurrence of previously resected neuroendocrine tumour in a young man who had undergone distal pancreatectomy.

Expression of Sonic hedgehog pathway genes is altered in colonic neoplasia.

The Hedgehog (Hh) signalling pathway is crucial for normal development and patterning of numerous human organs including the gut. Hh proteins are also expressed during gastric gland development and gastric epithelial differentiation in adults. Recently, dysregulation of these developmentally important genes has been implicated in cancer, leading to the present study of the expression of Hh signalling proteins in colon cancer.