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Eluri S.,University of North Carolina at Chapel Hill | Brugge W.R.,Massachusetts General Hospital | Daglilar E.S.,Massachusetts General Hospital | Jackson S.A.,Interpace Diagnostics Corporation | And 5 more authors.
American Journal of Gastroenterology | Year: 2015

Risk stratification in Barrett's esophagus (BE) is challenging. We evaluated the ability of a panel of genetic markers to predict progression to high-grade dysplasia (HGD) or esophageal adenocarcinoma (EAC).METHODS:In this case-control study, we assessed a measure of genetic instability, the mutational load (ML), in predicting progression to HGD or EAC. Cases had nondysplastic BE or low-grade dysplasia (LGD) at baseline and developed HGD/EAC ≥1 year later. Controls were matched 2:1, had nondysplastic BE or LGD, and no progression at follow-up. Formalin-fixed, paraffin-embedded tissue was microdissected for the epithelium. Loss of heterozygosity (LOH) and microsatellite instability (MSI) were assessed. ML was calculated from derangements in 10 genomic loci. High-clonality LOH mutations were assigned a value of 1, low-clonality mutations were assigned a value of 0.5, and MSI 0.75 at the first loci, and 0.5 for additional loci. These values were summed to the ML. Receiver operator characteristic (ROC) curves were created.RESULTS:There were 69 patients (46 controls and 23 cases). Groups were similar in age, follow-up time, baseline histology, and the number of microdissected targets. Mean ML in pre-progression biopsies was higher in cases (2.21) than in controls (0.42; P<0.0001). Sensitivity was 100% at ML ≥0.5 and specificity was 96% at ML ≥1.5. Accuracy was highest at 89.9% for ML ≥1. ROC curves for ML ≥1 demonstrated an area under the curve (AUC) of 0.95.CONCLUSIONS:ML in pre-progression BE tissue predicts progression to HGD or EAC. Although further validation is necessary, ML may have utility as a biomarker in endoscopic surveillance of BE. © 2015 by the American College of Gastroenterology.

PubMed | Akesogen, Genospace, Llc and PathGroup
Type: Journal Article | Journal: Cancer genetics | Year: 2016

The development of targeted therapies based on specific genomic alterations has altered the treatment and management of lung and colorectal cancers. Chromosomal microarray (CMA) has allowed identification of copy number variations (CNVs) in lung and colorectal cancers in great detail, and next-generation sequencing (NGS) is used extensively to analyze the genome of cancers for molecular subtyping and use of molecularly guided therapies. The main objective of this study was to evaluate the utility of combining CMA and NGS for a comprehensive genomic assessment of lung and colorectal adenocarcinomas, especially for detecting drug targets. We compared the results from NGS and CMA data from 60 lung and 51 colorectal tumors. From CMA analysis, 33% were amplified, 89% showed gains, 75% showed losses and 41% demonstrated loss of heterozygosity; pathogenic variants were identified in 81% of colon and 67% lung specimens through NGS. KRAS mutations commonly occurred with loss in TP53 and there was significant loss of BRCA1 and NF1 among male patients with lung cancer. For clinically actionable targets, 23% had targetable CNVs when no pathogenic variants were detected by NGS. The data thus indicate that combining the two approaches provides significant benefit in a routine clinical setting not available by NGS alone.

BRENTWOOD, Tenn.--(BUSINESS WIRE)--PathGroup, one of the largest private providers of anatomic pathology and clinical lab services in the U.S., today announced a new partnership with the Centers for Disease Control and Prevention (CDC) and the California Department of Public Health that standardizes nationwide state cancer registry data and reporting, enabling physicians, surgeons and researchers to make data-driven treatment decisions with real-time information and analyses. Facilitated by the

Policarpio-Nicolas M.L.C.,University of Texas Health Science Center at San Antonio | Avery D.L.,PathGroup | Hartley T.,University of Texas Health Science Center at San Antonio
CytoJournal | Year: 2015

The most common site of metastasis to ascitic fluid in females is from a mullerian (ovarian) primary, whereas in males it is from the gastrointestinal tract. Metastatic Merkel cell carcinoma (MCC) to the ascitic fluid is extremely rare and may present as a diagnostic challenge on effusion cytology. In a review of the literature, there are only two case reports of metastatic MCC in pleural effusion. To the best of our knowledge, we present the first cytological diagnosis of MCC metastatic to the ascitic fluid. We describe the cytologic findings as well as the immunohistochemical stains supportive of the diagnosis. Given the fatal prognosis of this tumor compared to melanoma and rarity of its occurrence in ascitic fluid, awareness of this tumor and use of immunohistochemical stains are critical in arriving at the diagnosis.

Lennon A.,PathGroup
Clinical laboratory science : journal of the American Society for Medical Technology | Year: 2011

Some clinical laboratories require workers who have basic knowledge in molecular techniques (such as fluorescent in situ hybridization and polymerase chain reaction). Exclusively molecular diagnostic laboratories need workers to be competent in a variety of cutting edge molecular technologies, such as DNA sequencing, array-based comparative genomic hybridization, quantitative polymerase chain reaction, and many other techniques. Having only one certification for molecular biology at the entry level, as newly prescribed by the Board of Certification, doesn't accurately define the two very differently trained types of people these differing types of laboratories require. Creating a second molecular certification, at the specialist level, would address this issue positively.

Bhaskara S.,Vanderbilt University | Knutson S.K.,Vanderbilt University | Jiang G.,Vanderbilt University | Chandrasekharan M.B.,Vanderbilt University | And 16 more authors.
Cancer Cell | Year: 2010

Hdac3 is essential for efficient DNA replication and DNA damage control. Deletion of Hdac3 impaired DNA repair and greatly reduced chromatin compaction and heterochromatin content. These defects corresponded to increases in histone H3K9,K14ac; H4K5ac; and H4K12ac in late S phase of the cell cycle, and histone deposition marks were retained in quiescent Hdac3-null cells. Liver-specific deletion of Hdac3 culminated in hepatocellular carcinoma. Whereas HDAC3 expression was downregulated in only a small number of human liver cancers, the mRNA levels of the HDAC3 cofactor NCOR1 were reduced in one-third of these cases. siRNA targeting of NCOR1 and SMRT (NCOR2) increased H4K5ac and caused DNA damage, indicating that the HDAC3/NCOR/SMRT axis is critical for maintaining chromatin structure and genomic stability. © 2010 Elsevier Inc.

Fox M.D.,NorthShore University HealthSystem | Billings S.D.,Cleveland Clinic | Gleason B.C.,PathGroup | Thomas A.B.,NorthShore University HealthSystem | Cibull T.L.,NorthShore University HealthSystem
Journal of Cutaneous Pathology | Year: 2013

Cutaneous meningiomas are divided into three groups. Type I lesions present at birth and are derived from ectopic arachnoid cells. Type II lesions usually present in adults and are derived from arachnoid cells surrounding nerve bundles. Type III lesions are due to direct extension or metastasis from dural-based neoplasms. Dural-based meningiomas are known to express p63. The aim of our study is to examine the expression of p63 in type II and type III meningioma. Two cases of cutaneous meningioma (type II and type III) were evaluated for the expression of p63, EMA, CK 5/6, S100 and CD31. The cells of interest were spindled to epithelioid and arranged in a whorling pattern. Immunohistochemical staining showed expression of EMA and p63 in both cases, while stains for CK 5/6, S100 and CD31 were negative. Among cutaneous tumors, p63 is considered a marker of epithelial derivation, as it is positive in epidermal and adnexal neoplasms. It is important to be aware of p63 expression in the context of cutaneous meningioma to avoid misinterpretation as an epithelial tumor. On the basis of our small study, it is unlikely that p63 expression would be helpful in distinguishing between type II and type III meningioma, as both may be p63-positive. © 2013 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Matsukuma K.,PathGroup
American Journal of Surgical Pathology | Year: 2016

We have identified 8 cases of gastritis characterized by the presence of purple to black granular deposits in the superficial mucosa associated with marked reactive epithelial changes. In each case, the patient had taken OsmoPrep, a tablet form of sodium phosphate used for bowel preparation just before upper endoscopy and had undergone concurrent colonoscopy. Endoscopic findings ranged from normal gastric mucosa to severe inflammation, congestion, and friability. No other gastrointestinal sites were noted to contain the deposits or show similar mucosal injury. On initial histologic review, the deposits raised the differential diagnosis of elemental iron and mucosal calcinosis. However, none of the patients was noted to be taking iron supplements, and none had a history of renal disease or other cause of calcium dysmetabolism. Histochemical stains revealed the deposits were negative on Perls’ iron stain (8/8 cases), positive on von Kossa stain (7/8 cases), and negative on Alizarin Red stain (8/8 cases)—a histochemical profile compatible with sodium phosphate but inconsistent with mucosal calcium. A crushed OsmoPrep tablet was subjected to processing and demonstrated similar histologic features and histochemical profile. In addition, biopsies of 20 consecutive patients who did not take OsmoPrep and who underwent concurrent endoscopy and colonoscopy were reviewed, and no deposits with similar histochemical profile were identified. In summary, we have characterized a unique form of gastritis associated with OsmoPrep use. Attention to clinical history and use of a select panel of histochemical stains allow for accurate diagnosis. Copyright © 2016 Wolters Kluwer Health, Inc. All rights reserved.

PubMed | University of California at San Diego, PathGroup and Aurora University
Type: Journal Article | Journal: Clinical and translational science | Year: 2016

Hypoplastic left heart syndrome (HLHS) is a heterogeneous, lethal combination of congenital malformations characterized by severe underdevelopment of left heart structures, resulting in a univentricular circulation. The genetic determinants of this disorder are largely unknown. Evidence of copy number variants (CNVs) contributing to the genetic etiology of HLHS and other congenital heart defects has been mounting. However, the functional effects of such CNVs have not been examined, particularly in cases where the variant of interest is found in only a single patient.Whole-genome SNP microarrays were employed to detect CNVs in two patient cohorts (N = 70 total) predominantly diagnosed with some form of nonsyndromic HLHS. We discovered 16 rare or private variants adjacent to or overlapping 20 genes associated with cardiovascular or premature lethality phenotypes in mouse knockout models. We evaluated the impact of selected variants on the expression of nine of these genes through quantitative PCR on cDNA derived from patient heart tissue. Four genes displayed significantly altered expression in patients with an overlapping or proximal CNV verses patients without such CNVs.Rare and private genomic imbalances perturb transcription of genes that potentially affect cardiogenesis in a subset of nonsyndromic HLHS patients.

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