Clinical validation of the Ion Torrent Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer as a stand-alone assay for single-nucleotide variants, insertions/deletions, and fusion genes: Challenges, performance, and perspectives.

OBJECTIVES: Myeloid neoplasms require comprehensive characterization of genetic abnormalities, including single-nucleotide variants, small insertions and deletions, and fusions and translocations for management. The Oncomine Myeloid Assay GX v2 (Thermo Fisher Scientific) analyzes 17 full genes, 28 hotspot genes, 30 fusion driver genes, and 5 expression genes. METHODS: The validation set included 192 DNA samples, 28 RNA samples, and 9 cell lines and contrived controls. The DNA and RNA were extracted from both peripheral blood and bone marrow. Library preparation, templating, and sequencing was performed on the fully automated Genexus Integrated Sequencer (Thermo Fisher Scientific). The sequencing data were analyzed by manual curation, default Oncomine filters and the Oncomine Reporter (Thermo Fisher Scientific). RESULTS: Of the 600 reference pathogenic DNA variants targeted by the assay, concordance was seen in 98.3% of unfiltered variant call format files. Precision and reproducibility were 100%, and the lower limit of detection was 2% variant allele frequency for DNA. Inability to detect variants in long homopolymer regions intrinsic to the Ion Torrent chemistry led to 7 missed variants; 100% concordance was seen with reference RNA samples. CONCLUSIONS: This extensive clinical validation of the Oncomine Myeloid Assay GX v2 on the Genexus Integrated Sequencer with its built-in bioinformatics pipeline and Ion Torrent Oncomine Reporter shows robust performance in terms of variant calling accuracy, precision, and reproducibility, with the advantage of a rapid turnaround time of 2 days. The greatest limitation is the inability to detect variants in long homopolymer regions.

Defining the Nature and Clinicopathologic Significance of Mallory-Denk-like Inclusions in Ovarian Fibromas: A Potential Degenerative Phenomenon Associated With Torsion.

Mallory-Denk bodies (MBD), described in alcoholic hepatitis, are composed of intermediate filaments admixed with other proteins. These cytoplasmic inclusions are irregularly shaped and eosinophilic as seen under the light microscope. MBD-like inclusions have rarely been described outside the hepatobiliary tree. Though rare, intracytoplasmic inclusions have been reported in ovarian fibromas. This study evaluates a series of torsed ovarian fibromas with intracytoplasmic inclusions resembling MDBs. Forty-three ovarian fibromas were retrieved from the pathology archives. The H&E slides were evaluated for the presence of MBD-like inclusions and histologic evidence of torsion. The cases with histologic features of torsion were included in the study group while the nontorsed fibromas formed the control group. Among the 15 cases of fibromas with torsion, MBD-like intracytoplasmic inclusions were seen in 5 cases, predominantly in the interface between necrotic areas and viable stroma. None of the cases from the control group showed any inclusions. There was no significant difference in the size of the fibroma or patient demographics between cases with and without inclusions. The inclusions were positive for cytokeratin and ubiquitin while being negative for per acidic Schiff and periodic acid-Schiff with diastase reaction, in the 3 cases selected for immunohistochemistry and special stains. Electron microscopy of the index case revealed a predominance of type 3 Mallory hyaline. This is the first report describing MDB-like inclusions in ovarian fibromas. These MDB-like inclusions appear to be limited to a fraction of ovarian fibromas that underwent torsion, suggesting that these inclusions likely result from subacute hypoxic damage to the cells.

Pitfalls of using polymerase chain reaction-based assays for JAK2 and CALR exon 9 variant testing in myeloproliferative neoplasms: Knowing when to go the extra mile!

OBJECTIVES: The BCR::ABL1 negative myeloproliferative neoplasms are sequentially tested for JAK2 p.V617F, followed by CALR exon 9 pathogenic variants. Historically, these variants were thought to be mutually exclusive. However, recent reports indicate coexisting JAK2 p.V617F and CALR exon 9 somatic variants. METHODS: Analysis of JAK2 p.V617F and CALR exon 9 variant was performed by polymerase chain reaction (PCR)-based assays. Subsequent testing was performed on the Genexus integrated sequencer (ThermoFisher) using the Oncomine myeloid assay GX v2. RESULTS: CALR exon 9 variants were positive in 3 cases, while 2 were positive for JAK2 p.V617F on PCR-based assays. Next-generation sequencing confirmed the JAK2 P.V617F status in all cases. CALR variants resulting in in-frame deletions were identified in 2 cases at a variant allele frequency of 52.16% and 50.91%, while the third case had an intronic CALR variant c.-48G>A at a variant allele frequency of 51.1%. Thus, CALR variants in all 3 cases were interpreted as potentially germline. Of the 228 cases that underwent JAK2 p.V617F and CALR cotesting in the past 2 years, only these 2 cases were positive for both JAK2 p.V617F and CALR exon 9 variants. CONCLUSIONS: These cases highlight the importance of understanding the pitfalls of molecular techniques in current practice.

PIK3CA-related overgrowth spectrum (PROS) presenting as isolated macrodactyly.

PIK3CA-related overgrowth spectrum (PROS) is a heterogeneous group of diseases, with varied clinical presentations ranging from isolated segmental overgrowths to megalencephaly and vascular malformations, all resulting from post-zygotic activating mutations in PIK3CA. Isolated macrodactyly of upper limb is extremely rare, accounting only for 0.9%-1% of all congenital anomalies of the upper limb. This report describes a case of congenital, isolated, nonprogressive macrodactyly of the right index finger and thumb, in an adult patient that was treated with debulking surgery. The microscopic features were compatible with lipomatosis of nerve. Due to the prompt and pertinent molecular testing, which identified a somatic PIK3CA variant, c.3140A > G, p.H1047R., the case was classified as a PROS. The availability of mTOR inhibitors offers additional treatment possibilities in cases with progressive disease. This case report highlights the importance of molecular testing to identify PROS, to further the knowledge of this continually expanding entity.

A study of somatic BRCA variants and their putative effect on protein properties in malignant mesothelioma.

Objectives: The aim of this study is to analyze the prevalence of somatic mutations in BRCA1 and BRCA2 in malignant mesothelioma and their putative impact on protein properties. Methods: Eighteen cases of malignant mesothelioma were retrieved from the archives and for next generation sequencing analysis of BRCA1 and BRCA2 genes. Variants were analyzed using Ensembl VEP17, Polyphen 2.0 software, SIFT software, MutpredV2, and SWISS-MODEL homology-modeling pipeline server. Results: BRCA2 variants were found in significantly higher percentage (22%) of cases (p=0.02). Five missense variants were identified. These were p.A2351P, p.T2250A, p.A895V, pG1771D, and p.R2034C. The SIFT scores of all except one were ≥ 0.03. The Polyphen scores of these four alterations were ≤0.899. In case of p.A2315, the SIFT score was 0.01, while the Polyphen 2 score was 0.921. MutPred2 scores were ≤0.180 for all. Loss of intrinsic disorder was predicted (Pr=0.32, p=0.07) for p.R2034C, while gain of intrinsic disorder was predicted for p.A2351P (Pr=0.36, p=0.01) and p.G1771D (Pr=0.34, p=0.02). Conclusions: BRCA2 somatic variants were identified in 22% cases of malignant mesotheliomas in this study. The variants localize more frequently to the disordered regions of the protein and are predicted to affect the level of disorder.

Diffuse WT1 Positivity in Smooth Muscle Component Supports Dual Differentiation of Mesothelial Cells in the Histogenesis of Leiomyoadenomatoid Tumors-A Report of two Cases.

Leiomyoadenomatoid tumors of the epididymis are exceedingly rare biphasic tumors composed of an adenomatoid component in the form of gland-like structures lined by single flat or cuboidal cells admixed with smooth muscle. Radiological and gross findings cannot distinguish leiomyoadenomatoid tumors from the more common classic adenomatoid tumors or leiomyomas, and careful microscopic examination is critical in the identification of this esoteric variant. The histogenesis of this entity remains ambiguous. Common hypotheses include a collision tumor, a variant of an adenomatoid tumor with a smooth muscle component, or an adenomatoid tumor arising in the background of reactive smooth muscle hyperplasia. We present 2 cases of leiomyoadenomatoid tumors with diffuse nuclear WT1 positivity in both the adenomatoid and smooth muscle components, supporting the mesothelial origin of these tumors.

MPO Expression of Background Neutrophils in MPO Negative Acute Promyelocytic Leukemia, An Easy Clue to Corroborate a Challenging Diagnosis: A Case Report and Review of Literature.

Acute promyelocytic leukemia (APL) is characterized by the pathogenic driver fusion transcript PML-RARA resulting from the t(15;17) translocation. Early recognition of APL with prompt ATRA induction has a decisive impact on the early death rate. The preliminary diagnosis of APL relies heavily on cytomorphology and flow cytometry. In APL with variant morphology, such as the microgranular variant, immunophenotype, especially the bright MPO positivity is the basis of diagnosis. Till date, only five cases of APL with reduced/absent MPO have been described in literature. The identification of MPO deficiency based on genetic testing would involve at the least a MPO gene scanning with NGS, followed by microarray to identify somatic uniparental disomy in heterozygotes. This testing is not only redundant given the scant clinical implications of heterozygous MPO deficiency but also time consuming. An easy way to identify background MPO deficiency confounding the immunophenotype of a myeloid neoplasm is the MPO expression in background neutrophils gated on the initial flow cytometry. A dim MPO in the background neutrophils, in the morphological setting of APL, can identify underlying MPO deficiency, clarifying the immunophenotypic ambiguity and thus establishing an unequivocal diagnosis as seen in the current case.

ROS1 altered breast cancers - a distinctive molecular subtype of PR- metastatic breast cancers: Expanding the scope of targeted therapeutics.

BACKGROUND: Breast cancer, one of the leading causes of cancer-related mortality in women worldwide, exhibits wide-ranging histo-morphologic, clinical and molecular diversity. OBJECTIVE: This study compares the genetic alterations of breast tumors with the histo-morphological, hormone receptor status and metastatic "organotropism". MATERIALS AND METHODS: Twenty-two cases of primary invasive breast carcinoma with local/distant metastasis were retrieved from the pathology archives. The status of estrogen and progesterone receptors by immunohistochemistry was recorded along with other pertinent case data. Next generation sequencing was performed on formalin-fixed paraffin embedded blocks of tumor. RESULTS: The mean age of the study subjects was 57.9 ± 13.3 years. TP53 mutation was the most common gene alteration in this study and was seen in 40.9% cases. ROS1 gene was mutated in 44.4% PR negative breast cancers while being wild type in the twelve PR positive tumors. (p = 0.021).STRING interaction network constructed with ROS1 and PR revealed a significantly higher number of interactions in this network than expected (p-value 0.000973). CONCLUSION: This study highlights the significantly higher incidence of ROS1 gene alterations in metastatic PR- breast cancers, with STRING network analysis revealing higher nodal interaction in the nodal network comprised of PR and ROS1 exclusive of ER.

The mutational landscape of upper gastrointestinal adenocarcinomas- A study of similarities and differences.

PURPOSE: The gastrointestinal tract is home to a wide variety of neoplasms. Gastrointestinal adenocarcinomas display distinct prognostic patterns. With the advent of next generation sequencing, attempts are being made to delineate distinct molecular characteristics of these adenocarcinomas from adjoining anatomical sites. METHODS: Thirty-seven cases of upper gastrointestinal adenocarcinomas including those of the esophagus, gastroesophageal junction, stomach, small intestine and gallbladder were retrieved. Next generation sequencing data consisting of base substitutions, copy number variations, indels and rearrangements, in 324 genes, were analyzed for recurrent genetic abnormalities. Statistical analysis was performed using IBM SPSS25 and SAS software. RESULTS: Genetic alterations were found in 181 genes. APC mutations were found in 50% of the esophageal adenocarcinomas, 5% of the gastric adenocarcinomas and 33.3% of the small intestinal adenocarcinomas (p = 0.04). PIK3 gene family mutations were found in 10% of the gastric adenocarcinomas, 66% of the gall bladder adenocarcinomas and 66% of the small intestinal adenocarcinomas (p = 0.002). The mutations were found exclusively in the PIK3 class 1 family. TP53 mutations were more common in tumors with intact DNA mismatch repair protein expression as assessed by immunohistochemistry (p = 0.042). CONCLUSION: In this study, APC gene mutations were found to be more frequent in esophageal and small intestinal adenocarcinomas than previously reported. PIK3 class 1 gene family mutations were found to be more frequent in gallbladder and small intestinal adenocarcinomas. An inverse relationship was found between TP53 mutations and loss of DNA mismatch repair protein expression.

Yolk sac differentiation in urothelial carcinoma - A rare variant originating from aberrant differentiation of sarcomatoid components.

Yolk sac differentiation occurs in somatic neoplasms of the gastrointestinal and gynecologic tracts; it has rarely been reported in urothelial carcinoma. Here, we report three cases of yolk sac differentiation in sarcomatoid urothelial carcinoma. The epithelioid component of the sarcomatoid urothelial carcinoma showed divergent differentiation, including squamous, conventional glandular, small cell carcinoma, and yolk sac components. The sarcomatoid component showed malignant spindle cells admixed with focal chondroid and rhabdoid elements. In all three cases, the yolk sac areas were admixed with the sarcomatoid component and showed a glandular pattern, with vacuolated, eosinophilic cytoplasm. These areas were positive for SALL4, variably positive for glypican 3 and AFP, and negative for the conventional urothelial markers GATA3, p63, and 34ßE12. Yolk sac differentiation is an extremely rare occurrence in sarcomatoid urothelial carcinoma.

Bronchiolar adenomas (BA) - A detailed radio-pathologic analysis of six cases and review of literature.

Bronchiolar adenomas (BAs)/ciliated muco-nodular papillary tumors (CMPTs), are small, peripheral lung nodules arising predominantly in the elderly that follow a benign course. They can be mistaken for adenocarcinomas on frozen section. Immunohistochemistry (IHC) for basal cell markers highlights the continuous layer of basal cells underlying the tumor cells in BAs. BAs are further subdivided into proximal-type and distal type. Six BAs were retrieved from the pathology archives. The cases were classified based on morphology into proximal and distal BAs. The clinical and radiological features were reviewed. Immunohistochemistry and special stains were performed. The most common radiological picture of BA/CMPT was of a solid nodule with SUVmax < 3 as seen in 60% cases. 40% cases showed cavitation on CT. On histological examination, four cases were morphologically classified as proximal BAs and two as distal BAs. In proximal BAs, TTF1 was focally positive only in the basal cells in three of four. The mucin stained acidic. In distal BAs, TTF1 was diffusely positive in both basal and luminal cells. There was scant intracellular neutral mucin. Both the distal BAs had concomitant neuroendocrine tumors in the same lobe. Though the number of cases evaluated in this study is too low to be statistically significant, this study provides additional evidence to the concept of BA classification based on site specific histology and supplementary immunohistochemistry and reiterates the radiological features that may help distinguish it from malignant lesions.

Morphological and immunophenotypical analysis of the spindle cell component in adenomyomatous hyperplasia of the gallbladder.

BACKGROUND: Adenomyomatous hyperplasia (AMH) of the gallbladder, reported in 1-8.7% of cholecystectomies, consists of cystically dilated sinuses/glands with a surrounding spindle cell proliferation which is thought to be composed of smooth muscle cells. Myofibroblasts are contractile cells that secrete a variety of biochemical modulators causing a "field-effect". Myofibroblasts can be immunohistochemically distinguished from smooth muscle cells by their desmin negativity. METHODS: Eighteen cases of AMH and five cases each of chronic follicular cholecystitis, chronic cholecystitis, gallbladder carcinoma and 10 colonic diverticular disease were stained with actin and desmin. The percentage of myofibroblasts was estimated by the difference between actin and desmin staining in the same field. Statistical anlysis was performed using SPSS 22.0. RESULTS: The percentage of actin staining was significantly higher in AMH and gallbladder carcinoma compared to chronic follicular and chronic cholecystitis (p = 0.04). The percentage of desmin staining did not show any significant difference between the four groups. The estimated myofibroblastic population was significantly higher in AMH when compared to chronic follicular and chronic cholecystitis (p = 0.005). CONCLUSION: The spindle cell proliferation around cystically dilated glands in AMH is composed predominantly of myofibroblasts and of smooth muscle cells as previously described. This finding suggest a derangement in epithelial-stromal interactions as the underlying pathophysiology in AMH.

A right para-tracheal mass extending into the anterior mediastinum: An anesthetic management conundrum.

The anesthetic management of patients with a mediastinal mass represent a challenge due to the potential for difficult ventilation and intubation, as well as the risk of cardiovascular collapse upon induction of general anesthesia. Different strategies and alternatives have been described. We present the case of a 70-year-old man with a right para-tracheal mass extending into the anterior mediastinum with 90% mid-tracheal lumen obstruction who was successfully managed with venous-venous extra-corporeal membrane oxygenation (ECMO) during mass debulking and tracheal stent placement.

Analysis of Genetic Alterations in Cutaneous Malignant Melanomas Unveils Unique Loco-Regional Variations and Novel Predictors of Metastatic Potential.

ABSTRACT: Cutaneous malignant melanoma is an aggressive cancer that contributes significantly to cancer-related mortality. Over the years, a deeper scrutiny of melanoma biology has led to identification of diverse evolutionary patterns involving various genetic pathways. This study attempts to further understand the genetic landscape of cutaneous malignant melanoma in terms of loco-regional variations and malignant potential. Thirty-five cases of cutaneous malignant melanoma were retrieved from the archives and were classified based on location of the primary tumor and presence or absence of metastatic disease. Next-generation sequencing data consisting of base substitutions, copy number variations, indels, and rearrangements in a total of 324 genes were analyzed for recurrent genetic alterations. Statistical analysis was performed using IBM SPSS26 software. Mutations in KDM gene family were found in 62.5% of the melanomas in the head and neck as compared with 10% in melanomas of the extremity and trunk (P = 0.03). Mutations in the RAS gene family were found in 70% of melanomas in the extremities as compared to 12.5% in melanomas of the head and neck (P = 0.003). BTK gene mutations were found exclusively in melanomas of the head and neck (P = 0.032). CREBBP mutations were seen in 50% of the nonmetastatic melanomas as compared with 3.57% of metastatic melanomas (P = 0.005). This study highlights the loco-regional variations in cutaneous malignant melanoma for genetic alterations involving the KDM, RAS, and BTK gene family. In addition, the CREBBP mutational status is identified as a potential prognostic marker for predicting metastatic potential in cutaneous malignant melanomas.

Primary Histiocytic Sarcoma in Adult Polycystic Kidney Disease: Case Report and Review of Literature.

Genetically driven tissue destruction followed by remodeling in adult polycystic kidney disease (APKD) raises the possibility of malignant transformation. Renal cell carcinoma (RCC) associated with APKD has been frequently reported in the literature; however, only a few cases of nonepithelial neoplasms arising in APKD have been described so far. Histiocytic sarcoma (HS) is a lymphohematopoietic malignant neoplasm that accounts for less than 1% of hematologic malignancies. In this article, we describe a case of primary HS occurring in a 61-year-old man with end-stage renal disease secondary to APKD. This is the first reported case of primary HS in the setting of APKD. The aberrant h-caldesmon expression seen in this case is another novel finding that has previously not been described. This case highlights the importance of morphology in guiding diagnostic workup and reiterates the necessity of maintaining a high index of suspicion for neoplastic entities in APKD.

The Utility of Elevated Serum Lactate Dehydrogenase in Current Clinical Practice.

OBJECTIVE: Because of its wide tissue distribution, elevation of serum lactate dehydrogenase (LD) is a nonspecific finding. Although serum LD is still included in the prognosis and staging of metastatic melanoma and germ cell tumors, its nonspecificity has led to decreased usefulness. METHODS: In this study, we analyzed the serum LD assays performed in a 726-bed hospital during a 1-year period and reviewed charts of patients with serum LD of >3 standard deviations (SD). RESULTS: Of 312 patients with elevated serum LD, only 9 were patients with melanoma and germ cell tumors. The other 303 patients had other malignancies, chronic conditions, and sepsis. CONCLUSION: Elevated serum LD (even >3 SD) is an extremely nonspecific finding that does not contribute to clinical management in a majority of patients. As such, serum LD testing should be retired from routine clinical order sets and restricted in use.

Title- Genomic landscape of squamous cell carcinoma- Different genetic pathways culminating in a common phenotype.

INTRODUCTION: Squamous cell carcinomas (SqCCs) are the most common solid tumors in humans and are found across multiple organ systems. Although, integrated analysis of genetic alterations divulge similarities between SqCCs from various body sites, certain genes appear to be more frequently mutated in a given SqCC. These subtle differences may hold the key to determining the differentiation characteristics and predicting aggressiveness of tumors. MATERIALS AND METHOD: Fifty-four cases of SqCCs, in which the primary location of the tumor could be ascertained by clinical and radiological findings, were included in this study. Next generation sequencing data was analyzed for recurrent genetic abnormalities. RESULTS: Genetic alterations were found in 219 genes in the 54 cases studied. TP53 mutations were found to be more frequent in pulmonary SqCCs (86.5%) as compared to non-pulmonary SqCCs (58.8%) (p<0.05). NOTCH gene family mutations and CREBBP mutations were limited to non-pulmonary SqCC (p<0.005) and were mutated in 41.2% and 17.6% cases. CONCLUSION: A detailed comparative analysis of the genetic alterations identified by sequencing identified higher frequency of TP53 mutations in lung SqCCs as compared to non-pulmonary SqCCs. NOTCH and CREBPP mutations were found to be absent in lung and head and neck SqCCs and more frequent in SqCCs from other locations.

Lost in the Clinics and Found in the Morgue: A Case of Peripheral T-cell Lymphoma Masquerading as Pneumonia.

In modern medicine, there is an increasing dependence on noninvasive imaging modalities, for diagnosis and management of diseases. Though there are definite advantages to this, they are at times offset by diagnostic pitfalls especially in entities with elusive clinical presentation.Peripheral T-cell lymphoma-not otherwise specified (PTCL-NOS) is an aggressive subtype of T-cell lymphomas that does not meet criteria for a specific subtype. Peripheral T-cell lymphoma usually has varied clinical presentations depending on the site of involvement. Vast majority of PTCL patients present with systemic disease, generalized lymphadenopathy and constitutional symptoms. Pulmonary involvement is relatively rare and is seen in approximately 10% of patients.Here in we highlight a rare case of PTCL, masquerading as pneumonia due to extensive pulmonary involvement that went undiagnosed and was discovered at autopsy. This case of malignant lymphoma of T-cell origin involving the lung, which is very rare, highlights the continued importance of medical autopsies not only as a teaching tool but also as an important adjunct to investigative medicine in uncovering lapses that can subsequently be avoided to improve patient care and decrease mortality.

Retinoblastoma co-repressor 1 (RB) and cyclin-dependent kinase inhibitor (CDKN) as a multi-gene panel for differentiating pulmonary from non-pulmonary origin in metastatic neuroendocrine carcinomas.

BACKGROUND: Neuroendocrine carcinomas (NECs) arise from neuroendocrine cells present throughout the body, and often present with metastases even with small and undetectable primary tumors. Additionally, neuroendocrine differentiation can be seen in carcinomas of non-neuroendocrine origin further complicating the landscape of metastatic NECs. Organ specific immunohistochemical markers such as TTF1, CDX2 and PAX8 are often lost in high grade tumors and may be non-contributory in localizing the primary site. Though NECs share a common cellular origin, they exhibit great variability in biologic behavior, prognosis and treatment based on the primary organ of origin. DESIGN: Twenty one cases of metastatic NECs were retrieved from our archives and were classified based on location of the primary tumor derived from clinical and radiological findings. Next generation sequencing data was retrieved and analyzed for recurrent genetic abnormalities in these cases. Statistical analysis was performed using IBM SPSS25 software. RESULTS: RB1 mutations were exclusive to NECs metastasizing from lung primary and were detected in 5 of 12 (41.6 %) cases (p = 0.04). CDKN gene family (CDKN1B and 2 A) mutations were limited to metatstatic NECs of non-pulmonary origin and were detected in 4 of 9 (44.4 %) cases (p = 0.02). CONCLUSION: The location of the primary tumor in metastatic NECs appears to have significant prognostic and therapeutic implications. But due to the morphological homogeneity, higher grade of tumor, variable sensitivity of immunohistochemical markers, and small, often undetectable primary tumors, the localization of the primary tumor in cases of metastatic NECs is a challenge. In this study, RB1 and CDKN gene family mutations are identified as possible markers for differentiating pulmonary and non-pulmonary origin in metatstatic NECs.