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Ilyas M. Next-Generation Sequencing in Diagnostic Pathology. Pathobiology 2017; 84:292-305. [PMID: 29131018 DOI: 10.1159/000480089] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 08/06/2017] [Indexed: 12/26/2022] Open
Abstract
Interrogation of tissue informs on patient management through delivery of a diagnosis together with associated clinically relevant data. The diagnostic pathologist will usually evaluate the morphological appearances of a tissue sample and, occasionally, the pattern of expression of a limited number of biomarkers. Recent developments in sequencing technology mean that DNA and RNA from tissue samples can now be interrogated in great detail. These new technologies, collectively known as next-generation sequencing (NGS), generate huge amounts of data which can be used to support patient management. In order to maximize the utility of tissue interrogation, the molecular data need to be interpreted and integrated with the morphological data. However, in order to interpret the molecular data, the pathologist must understand the utility and the limitations of NGS data. In this review, the principles behind NGS technologies are described. In addition, the caveats in the interpretation of the data are discussed, and a scheme is presented to "classify" the types of data which are generated. Finally, a glossary of new terminology is included to help pathologists become familiar with the lexicon of NGS-derived molecular data.
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Wong DD, Low IC, Peverall J, Robbins PD, Spagnolo DV, Nairn R, Carey-Smith RL, Wood D. MDM2/CDK4 gene amplification in large/deep-seated 'lipomas': incidence, predictors and clinical significance. Pathology 2016; 48:203-9. [PMID: 27020493 DOI: 10.1016/j.pathol.2016.02.007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2015] [Revised: 11/26/2015] [Accepted: 12/06/2015] [Indexed: 11/30/2022]
Abstract
This study of 140 cases assessed the incidence of MDM2/CDK4 gene amplification in lipomatous neoplasms with histological features of a lipoma but which were of clinical concern due to large size (≥50 mm) and/or deep-seated (subfascial) location. Univariate and multivariate statistical analyses were used to identify clinical, radiological and pathological predictors of gene amplification. Differences in local recurrence rates between amplified and non-amplified cases were assessed using survival analysis. The findings indicate that the incidence of MDM2/CDK4 amplification in this setting is low at 5% (95%CI 1.4-8.6%). Variables associated with amplification on univariate analysis were tumour site (thigh, p = 0.004), size (>100 mm, p = 0.033) and presence of equivocal atypia (p = 0.001). Independent predictors on multivariate analysis were size (OR 3.9, 95%CI 1.4-11.3, p = 0.012) and presence of equivocal atypia (OR 12.5, 95%CI 1.9-80.3, p = 0.008). There was no significant difference in local recurrence rates between amplified and non-amplified cases (p = 0.461) based on a median follow-up time of 31 months. Assessment for MDM2/CDK4 amplification, therefore, should be considered in 'lipomas' which are >100 mm in size, show equivocal atypia and arise in the thigh. However, the clinical significance of gene amplification in this setting is unclear and requires confirmation in larger studies.
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Affiliation(s)
- Daniel D Wong
- Department of Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia; School of Pathology and Laboratory Medicine, University of Western Australia, Crawley, WA, Australia.
| | - Irene C Low
- Department of Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia
| | - Joanne Peverall
- Department of Diagnostic Genomics, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia
| | - Peter D Robbins
- Department of Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia
| | - Dominic V Spagnolo
- Department of Anatomical Pathology, PathWest Laboratory Medicine, QEII Medical Centre, Nedlands, WA, Australia
| | - Robert Nairn
- Department of Radiology, Sir Charles Gairdner Hospital, Nedlands, WA, Australia
| | | | - David Wood
- Perth Orthopaedic Institute, Nedlands, WA, Australia
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Squamous Cell Carcinoma Arising From Massive Localized Lymphedema of Scrotum Mimicking Scrotal Smooth Muscle Hamartoma of Dartos: A Case Report. Am J Dermatopathol 2015; 37:551-4. [PMID: 26091513 DOI: 10.1097/dad.0000000000000135] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Massive localized lymphedema (MLL) is an uncommon benign skin lesion typically presenting with prominent edema and vascular proliferation in the adipose tissue of lower limbs. When rarely occurring in scrotum, it instead is characterized by a striking proliferation of dermal smooth muscle bundles mimicking acquired smooth muscle hamartoma of dartos. The authors report a rare case of scrotal MLL. A 57-year-old obese man with a history of previous surgery for rectal adenocarcinoma, 20 years earlier, presented with progressive nodular enlargement of the scrotum for 2 years, causing discomfort, difficulty in ambulation, and cosmetic problems. The preoperative radiographic investigation revealed thickening of the scrotal wall with multiple soft-tissue nodules. The patient underwent a wide excision of the scrotal wall, perineum, and penile skin. The pathological examination showed a scrotal MLL associated with well-differentiated squamous cell carcinoma. The authors speculate that prior radiotherapy and surgery together with morbid obesity led to long-standing lymphedema that triggered the proliferation of smooth muscle cells, chronic epidermal change, and finally squamous cell carcinoma.
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Mussi CE, Daolio P, Cimino M, Giardina F, De Sanctis R, Morenghi E, Parafioriti A, Bartoli MS, Bastoni S, Cozzaglio L, Colombo P, Quagliuolo V. Atypical Lipomatous Tumors: Should They be Treated Like Other Sarcoma or Not? Surgical Consideration from a Bi-Institutional Experience. Ann Surg Oncol 2014; 21:4090-7. [DOI: 10.1245/s10434-014-3855-7] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2014] [Indexed: 11/18/2022]
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ElMoneim HMA, El Sherbiny YM. Evaluation of immunohistochemical expression of MDM2 protein in comparison with MDM2 gene amplification in diagnosing lipomatous tumors. EGYPTIAN JOURNAL OF PATHOLOGY 2011; 31:92-97. [DOI: 10.1097/01.xej.0000406597.88861.1e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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Molecular Testing for Lipomatous Tumors: Critical Analysis and Test Recommendations Based on the Analysis of 405 Extremity-based Tumors. Am J Surg Pathol 2010; 34:1304-11. [DOI: 10.1097/pas.0b013e3181e92d0b] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Bogusz AM, Hussey SM, Kapur P, Yan Peng, Tunc Gokaslan S. Massive Localized Lymphedema With Unusual Presentations: Report of 2 Cases and Review of the Literature. Int J Surg Pathol 2008; 19:212-6. [DOI: 10.1177/1066896908320833] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Massive localized lymphedema is a benign soft tissue lesion that usually presents as a large mass in morbidly obese adults. The diagnosis may be challenging as it can mimic other lesions, including well-differentiated liposarcoma. We report 2 cases of massive localized lymphedema with unusual presentation. The first case is a recurrent massive localized lymphedema in the right thigh of a 40-year-old morbidly obese woman. In addition to typical massive localized lymphedema features such as prominent edema and vascular proliferation in the adipose tissue, we observed prominent and abundant multinucleated stromal floret-like giant cells, arborizing network of capillaries, and areas of hyalinized collagen. Our second case is in a rare location (scrotum extending into penile soft tissue) in an overweight 55-year-old male. This lesion exhibits striking smooth muscle hyperplasia. Lack of staining by antibodies against murine double minute 2 protein and cyclin dependent kinase 4 and absence of high mobility group AT- hook 2 transcription factor rearrangement by fluorescence in situ hybridization support our diagnosis of massive localized lymphedema in both cases.
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Affiliation(s)
- Agata M. Bogusz
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sean M. Hussey
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Payal Kapur
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - Yan Peng
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas
| | - S. Tunc Gokaslan
- Department of Pathology, The University of Texas Southwestern Medical Center, Dallas, Texas,
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Hameed M. Pathology and genetics of adipocytic tumors. Cytogenet Genome Res 2007; 118:138-47. [DOI: 10.1159/000108294] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2006] [Accepted: 03/26/2007] [Indexed: 11/19/2022] Open
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Cleynen I, Brants JR, Peeters K, Deckers R, Debiec-Rychter M, Sciot R, Van de Ven WJM, Petit MMR. HMGA2 regulates transcription of the Imp2 gene via an intronic regulatory element in cooperation with nuclear factor-kappaB. Mol Cancer Res 2007; 5:363-72. [PMID: 17426251 DOI: 10.1158/1541-7786.mcr-06-0331] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
IMP2 (insulin-like growth factor-II mRNA binding protein 2) is an oncofetal protein that is aberrantly expressed in several types of cancer. We recently identified the Imp2 gene as a target gene of the architectural transcription factor HMGA2 (high mobility group A2) and its tumor-specific truncated form HMGA2Tr. In this study, we investigated the mechanism via which HMGA2 regulates Imp2 gene expression. We show that HMGA2 and HMGA2Tr directly regulate transcription of the Imp2 gene by binding to an AT-rich regulatory region located in the first intron. In reporter experiments, we show that this AT-rich regulatory region mimics the response of the endogenous Imp2 gene to HMGA2 and HMGA2Tr. Furthermore, we show that a consensus nuclear factor-kappaB (NF-kappaB) binding site located immediately adjacent to the AT-rich regulatory region binds NF-kappaB and that NF-kappaB and HMGA2 cooperate to regulate Imp2 gene expression. Finally, we provide evidence that there is a strong and statistically significant correlation between HMGA2 and IMP2 gene expression in human liposarcomas.
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Affiliation(s)
- Isabelle Cleynen
- Department of Human Genetics, Flanders Interuniversity Institute for Biotechnology, University of Leuven, Herestraat 49, Box 602, B-3000 Leuven, Belgium
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Abstract
BACKGROUND Both trauma and lipomas are frequently encountered in day-to-day clinical practice. Although lipomas are defined both clinically and pathologically as benign fatty tissue tumours, their aetiology is still not clear. METHODS In this study 19 patients with 23 posttraumatic lipomas were analysed retrospectively with reference to ultrasound and MRI diagnosis, history, laboratory results and histopathological investigations. RESULTS The mean age of the patients was 50.5 years (+/-15.5). The causative soft tissue trauma dated back an average of 2.6 years. When the histories were taken, 16 of the 19 patients reported vast, slow-resorbing posttraumatic haematomas. Nine of the 23 lipomas were sited in the upper extremity, 3 in the lower extremity, 9 in the trunk and 2 in the face. All were located epifascially. In 22 cases the lipomas were excised, and in 1 case the lipoma was removed by liposuction. Histological examination demonstrated capsulated benign fatty tissue tumours in 19 cases and uncapsulated benign fatty tissue tumours in 4. The average body mass index (BMI) was 29 kg/m(2). Removal of the tumour resulted in a good aesthetic result in all patients. CONCLUSIONS The link between a blunt soft tissue injury and the development of a posttraumatic lipoma is still the subject of controversy; there are two mechanisms that seem more likely than any others proposed: (1) the "pseudolipoma" as the result of a prolapse of fatty tissue as an immediate result of trauma and (2) the development of a lipoma by way of differentiation of pre-adipocytes mediated by cytokines released by a posttraumatic haematoma. There appears to be a correlation between an increased partial thromboplastin time (PTT) and the development of posttraumatic lipomas. The generalised increase in the volume of body fat documented by the elevated BMI supports the idea that lipomas arise from the prolapse of adipose tissue. However, there is no single mechanistic explanation for the development of posttraumatic lipomas. They are probably caused by multiple factors and not by isolated pathological mechanisms.
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Affiliation(s)
- M C Aust
- Klinik für Plastische-, Hand- und Wiederherstellungschirurgie, Medizinische Hochschule Hannover, Carl-Neubergstr. 1, 30625 Hannover, Deutschland
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Cunningham KS, Veinot JP, Feindel CM, Butany J. Fatty lesions of the atria and interatrial septum. Hum Pathol 2006; 37:1245-51. [PMID: 16949930 DOI: 10.1016/j.humpath.2006.04.028] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/02/2005] [Revised: 04/25/2006] [Accepted: 04/27/2006] [Indexed: 10/24/2022]
Abstract
Lipomatous lesions of the heart involving the atria and interatrial septum are not well known. Most such lesions do not become clinically significant; however, intractable arrhythmias, blood flow obstruction, and valvular disruption may result from extensive fatty infiltration of the atrial wall or from the mass effect of benign or malignant lipomatous tumors. Some fatty lesions may be difficult to characterize radiologically, and misdiagnosis may lead to unnecessary surgical interventions. We describe the pathology of the most common fatty lesions and underscore some of the radiographic and surgical issues pertaining to the diagnosis and management of these masses.
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Affiliation(s)
- Kristopher S Cunningham
- Department of Pathology, University Health Network, University of Toronto, Toronto, Ontario, Canada M5G 2C4
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Boultwood J, Wainscoat JS. High-mobility group A (HMGA) genes: from solid to liquid tumours? Leukemia 2004; 19:195-6. [PMID: 15618962 DOI: 10.1038/sj.leu.2403606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- J Boultwood
- LRF Molecular Haematology Unit, University of Oxford, John Radcliffe Hospital, Oxford, UK.
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