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1.
Am J Pathol ; 2024 Jun 13.
Article in English | MEDLINE | ID: mdl-38879079

ABSTRACT

Endometrial cancer is the fourth most common cancer in women in the United States; the lifetime risk for developing this disease is approximately 2.8%. Precise histologic evaluation and molecular classification of endometrial cancer are important for effective patient management and determining the best treatment modalities. This study introduces EndoNet, which uses convolutional neural networks for extracting histologic features and a vision transformer for aggregating these features and classifying slides based on their visual characteristics into high- and low-grade cases. The model was trained on 929 digitized hematoxylin and eosin-stained whole-slide images of endometrial cancer from hysterectomy cases at Dartmouth-Health. It classifies these slides into low-grade (endometrioid grades 1 and 2) and high-grade (endometrioid carcinoma International Federation of Gynecology and Obstetrics grade 3, uterine serous carcinoma, or carcinosarcoma) categories. EndoNet was evaluated on an internal test set of 110 patients and an external test set of 100 patients from The Cancer Genome Atlas public database. The model achieved a weighted average F1 score of 0.91 (95% CI, 0.86 to 0.95) and an area under the curve of 0.95 (95% CI, 0.89 to 0.99) on the internal test, and 0.86 (95% CI, 0.80 to 0.94) for F1 score and 0.86 (95% CI, 0.75 to 0.93) for area under the curve on the external test. Pending further validation, EndoNet has the potential to support pathologists without the need of manual annotations in classifying the grades of gynecologic pathology tumors.

2.
J Cutan Pathol ; 50(7): 632-636, 2023 Jul.
Article in English | MEDLINE | ID: mdl-37057381

ABSTRACT

Cutaneous myoepithelioma is a rare benign soft tissue neoplasm of myoepithelial cells involving the skin and subcutis. These tumors can be diagnostically challenging. The plasticity of myoepithelial cells leads to wide variability in the cytomorphology, immunophenotype, and genetic features of myoepithelioma. Their protean presentations may mimic malignant neoplasms. Therefore, distinction from malignancy is essential. Herein, we report a case of cutaneous myoepithelioma presenting similarly to Ewing sarcoma, with small round blue cells and an EWSR1 rearrangement. Our case highlights the important morphologic, immunohistochemical, and cytogenetic features of this benign basaloid cutaneous tumor.


Subject(s)
Connective Tissue Diseases , Myoepithelioma , Skin Neoplasms , Soft Tissue Neoplasms , Humans , Myoepithelioma/pathology , Biomarkers, Tumor/genetics , Skin Neoplasms/pathology , Soft Tissue Neoplasms/pathology , Gene Rearrangement , RNA-Binding Protein EWS/genetics
3.
J Cutan Pathol ; 48(2): 302-308, 2021 Feb.
Article in English | MEDLINE | ID: mdl-32592167

ABSTRACT

Primary cutaneous Ewing sarcoma is a very rare entity with less than 100 cases reported in the literature, sharing the same morphological and immunohistochemical characteristics as their osseous counterparts. Herein, to the best of our knowledge, we report the first case in English literature of a molecularly confirmed Ewing sarcoma with diffuse and strong SOX10 immunoreactivity. This exceedingly rare immunohistochemical finding along with the rarity of this tumor could easily lead to a misdiagnosis with significant repercussions. Our case highlights the difficulty in diagnosing primary cutaneous Ewing sarcoma as well as the pivotal role molecular diagnostics can play in specific scenarios.


Subject(s)
Neoplasm Proteins/metabolism , SOXE Transcription Factors/metabolism , Sarcoma, Ewing , Skin Neoplasms , Adult , Humans , Male , Sarcoma, Ewing/diagnosis , Sarcoma, Ewing/metabolism , Sarcoma, Ewing/pathology , Skin Neoplasms/diagnosis , Skin Neoplasms/metabolism , Skin Neoplasms/pathology
4.
Adv Anat Pathol ; 27(1): 3-10, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31567128

ABSTRACT

Non-small cell lung cancer (NSCLC), since the recognition of epidermal growth factor receptor (EGFR) mutations that sensitized tumors to EGFR tyrosine kinase inhibitors, has been a poster child for precision oncology in solid tumors. The emergence of resistance to the EGFR tyrosine kinase inhibitors led to the unveiling of multiple resistance mechanisms that are now recognized to be frequent mechanisms across multiple tumor types. Coevolution of technological advancements in testing methods available to clinical laboratories now has identified a growing number of molecularly defined subsets of NSCLC that have new therapeutic implications. In addition, identifying patients eligible for immunotherapy is another goal for precision oncology. Recently, studies suggest that TMB may be a promising biomarker for selecting patients with NSCLC for immunotherapy. This review focuses on emerging potentially targetable alterations specifically in RET, ERBB2 (HER2), MET, and KRAS and current evidence and controversies surrounding TMB testing.


Subject(s)
Carcinoma, Non-Small-Cell Lung/genetics , Lung Neoplasms/genetics , Oncogenes , Biomarkers, Tumor , Clinical Trials as Topic , Humans , Immunotherapy , Molecular Targeted Therapy
5.
Histopathology ; 73(6): 963-968, 2018 Dec.
Article in English | MEDLINE | ID: mdl-30003571

ABSTRACT

AIMS: Isocitrate dehydrogenase 1 (IDH1) is a metabolic enzyme that converts isocitrate to α-ketoglutarate. IDH1 mutations are associated with the accumulation of the oncometabolite D-2-hydroxyglutarate, which acts as an epigenetic modifier, and the development of multiple malignancies. METHODS AND RESULTS: From May 2013 to June 2017, 252 melanoma samples from 214 patients with advanced or distant metastatic disease were tested for somatic mutations with the 50-gene AmpliSeq version 2 Cancer Hotspot Panel. Two hundred and twenty-six samples were sequenced successfully from 206 patients with 26 samples being characterised as quantity not sufficient. Melanomas from 10 separate patients (4.9%) were positive for IDH1 R132C (nine) or R132S (one). In six cases, the tumours also had a co-existing NRAS mutation (p.Q61R, Q61L and Q61K in two patients each) (P = 0.0044), whereas three patients had BRAF non-V600E mutations (V600K, V600G and V600R). Two cases had a TP53 variant, two cases an ATM variant, one a CDKN2A variant and one had an APC variant. The patients' ages ranged from 45 to 82 years (mean = 65.3, median = 65 years) and three of 10 patients were female (M:F ratio = 2:3). Three patients were stage 3 and seven were stage 4. Two are deceased, five are alive with stable disease (four on pembrolizumab) and three have no evidence of disease. CONCLUSION: IDH mutations may define a unique subset of melanoma patients who are eligible for IDH1 targeted therapies or combined therapies, such as MEK inhibitors when there is co-existing NRAS mutations, or immunotherapy.


Subject(s)
GTP Phosphohydrolases/genetics , Isocitrate Dehydrogenase/genetics , Melanoma/genetics , Membrane Proteins/genetics , Skin Neoplasms/genetics , Aged , Aged, 80 and over , Female , Humans , Male , Melanoma/pathology , Middle Aged , Mutation , Skin Neoplasms/pathology
6.
Exp Mol Pathol ; 104(1): 26-28, 2018 02.
Article in English | MEDLINE | ID: mdl-29248665

ABSTRACT

Mixed morphology lung tumors are rare; this is the second report of a combined NSCLC and atypical carcinoid tumor. Next generation sequencing was performed on both histologically distinct patterns which identified that both components harbored a BRAF p.V600E mutation. Molecular studies inform our knowledge of the biology and aid in treatment decisions for mixed morphology lung cancers.


Subject(s)
Adenocarcinoma/genetics , Carcinoid Tumor/genetics , Lung Neoplasms/genetics , Mutation , Proto-Oncogene Proteins B-raf/genetics , Adenocarcinoma/enzymology , Adenocarcinoma/pathology , Adenocarcinoma of Lung , Aged , Carcinoid Tumor/enzymology , Carcinoid Tumor/pathology , Carcinoma, Neuroendocrine/enzymology , Carcinoma, Neuroendocrine/genetics , Carcinoma, Neuroendocrine/pathology , High-Throughput Nucleotide Sequencing , Humans , Lung Neoplasms/enzymology , Lung Neoplasms/pathology , Male , Polymorphism, Single Nucleotide , Proto-Oncogene Proteins B-raf/metabolism
7.
Am J Pathol ; 186(3): 671-7, 2016 Mar.
Article in English | MEDLINE | ID: mdl-26797085

ABSTRACT

Benign ovarian Brenner tumors often are associated with mucinous cystic neoplasms, which are hypothesized to share a histogenic origin and progression, however, supporting molecular characterization is limited. Our goal was to identify molecular mechanisms linking these tumors. DNA from six Brenner tumors with paired mucinous tumors, two Brenner tumors not associated with a mucinous neoplasm, and two atypical proliferative (borderline) Brenner tumors was extracted from formalin-fixed, paraffin-embedded tumor samples and sequenced using a 358-gene next-generation sequencing assay. Variant calls were compared within tumor groups to assess somatic mutation profiles. There was high concordance of the variants between paired samples (40% to 75%; P < 0.0001). Four of the six tumor pairs showed KRAS hotspot driver mutations specifically in the mucinous tumor. In the two paired samples that lacked KRAS mutations, MYC amplification was detected in both of the mucinous and the Brenner components; MYC amplification also was detected in a third Brenner tumor. Five of the Brenner tumors had no reportable potential driver alterations. The two atypical proliferative (borderline) Brenner tumors both had RAS mutations. The high degree of coordinate variants between paired Brenner and mucinous tumors supports a shared origin or progression. Differences observed in affected genes and pathways, particularly involving RAS and MYC, may point to molecular drivers of a divergent phenotype and progression of these tumors.


Subject(s)
Brenner Tumor/genetics , Neoplasms, Cystic, Mucinous, and Serous/genetics , Ovarian Neoplasms/genetics , Proto-Oncogene Proteins c-myc/genetics , Proto-Oncogene Proteins p21(ras)/genetics , Adult , Aged , Aged, 80 and over , Brenner Tumor/pathology , DNA, Neoplasm/chemistry , DNA, Neoplasm/genetics , Female , High-Throughput Nucleotide Sequencing , Humans , Middle Aged , Mutation , Neoplasms, Cystic, Mucinous, and Serous/pathology , Ovarian Neoplasms/pathology , Phenotype , Sequence Analysis, DNA
8.
Exp Mol Pathol ; 103(3): 279-287, 2017 12.
Article in English | MEDLINE | ID: mdl-29169801

ABSTRACT

Histopathology is the gold standard for diagnosing melanocytic lesions; however, distinguishing benign versus malignant is not always clear histologically. Single nucleotide polymorphism (SNP) microarray analysis may help in making a definitive diagnosis. Here, we share our experience with the Oncoscan FFPE Assay and demonstrate its diagnostic utility in the context of ambiguous melanocytic lesions. Eleven archival melanocytic lesions, including three benign nevi, four melanomas, three BAP1-deficient Spitzoid nevi and one nevoid melanoma were selected for validation. SNP-array was performed according to the manufacturer's protocol, using the recommended 80ng of DNA; however, as little as 15ng was used if the extraction yield was lower. Concordance was assessed with H&E and various combinations of BAP1 and p16 immunohistochemical stains (IHC) and external reference laboratory chromosomal microarray results. After validation, the SNP array was utilized to make definitive diagnoses in four challenging cases. Oncoscan SNP array findings were in concordance with H&E, IHC, and reference laboratory chromosomal microarray testing. The SNP-based microarray can accurately detect copy number changes and aid in making a more definitive diagnosis of challenging melanocytic lesions. This can be accomplished using significantly less DNA than is required by other microarray technologies.


Subject(s)
Melanoma/diagnosis , Neoplasms/diagnosis , Nevus, Epithelioid and Spindle Cell/genetics , Nevus/diagnosis , Diagnosis, Differential , Humans , Melanocytes/pathology , Melanoma/genetics , Melanoma/pathology , Microarray Analysis , Neoplasms/genetics , Neoplasms/pathology , Nevus/genetics , Nevus/pathology , Nevus, Epithelioid and Spindle Cell/pathology , Polymorphism, Single Nucleotide/genetics , Tumor Suppressor Proteins/genetics , Ubiquitin Thiolesterase/genetics
9.
Exp Mol Pathol ; 102(1): 47-49, 2017 02.
Article in English | MEDLINE | ID: mdl-27939577

ABSTRACT

Clinical laboratories are expected to reliably identify human papilloma virus (HPV) associated oropharyngeal squamous cell carcinoma (OPSCC) for prognostic and potential therapeutic applications. In addition to surrogate p16 immunohistochemistry (IHC) testing, DNA-based HPV-specific testing strategies are widely utilized. Recognizing the efficiency of the Roche Cobas 4800 platform for testing gynecological cytology specimens for high-risk HPV, we elected to evaluate the potential utility of this platform for testing formalin-fixed paraffin-embedded (FFPE) OPSCC tissue. Using the Roche Linear Array assay for comparison, we tested twenty-eight samples (16 primary OPSCC, 2 lymph node metastases from primary OPSCC, 1 oral tongue carcinoma, 3 benign squamous papillomas, and 3 non-oropharyngeal carcinoma tissues). Excluding two invalid results, the Roche Cobas 4800 testing resulted in excellent inter-assay concordance (25/26, 96.2%) and 100% concordance for HPV-16/HPV-18 positive samples. This data suggests that the Roche Cobas 4800 platform may be a cost-effective method for testing OPSCC FFPE tissues in a clinical molecular pathology laboratory setting.


Subject(s)
Carcinoma, Squamous Cell/diagnosis , Human Papillomavirus DNA Tests/methods , Oropharyngeal Neoplasms/diagnosis , Papillomaviridae/genetics , Papillomavirus Infections/diagnosis , Biomarkers, Tumor/genetics , Biomarkers, Tumor/metabolism , Carcinoma, Squamous Cell/metabolism , Carcinoma, Squamous Cell/virology , Cyclin-Dependent Kinase Inhibitor p16/metabolism , DNA, Viral/genetics , Formaldehyde , Host-Pathogen Interactions , Human Papillomavirus DNA Tests/instrumentation , Humans , Immunohistochemistry , Oropharyngeal Neoplasms/metabolism , Oropharyngeal Neoplasms/virology , Papillomaviridae/classification , Papillomaviridae/physiology , Papillomavirus Infections/metabolism , Papillomavirus Infections/virology , Paraffin Embedding , Reproducibility of Results , Risk Factors , Sensitivity and Specificity , Tissue Fixation/methods
10.
Genet Med ; 18(12): 1206-1213, 2016 12.
Article in English | MEDLINE | ID: mdl-27124787

ABSTRACT

PURPOSE: The College of American Pathologists offers blinded proficiency testing (PT) for laboratories performing HFE genetic tests for hereditary hemochromatosis (common C282Y and H63D variants). This study used 10 years of PT data to determine laboratory performance for HFE analytical genotyping and clinical interpretation. METHODS: Laboratories were graded for accuracy of genotype determination (six possible C282Y/H63D genotypes) and clinical interpretation regarding whether the genotype was likely to have contributed to iron overload in a hypothetical patient. RESULTS: The analytical genotyping error rate was low (0.73%) in 7,663 results (from 257 unique laboratories). Genotyping errors were significantly higher in C282Y heterozygous, H63D homozygous, and C282Y homozygous samples, in non-American laboratories, and in laboratories with lower testing volume. Analytical sensitivity and specificity were >98.5 and >99.5%. The interpretive error rate (4.3%) was higher than the genotyping error rate, with two problematic genotypes (C282Y heterozygous and H63D homozygous) accounting for 77% of total interpretive errors. There was a time-dependent improvement in the interpretation of the clinical significance of HFE genotypes. CONCLUSIONS: HFE molecular genetic testing, performed by non-US Food and Drug Administration-approved laboratory-developed tests, demonstrated excellent accuracy, sensitivity, and specificity. Clinical interpretations were more heterogeneous, probably owing to the low clinical penetrance of some common HFE genotypes.Genet Med 18 12, 1206-1213.


Subject(s)
Genetic Testing , Hemochromatosis Protein/genetics , Hemochromatosis/diagnosis , Hemochromatosis/genetics , Genotype , Hemochromatosis/pathology , Humans , Mutation, Missense
11.
Clin Chem ; 62(1): 252-61, 2016 Jan.
Article in English | MEDLINE | ID: mdl-26585927

ABSTRACT

BACKGROUND: Crizotinib has antitumor activity in ALK (anaplastic lymphoma receptor tyrosine kinase)-rearranged non-small cell lung cancer (NSCLC). The current diagnostic test for ALK rearrangement is breakapart fluorescence in situ hybridization (FISH), but FISH has low throughput and is not always reflective of protein concentrations. The emergence of multiple clinically relevant biomarkers in NSCLC necessitates efficient testing of scarce tissue samples. We developed an anaplastic lymphoma kinase (ALK) protein assay that uses multiplexed selected reaction monitoring (SRM) to quantify absolute amounts of ALK in formalin-fixed paraffin-embedded (FFPE) tumor tissue. METHODS: After validation in formalin-fixed cell lines, the SRM assay was used to quantify concentrations of ALK in 18 FFPE NSCLC samples that had been tested for ALK by FISH and immunohistochemistry. Results were correlated with patient response to crizotinib. RESULTS: We detected ALK in 11 of 14 NSCLC samples with known ALK rearrangements by FISH. Absolute ALK concentrations correlated with clinical response in 5 of 8 patients treated with crizotinib. The SRM assay did not detect ALK in 3 FISH-positive patients who had not responded to crizotinib. In 1 of these cases, DNA sequencing revealed a point mutation that predicts a nonfunctional ALK fusion protein. The SRM assay did not detect ALK in any tumor tissue with a negative ALK status by FISH or immunohistochemistry. CONCLUSIONS: ALK concentrations measured by SRM correlate with crizotinib response in NSCLC patients. The ALK SRM proteomic assay, which may be multiplexed with other clinically relevant proteins, allows for rapid identification of patients potentially eligible for targeted therapies.


Subject(s)
Antineoplastic Agents/therapeutic use , Carcinoma, Non-Small-Cell Lung/drug therapy , Gene Expression Regulation, Neoplastic , Lung Neoplasms/drug therapy , Pyrazoles/therapeutic use , Pyridines/therapeutic use , Receptor Protein-Tyrosine Kinases/analysis , Receptor Protein-Tyrosine Kinases/genetics , Anaplastic Lymphoma Kinase , Antineoplastic Agents/pharmacology , Carcinoma, Non-Small-Cell Lung/diagnosis , Carcinoma, Non-Small-Cell Lung/genetics , Cell Line, Tumor , Crizotinib , Gene Expression Regulation, Neoplastic/drug effects , Humans , Immunohistochemistry , In Situ Hybridization, Fluorescence , Lung Neoplasms/diagnosis , Lung Neoplasms/genetics , Pyrazoles/pharmacology , Pyridines/pharmacology , Receptor Protein-Tyrosine Kinases/antagonists & inhibitors
12.
Exp Mol Pathol ; 100(3): 421-5, 2016 06.
Article in English | MEDLINE | ID: mdl-27095739

ABSTRACT

BACKGROUND: Metastatic breast cancer is a genetically heterogeneous disease and effective therapies for advanced stage disease are limited. METHODS: In this study, distant metastases of 22 formalin-fixed, paraffin-embedded (FFPE) breast cancer samples were sequenced using the Ion Torrent PGM and the 50 gene AmpliSeq Cancer Hotspot Panel v2 from 10ng of extracted DNA using 318 chips. Data analysis was performed with the Ion Torrent Variant Caller Plugin (hg19) and Golden Helix's SVS software for annotation and prediction of the significance of the variants. RESULTS: All patients were female with a median age of 61years (range 37-85years). Metastatic sites included liver (n=6, 27%), skin (n=5, 23%), brain (n=4, 18%), lymph node (n=3, 14%), lung (n=2, 9%), retroperitoneum (n=1, 4.5%), and colon (n=1, 4.5%). Overall, 28 variants in 11 genes were observed. Five (23%) samples showed no alterations and 17 (77%) showed at least one potentially biologically significant variant (BSV) defined as having FDA-approved drugs or clinical trials evaluating their significance. BSVs included mutations in the following genes: TP53 (n=8), APC (n=4), PIK3CA (n=5), MET (n=2), ERBB2 (n=2), AKT1 (n=1), CDKN2A (n=1), KRAS (n=1), and FGFR3 (n=1). CONCLUSIONS: Potentially actionable mutations were identified in the majority of breast cancer metastases. Evaluating metastatic breast tumors using a NGS approach provides a better understanding of the mechanisms behind tumor progression and evolution and also identifies additional potentially beneficial therapeutic targets for patient management or eligibility for clinical trials.


Subject(s)
Breast Neoplasms/genetics , Genetic Predisposition to Disease/genetics , High-Throughput Nucleotide Sequencing/methods , Mutation , Adenomatous Polyposis Coli Protein/genetics , Adult , Aged , Aged, 80 and over , Breast Neoplasms/pathology , Class I Phosphatidylinositol 3-Kinases , Female , Humans , Middle Aged , Neoplasm Metastasis , Phosphatidylinositol 3-Kinases/genetics , Proto-Oncogene Proteins c-met/genetics , Receptor, ErbB-2/genetics , Tumor Suppressor Protein p53/genetics
13.
J Cutan Pathol ; 43(8): 707-10, 2016 Aug.
Article in English | MEDLINE | ID: mdl-27090873

ABSTRACT

Mammary-like glands are normal appendages of anogenital skin and can give rise to epithelial and stromal tumors that closely resemble breast tumors. Cowden syndrome is an autosomal-dominant cancer-predisposition syndrome that is associated with increased risk of various benign and malignant tumors including breast cancers. Here, we report the first case of a proliferative lesion of mammary-like glands in the setting of Cowden syndrome. A 27-year-old female with Cowden syndrome (R130Q-PTEN mutation) presented with a 1-cm tender, polypoid perianal lesion. An excisional biopsy revealed a circumscribed, lobulated lesion with fibromyxoid stroma and epithelial hyperplasia with apocrine and columnar cell changes that was arranged in papillary, micropapillary and focal cribriform architecture. The features strikingly resembled proliferative changes commonly seen in the breast. Interestingly, the patient subsequently developed an atypical complex sclerosing lesion of the breast. Given the increased risk of breast neoplasia in Cowden syndrome, and the morphologic relationship between breast glands and mammary-like glands, this case raises the possibility of an increased risk of neoplasia arising in mammary-like glands in the setting of Cowden syndrome.


Subject(s)
Anal Canal/pathology , Hamartoma Syndrome, Multiple/pathology , Adult , Female , Humans , Hyperplasia/pathology
14.
Oncologist ; 20(9): 1011-8, 2015 Sep.
Article in English | MEDLINE | ID: mdl-26205736

ABSTRACT

BACKGROUND: Although genetic profiling of tumors is a potentially powerful tool to predict drug sensitivity and resistance, its routine use has been limited because clinicians are often unfamiliar with interpretation and incorporation of the information into practice. We established a Molecular Tumor Board (MTB) to interpret individual patients' tumor genetic profiles and provide treatment recommendations. PATIENTS AND METHODS: DNA from tumor specimens was sequenced in a Clinical Laboratory Improvement Amendments-certified laboratory to identify coding mutations in a 50-gene panel (n = 34) or a 255-gene panel (n = 1). Cases were evaluated by a multidisciplinary MTB that included pathologists, oncologists, hematologists, basic scientists, and genetic counselors. RESULTS: During the first year, 35 cases were evaluated by the MTB, with 32 presented for recommendations on targeted therapies, and 3 referred for potential germline mutations. In 56.3% of cases, MTB recommended treatment with a targeted agent based on evaluation of tumor genetic profile and treatment history. Four patients (12.5%) were subsequently treated with a MTB-recommended targeted therapy; 3 of the 4 patients remain on therapy, 2 of whom experienced clinical benefit lasting >10 months. CONCLUSION: For the majority of cases evaluated, the MTB was able to provide treatment recommendations based on targetable genetic alterations. The most common reasons that MTB-recommended therapy was not administered stemmed from patient preferences and genetic profiling at either very early or very late stages of disease; lack of drug access was rarely encountered. Increasing awareness of molecular profiling and targeted therapies by both clinicians and patients will improve acceptance and adherence to treatments that could significantly improve outcomes. IMPLICATIONS FOR PRACTICE: Case evaluation by a multidisciplinary Molecular Tumor Board (MTB) is critical to benefit from individualized genetic data and maximize clinical impact. MTB recommendations shaped treatment options for the majority of cases evaluated. In the few patients treated with MTB-recommended therapy, disease outcomes were positive and support genetically informed treatment.


Subject(s)
Decision Support Techniques , Neoplasms/drug therapy , Neoplasms/genetics , Precision Medicine/methods , DNA, Neoplasm/analysis , DNA, Neoplasm/genetics , Female , High-Throughput Nucleotide Sequencing/methods , Humans , Male , Middle Aged , Neoplasms/diagnosis , Neoplasms/pathology , Pathology, Molecular/methods
15.
Genet Med ; 17(1): 58-62, 2015 Jan.
Article in English | MEDLINE | ID: mdl-24946157

ABSTRACT

PURPOSE: The purpose of this study was to analyze laboratory performance on proficiency testing surveys offered jointly by the College of American Pathologists/American College of Medical Genetics and Genomics biannually for the three common Ashkenazi Jewish founder mutations in the BRCA1 and BRCA2 genes. METHODS: Survey responses were analyzed for accuracy of genotype determination and the associated clinical interpretation. Data on an individual laboratory's participation over time, number of samples tested, turnaround time, and test methodology were also reviewed. RESULTS: Between 2003 and 2012, 23 US laboratories and 39 international laboratories participated. There were six genotyping errors, with a corresponding analytical sensitivity of 99.0% (479/484 challenges; 95% confidence interval: 97.6-99.7%) and an analytic specificity of 99.9% (870/871; 95% confidence interval: 99.4-99.9%). Among the 1,325 clinical interpretations, 92.5% (1,226/1,325; 95% confidence interval: 91.0-93.9%) matched the intended response. Most of the 99 discrepancies-81% (80/99)-incorrectly interpreted the risk for a negative test result as having a lifetime risk of breast cancer "that is the same as that in the general population" instead of "that cannot be determined without BRCA mutation testing of the affected relative." CONCLUSION: Clinical laboratories demonstrated excellent analytical sensitivity and specificity. The clinical interpretation requires additional education, focusing on the clinical interpretation of negative test results for these three mutations.


Subject(s)
Founder Effect , Genes, BRCA1 , Genes, BRCA2 , Genetic Testing , Jews/genetics , Mutation , Genetic Testing/methods , Genetic Testing/standards , Genotype , Health Care Surveys , Humans , Laboratory Proficiency Testing , Reproducibility of Results , Sensitivity and Specificity
16.
Int J Gynecol Pathol ; 34(1): 30-5, 2015 Jan.
Article in English | MEDLINE | ID: mdl-25473750

ABSTRACT

Primary carcinoid tumors are rare neoplasms of the ovary. Of the 4 histologic subtypes, ovarian carcinoid tumors with insular patterns produce carcinoid syndrome in approximately one third of cases, versus strumal and trabecular carcinoids which very rarely cause typical carcinoid syndrome. A unique presentation of ovarian carcinoid tumors with concurrent severe constipation has been reported, which is thought to represent a new carcinoid syndrome. The proposed mechanism is the production of peptide YY by the tumor, a gastrointestinal hormone responsible for decreasing gut motility. We report a case of a 34-yr-old white woman who presented with constipation and weight loss for 1 yr, and was found to have a unilateral ovarian strumal carcinoid, which produced peptide YY as demonstrated by immunohistochemistry. The 13 previous case reports of ovarian carcinoids with constipation are reviewed and the clinicopathologic features are discussed. This report and literature review further solidifies this entity as a new type of carcinoid syndrome.


Subject(s)
Carcinoid Tumor/diagnosis , Constipation/diagnosis , Ovarian Neoplasms/diagnosis , Peptide YY/metabolism , Severity of Illness Index , Struma Ovarii/diagnosis , Adult , Carcinoid Tumor/epidemiology , Carcinoid Tumor/metabolism , Comorbidity , Constipation/epidemiology , Female , Gastrointestinal Motility/physiology , Humans , Ovarian Neoplasms/epidemiology , Ovarian Neoplasms/metabolism , Ovariectomy , Ovary/metabolism , Ovary/pathology , Ovary/surgery , Struma Ovarii/epidemiology , Struma Ovarii/metabolism , Syndrome , Treatment Outcome
17.
Clin Chem ; 60(1): 111-21, 2014 Jan.
Article in English | MEDLINE | ID: mdl-24193118

ABSTRACT

BACKGROUND: Lynch syndrome (LS) is the most common form of the hereditary colon cancer syndromes. Because of its high prevalence, a nationwide campaign has begun to screen all colorectal cancers for the genetic abnormalities associated with LS. CONTENT: Next to colorectal cancer, endometrial cancer is the most common form of malignancy found in women with LS. Identifying individuals who harbor the well-characterized mismatch-repair gene mutations via immunohistochemistry, microsatellite instability analysis, or direct gene sequencing is critical to managing the LS patient and to surveillance for the development of other associated tumor types. SUMMARY: Although many institutions have begun screening all colorectal tumors for LS, the evidence is sufficient to warrant the testing of all endometrial cancers for LS as well. Various testing algorithms, along with genetic-counseling efforts, can lead to a cost-efficient and beneficial screening program.


Subject(s)
Colorectal Neoplasms, Hereditary Nonpolyposis/diagnosis , Colorectal Neoplasms, Hereditary Nonpolyposis/pathology , Endometrial Neoplasms/diagnosis , Endometrial Neoplasms/pathology , Adaptor Proteins, Signal Transducing/genetics , Colorectal Neoplasms, Hereditary Nonpolyposis/genetics , Diagnosis, Differential , Endometrial Neoplasms/genetics , Female , Humans , Mass Screening , MutL Protein Homolog 1 , Nuclear Proteins/genetics
18.
Exp Mol Pathol ; 97(1): 116-9, 2014 Aug.
Article in English | MEDLINE | ID: mdl-24927872

ABSTRACT

BACKGROUND: HER2 fluorescence in-situ hybridization (FISH) is used in breast and gastro-esophageal carcinoma for determining HER2 gene amplification and patients' eligibility for HER2 targeted therapeutics. Traditional manual processing of the FISH slides is labor intensive because of multiple steps that require hands on manipulation of the slides and specifically timed intervals between steps. This highly manual processing also introduces inter-run and inter-operator variability that may affect the quality of the FISH result. Therefore, we sought to incorporate an automated processing instrument into our FISH workflow. METHODS: Twenty-six cases including breast (20) and gastro-esophageal (6) cancer comprising 23 biopsies and three excision specimens were tested for HER2 FISH (Pathvysion, Abbott) using the Thermobrite Elite (TBE) system (Leica). Up to 12 slides can be run simultaneously. All cases were previously tested by the Pathvysion HER2 FISH assay with manual preparation. Twenty cells were counted by two observers for each case; five cases were tested on three separate runs by different operators to evaluate the precision and inter-operator variability. RESULTS: There was 100% concordance in the scoring between the manual and TBE methods as well as among the five cases that were tested on three runs. Only one case failed due to poor probe hybridization. In total, seven cases were positive for HER2 amplification (HER2:CEP17 ratio >2.2) and the remaining 19 were negative (HER2:CEP17 ratio <1.8) utilizing the 2007 ASCO/CAP scoring criteria. Due to the automated denaturation and hybridization, for each run, there was a reduction in labor of 3.5h which could then be dedicated to other lab functions. CONCLUSION: The TBE is a walk away pre- and post-hybridization system that automates FISH slide processing, improves work flow and consistency and saves approximately 3.5h of technologist time. The instrument has a small footprint thus occupying minimal counter space. TBE processed slides performed exceptionally well in comparison to the manual technique with no disagreement in HER2 amplification status.


Subject(s)
Breast Neoplasms/genetics , Esophageal Neoplasms/genetics , In Situ Hybridization, Fluorescence/instrumentation , In Situ Hybridization, Fluorescence/methods , Receptor, ErbB-2/genetics , Stomach Neoplasms/genetics , Automation , Biopsy , Breast Neoplasms/pathology , Esophageal Neoplasms/pathology , Female , Gene Amplification , Humans , Reproducibility of Results , Stomach Neoplasms/pathology
19.
J Am Soc Cytopathol ; 13(4): 263-271, 2024.
Article in English | MEDLINE | ID: mdl-38677893

ABSTRACT

INTRODUCTION: The onset of the COVID-19 pandemic, with urgent implementation of safety protocols limiting the number of on-site personnel, essentially terminated the use of rapid on-site evaluation (ROSE) for computed tomography (CT)--guided lung biopsies at our institution. The diminished use of ROSE during the pandemic prompted us to reevaluate the potential value of ROSE for CT-guided lung biopsies. MATERIALS AND METHODS: We retrospectively identified all CT-guided lung biopsies from 2017 to 2022. Associations between the use of ROSE, adequate diagnostic and ancillary testing (programmed death-ligand 1 immunohistochemistry and next-generation sequencing) outcomes, and other factors such as the number of passes performed and lesion size, were evaluated. RESULTS: Nine hundred twelve CT-guided lung biopsies were performed from 2017 to 2022; 171 (19%) utilized ROSE. The use of ROSE had been steadily decreasing prior to the pandemic but was essentially eliminated with the onset of the pandemic. By univariable analysis, the employment of ROSE was more likely to be associated with an adequate final diagnosis (odds ratio = 2.14, 95% confidence interval: [1.24-3.70], P = 0.006) and successful molecular testing (odds ratio = 2.16, 95% confidence interval: [1.11-4.21], P = 0.024). However, those associations were not present in multivariable analyses that incorporated the number of passes performed or lesion size. There were no differences in diagnostic adequacy or ancillary testing yields when comparing the periods 2017-2019 and 2020-2022, despite declining use of ROSE. CONCLUSIONS: If ROSE is not requested for CT-guided lung biopsies, proceduralists should err on the side of performing more, rather than fewer, passes, particularly for smaller lesions.


Subject(s)
B7-H1 Antigen , COVID-19 , Image-Guided Biopsy , Immunohistochemistry , Lung , SARS-CoV-2 , Tomography, X-Ray Computed , Humans , COVID-19/pathology , COVID-19/diagnosis , Tomography, X-Ray Computed/methods , Retrospective Studies , Male , Female , Immunohistochemistry/methods , Middle Aged , B7-H1 Antigen/metabolism , Lung/pathology , Lung/diagnostic imaging , Aged , Image-Guided Biopsy/methods , SARS-CoV-2/isolation & purification , Adult , Pandemics , Lung Neoplasms/diagnosis , Lung Neoplasms/pathology
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