Validation and Implementation of a Somatic-Only Tumor Exome for Routine Clinical Application.

Next-generation sequencing-based genomic testing is standard of care for tumor workflows. However, its application across different institutions continues to be challenging given the diversity of needs and resource availability among different institutions globally. Moreover, the use of a variety of different panels, including those from a few individual genes to those involving hundreds of genes, results in a relatively skewed distribution of care for patients. It is imperative to obtain a higher level of standardization without having to be restricted to specific kits or requiring repeated validations, which are generally expensive. We show the validation and clinical implementation of the DH-CancerSeq assay, a tumor-only whole-exome-based sequencing assay with integrated informatics, while providing similar input requirements, sensitivity, and specificity to a previously validated targeted gene panel and maintaining similar turnaround times for patient care.

Chondrolipoma of the Breast: A Myofibroblastoma Variant or a Distinct Lesion?

The entity commonly referred to as chondrolipoma is a rare and enigmatic breast lesion with unclear histogenesis and a complete lack of molecular characterization. It is uncertain whether it represents a hamartoma, choristoma, or a distinct neoplasm, including possibly a variant of mammary-type myofibroblastoma. We report two additional chondrolipomatous lesions of the breast. The lesions had varying histologic and immunohistochemical features similar to myofibroblastoma, including the loss of retinoblastoma (Rb) protein expression in one lesion. Molecular analysis by chromosomal microarray analysis performed on a second lesion did not demonstrate a loss of 13q14 or 16q typical of myofibroblastoma. Our findings further support the concept that at least a subset of breast lesions that historically have been classified as chondrolipoma are related to myofibroblastoma. However, the lack of myofibroblastoma-specific molecular alterations in one lesion suggests chondrolipomas may also have varying origins.

Atypical Spindle Cell/Pleomorphic Lipomatous Tumor With Sarcomatous Transformation: Clinicopathologic and Molecular Analysis of 4 Cases.

Atypical spindle cell/pleomorphic lipomatous tumor (ASPLT) is a recently described adipocytic tumor predominantly affecting the subcutaneous soft tissues of adults. Previous studies have shown that ASPLT follows a benign clinical course with a 4% to 12% local recurrence rate and no risk of dedifferentiation. Herein, we describe the clinicopathologic and molecular findings of 4 cases of ASPLT showing unequivocal sarcomatous transformation. Three patients were male and one was female, aged 65, 70, 74, and 78 years. Two cases presented as mass-forming lesions, while 1 case was incidentally discovered. The tumors measured 30, 55, 80, and 110 mm and occurred in the chest wall (n = 2) or arm (n = 2); all were subcutaneous. Microscopically, they showed a biphasic appearance comprising a low-grade ASPLT component and a high-grade sarcomatous component. The low-grade components showed features in the spectrum of either atypical pleomorphic lipomatous tumor (n = 2) or atypical spindle cell lipomatous tumor (n = 2). The high-grade components displayed leiomyosarcoma-like (n = 2), pleomorphic liposarcoma-like (n = 1) or undifferentiated sarcoma-like (n = 1) morphology. On immunohistochemistry, tumors were negative for MDM2 and showed loss of RB1 expression. In addition, the leiomyosarcoma-like areas seen in 2 cases were positive for smooth muscle actin and H-caldesmon. Single-nucleotide polymorphism array, performed in 3 cases, showed deletions of TP53, RB1, and flanking genes in both components. In contrast, the sarcomatous components showed more complex genomic profiles with rare segmental gains and recurrent loss of PTEN (n = 3), ATM (n = 2), and CDKN2A/B (n = 2) among other genes. Whole exome sequencing identified a TP53 variant in one case and an ATRX variant in another, each occurring in both tumor components. Limited clinical follow-up showed no recurrence or metastasis after 1 to 13 months (median, 7.5 months) postsurgical excision. Altogether, our data support that ASPLT can rarely develop sarcomatous transformation and offer insights into the molecular mechanisms underlying this event.

A rapid, multiplex digital PCR assay to detect gene variants and fusions in non-small cell lung cancer.

Digital PCR (dPCR) is emerging as an ideal platform for the detection and tracking of genomic variants in cancer due to its high sensitivity and simple workflow. The growing number of clinically actionable cancer biomarkers creates a need for fast, accessible methods that allow for dense information content and high accuracy. Here, we describe a proof-of-concept amplitude modulation-based multiplex dPCR assay capable of detecting 12 single-nucleotide and insertion/deletion (indel) variants in EGFR, KRAS, BRAF, and ERBB2, 14 gene fusions in ALK, RET, ROS1, and NTRK1, and MET exon 14 skipping present in non-small cell lung cancer (NSCLC). We also demonstrate the use of multi-spectral target-signal encoding to improve the specificity of variant detection by reducing background noise by up to an order of magnitude. The assay reported an overall 100% positive percent agreement (PPA) and 98.5% negative percent agreement (NPA) compared with a sequencing-based assay in a cohort of 62 human formalin-fixed paraffin-embedded (FFPE) samples. In addition, the dPCR assay rescued actionable information in 10 samples that failed to sequence, highlighting the utility of a multiplexed dPCR assay as a potential reflex solution for challenging NSCLC samples.

Data-driven choice of a model selection method in joinpoint regression.

Selecting the number of change points in segmented line regression is an important problem in trend analysis, and there have been various approaches proposed in the literature. We first study the empirical properties of several model selection procedures and propose a new method based on two Schwarz type criteria, a classical Bayes Information Criterion (BIC) and the one with a harsher penalty than BIC (BIC3). The proposed rule is designed to use the former when effect sizes are small and the latter when the effect sizes are large and employs the partial R2 to determine the weight between BIC and BIC3. The proposed method is computationally much more efficient than the permutation test procedure that has been the default method of Joinpoint software developed for cancer trend analysis, and its satisfactory performance is observed in our simulation study. Simulations indicate that the proposed method performs well in keeping the probability of correct selection at least as large as that of BIC3, whose performance is comparable to that of the permutation test procedure, and improves BIC3 when it performs worse than BIC. The proposed method is applied to the U.S. prostate cancer incidence and mortality rates.

Sinonasal Myxoma: A Distinct Entity or a Myxoid Variant of Desmoid Fibromatosis?

Sinonasal myxoma (SNM) is a rare benign mesenchymal tumor that arises in the sinonasal cavity or maxilla and almost exclusively affects young children. Currently, it is considered a specific entity, but its molecular characteristics have not been reported. Lesions diagnosed as SNM and odontogenic myxoma/fibromyxoma were identified from the participating institutions, and the clinicopathologic features were recorded. Immunohistochemistry for ß-catenin was performed in all cases with available tissue. Next-generation sequencing was performed in all cases with SNM. Five patients with SNM were identified, including 3 boys and 2 girls with an age range of 20-36 months (mean: 26 months). The tumors were well defined, centered in the maxillary sinus, surrounded by a rim of woven bone, and composed of a moderately cellular proliferation of spindle cells oriented in intersecting fascicles in a variably myxocollagenous stroma that contained extravasated erythrocytes. Histologically, the tumors resembled myxoid desmoid fibromatosis. Three tested cases showed nuclear expression of ß-catenin. In 3 tumors, next-generation sequencing revealed intragenic deletions of APC exons 5-6, 9 and 15, or 16, respectively, with concurrent loss of the other wild-type copy of APC predicted to result in biallelic inactivation. The deletions were identical to those that occur in desmoid fibromatosis, and copy number analysis raised the possibility that they were germline. In addition, 1 case showed the possible deletion of APC exons 12-14, and another case exhibited a CTNNB1 p. S33C mutation. Ten patients with odontogenic myxoma/fibromyxoma were identified, including 4 women and 6 men (mean age: 42 years). Seven tumors involved the mandible and 3 the maxilla. Histologically, the tumors differed from SNM, and all cases lacked nuclear expression of ß-catenin. These findings suggest that SNM represents a myxoid variant of desmoid fibromatosis that often arises in the maxilla. The APC alterations might be germline, and therefore, genetic testing of the affected patients should be considered.

Utility of Retrospective Molecular Analysis in Diagnostically Challenging Mesenchymal Neoplasms.

Introduction: Molecular analysis plays a growing role in the diagnosis of mesenchymal neoplasms. The aim of this study was to retrospectively apply broad, multiplex molecular assays (a solid tumor targeted next-generation sequencing [NGS]) assay and single nucleotide polymorphism [SNP] microarray) to selected tumors, exploring the current utility and limitations. Methods: We searched our database (2010-2020) for diagnostically challenging mesenchymal neoplasms. After histologic review of available slides, tissue blocks were selected for NGS, SNP microarray, or both. DNA and RNA were extracted using the AllPrep DNA/RNA FFPE Kit Protocol on the QIAcube instrument. The NGS platform used was the TruSight Tumor 170 (TST-170). For SNP array, copy number variant (CNV) analysis was performed using the OncoScanTM CNV Plus Assay. Results: DNA/RNA was successfully extracted from 50% of tumors (n = 10/20). Specimens not successfully extracted included 6 core biopsies, 3 incisional biopsies, and 1 resection; 4 were decalcified (3 hydrochloric acid, 1 ethylenediaminetetraacetic acid). Higher tumor proportion and number of tumor cells were parameters positively associated with sufficient DNA/RNA extraction whereas necrosis and decalcification were negatively associated with sufficient extraction. Molecular testing helped reach a definitive diagnosis in 50% of tumors (n = 5/10). Conclusions: Although the overall utility of this approach is limited, these molecular panels can be helpful in detecting a specific "driver" alteration.

Shift Length and Shift Length Preference Among Acute Care Surgeons.

BACKGROUND: Work hour restrictions have been imposed by the Accreditation Council for Graduate Medical Education since 2003 for medical trainees. Many acute care surgeons currently work longer shifts but their preferred shift length is not known. METHODS: The purpose of this study was to characterize the distribution of the current shift length among trauma and acute care surgeons and to identify the surgeons' preference for shift length. Data collection included a questionnaire with a national administration. Frequencies and percentages are reported for categorical variables and medians and means with SDs are reported for continuous variables. A chi-square test of independence was performed to examine the relation between call shift choice and trauma center level (level 1 and level II), age, and gender. RESULTS: Data from 301 surgeons in 42 states included high-level trauma centers. Assuming the number of trauma surgeons in the United States is 4129, a sample of 301 gives the survey a 5% margin of error. The median age was 43 years (M = 46, SD = 9.44) and 33% were female. Currently, only 23.3% of acute care surgeons work a 12-hour shift, although 72% prefer the shorter shift. The preference for shorter shifts was statistically significant. There was no significant difference between call shift length preference and trauma center level, age, or gender. CONCLUSION: Most surgeons currently work longer than 12-hour shifts. Yet, there was a preference for 12-hour shifts indicating there is a gap between current and preferred shift length. These findings have the potential to substantially impact staffing models.

Indolent B-cell lymphoma with t(14;19) investigated from a molecular perspective.

T(14;19) is an unusual but distinct genomic alteration reported in low-grade B-cell lymphomas. This structural rearrangement places BCL3 in juxtaposition with IGH inducing proliferation and has been found in chronic lymphocytic leukemia/small lymphocytic lymphoma (CLL/SLL), marginal zone lymphoma (MZL), and other low-grade B-cell lymphomas. While there are some case series describing this in the context of other cytogenetic alterations, there are limited clinical cases examined from a molecular perspective. We herein describe a case of a low-grade B-cell lymphoma with t(14;19) resulting in IGH::BCL3 fusion on which we performed whole exome sequencing to investigate genetic variants that could contribute to its pathogenesis. We found pathogenic alterations including a variant in CXCR4 which has been shown to be recurrently mutated in different low-grade B-cell lymphomas including lymphoplasmacytic lymphoma (LPL) and MZL. We describe this interesting case in the context of its genomic findings and how it contributes to the literature as a whole.

Partisan Stability During Turbulent Times: Evidence from Three American Panel Surveys.

The past decade has witnessed profound changes in the tenor of American party politics. These changes, in tandem with growing affective polarization and residential segregation by party, raise the question of whether party identification is itself changing. Using three multi-wave panel surveys that stretch from the first Obama Administration through the Trump Administration, this paper takes a fresh look at the stability of party identification, using several different statistical approaches to differentiate true partisan change from response error. Perhaps surprisingly, the pace of partisan change observed between 2011 and 2020 is quite similar to the apparent rates of change in panel surveys dating back to the 1950s. Few respondents experience appreciable change in party identification in the short run, but the pace at which partisanship changes implies that substantial changes are relatively common over a voter's lifespan. Supplementary Information: The online version contains supplementary material available at 10.1007/s11109-022-09825-y.

Multiple gallstones causing ileus twenty years after cholecystectomy.

Gallstone ileus is an important form of small bowel obstruction that occurs in less than 0.5% of patients who present with obstruction. A biliary enteric fistula that evolves in the setting of chronic cholecystitis may allow the passage of a large gallstone into the gastrointestinal tract distal to the common duct. A single stone that is sufficient in size (at least 2-2.5 cm diameter) may then create a mechanical obstruction, most often at the ileocecal valve or the terminal ileum where the intestinal lumen narrows, and where peristalsis is less robust. We present an unusual case of gallstone ileus in a patient whose obstruction was caused by not one, but seven individual gallstones, collectively restricted in the jejunum at the point of a previous anastomosis and occurring twenty years after cholecystectomy.

Molecular analysis of NUT-positive poromas and porocarcinomas identifies novel break points of YAP1::NUTM1 fusions.

BACKGROUND: Poromas, and their malignant counterparts, porocarcinomas, harbor recurrent translocations involving YAP1-MAML2, YAP1-NUTM1, and infrequently WWTR1-NUTM1; YAP1-NUTM1 being the most common in porocarcinomas. NUT immunohistochemistry (IHC) can be used to identify NUTM1-translocated tumors. This study sought to investigate potential novel NUTM1-fusion partners among NUT IHC-positive poromas and porocarcinomas. METHODS: Thirteen NUT IHC-positive poroid tumors (four poromas and nine porocarcinomas) were identified within a multi-institutional international cohort. Next-generation sequencing (NGS) assessed for NUTM1 fusion partners. RESULTS: NGS detected a NUTM1 fusion in 12 of 13 cases: YAP1-NUTM1 (11/12 cases) and WWTR1-NUTM1 (1/12 cases). Two of the cases (2/12) with NUTM1 fusion were not called by the NGS algorithm but had at least one read-spanning YAP1-NUTM1 break point upon manual review. A NUTM1 fusion was not identified in one case; however, the sample had low RNA quality. The following fusion events were identified: YAP1 exon 4::NUTM1 exon 3 in six cases, YAP1 exon 6::NUTM1 exon 2 in one case, YAP1 exon 3::NUTM1 exon 3 in three cases, WWTR1 exon 3::NUTM1 exon 3 in one case, and YAP1 exon 8::NUTM1 exon 3 fusion in one case. CONCLUSION: While no novel NUTM1 fusion partners were identified within our cohort, 12 of 13 cases had discoverable NUTM1 fusions; YAP1-NUTM1 fusion was detected in 11 cases (92%) and WWTR1-NUTM1 in 1 case (8%). These data corroborate findings from other recent investigations and further substantiate the utility of NUT IHC in diagnosing a subset of poroid neoplasms. In addition, two of our cases harbored fusions of YAP1 exon 6 to NUTM1 exon 3 and YAP1 exon 8 to NUTM1 exon 2, which have not been reported before in poroid neoplasms and indicate novel break points of YAP1.

Molecular investigation of ALK-rearranged epithelioid fibrous histiocytomas identifies CLTC as a novel fusion partner and evidence of fusion-independent transcription activation.

Epithelioid fibrous histiocytoma (EFH) is a rare cutaneous neoplasm, which is characterized by the presence of rearrangements involving the ALK gene. Although EFH was long considered a variant of fibrous histiocytoma, the identification of its unique genetic signature confirmed that it represents a distinct entity. The aim of the present study was to examine a cohort of ALK-immunoreactive EFH cases to further characterize gene fusion partners. Next generation sequencing detected ALK fusions in 11 EFH cases identified in the pathology archives of two different institutions. The most common fusion partner was DCTN1 (N = 4) followed by CLTC (N = 2) and VCL (N = 2), while the remaining cases harbored fusions involving SPECC1L, PPFIBP1, and PRKAR1A. In one case no fusion was detected by NGS and FISH despite suitable sample quality. Notably, IHC demonstrated positive ALK expression and the level of aligned ALK reads was comparable to the fusion-positive cases. To the best of our knowledge, this is the first report of CLTC as a fusion partner in EFH. The two CLTC rearranged cases in our cohort also represent the first two EFH cases in the literature that involve exon 19 of ALK, instead of exon 20. These findings underscore the remarkable plasticity of ALK as an oncogenic driver and further expand the list of its potential fusion partners in EFH. Lastly this is also the first report of ALK-immunoreactive EFH with no underlying fusion suggesting a fusion independent transcription mechanism as seen in other tumors.

A Rare Case of Low-Grade Dedifferentiated Liposarcoma Presenting as a Pharyngeal Polyp: Avoiding a Pitfall With Significant Repercussions.

Dedifferentiated liposarcoma is a nonlipogenic sarcoma of variable histological grade that frequently arises in association with a well-differentiated liposarcoma. Dedifferentiation occurs in approximately 10% of well-differentiated liposarcomas and is most commonly encountered in the retroperitoneum. Dedifferentiated liposarcoma of the upper respiratory tract is an extremely rare occurrence. Herein, we report a very rare case of low-grade dedifferentiated liposarcoma of the pharynx that presented as a polyp mimicking a benign process clinically and microscopically. We discuss the relevant molecular findings and review the current literature.

A comparison of motorcycle instructor candidate selection practices in the United States.

INTRODUCTION: An essential aspect of motorcycle rider education is how the instructor selection process impacts student learning, sometimes referred to as the human element, as it is a significant factor influencing curriculum success. Student and program achievements are partially contingent on instructors who understand the curriculum and facilitate student learning during instruction. Previous research on motorcycle rider education has emphasized a need for the examination of instructor selection and development, stating that quality education is reliant on instructors who are competent and qualified. METHOD: By applying an exploratory study method, state and military Motorcycle Safety Education Program Managers and Instructor Trainers were examined and compared through telephonic interviews to develop a greater understanding of instructor candidate selection criteria and vetting processes. RESULTS: The results suggest that changes in instructor candidate selection systems may improve decisions about a candidate's job and organizational fit. CONCLUSIONS: Study conclusions indicate that use of multiple and thorough assessments to determine a candidate's motivation, social disposition, and emotional intelligence before preparation courses may better identify candidates and align potential job and organization fit within the discipline. Practical Application: Applications of the findings would include a standardized selection process with improved interviews and pre-course auditing, and candidate expectation management before the selection to attend preparation or certification courses. The efforts potentially decrease long-term costs and deficiencies when candidates have an inconsistent job or organizational fit, departing from organizations after short periods or by not providing consistent quality instruction to students. The study recommendations, when implemented, can improve most educational disciplines where instructors are selected for technical instructional positions where students risk injury or harm.

A Radio Drama's Effects on HIV Attitudes and Policy Priorities: A Field Experiment in Tanzania.

A growing body of evidence investigates how entertainment education influences knowledge about HIV, stigma toward those with HIV, and openness to disclosing one's HIV status. The present study shows that in addition to these effects, mass media interventions may influence audiences' policy priorities, such as their demand for local access to HIV/AIDS medical care. A condensed (2 hours) version of a popular Swahili radio drama was presented to rural Tanzanians as part of a placebo-controlled experiment, clustered at the village level. A random sample comprising 1,200 participants were interviewed at baseline and invited to attend a presentation of the radio drama, and 83% attended. Baseline respondents were reinterviewed 2 weeks later with a response rate of 95%. In addition to increasing listeners' knowledge and support for disclosure of HIV status, the radio drama produced sizable and statistically significant effects on listeners' preference for hypothetical candidates promising improved HIV/AIDS treatment.

Prejudice Reduction: Progress and Challenges.

The past decade has seen rapid growth in research that evaluates methods for reducing prejudice. This essay reviews 418 experiments reported in 309 manuscripts from 2007 to 2019 to assess which approaches work best and why. Our quantitative assessment uses meta-analysis to estimate average effects. Our qualitative assessment calls attention to landmark studies that are noteworthy for sustained interventions, imaginative measurement, and transparency. However, 76% of all studies evaluate light touch interventions, the long-term impact of which remains unclear. The modal intervention uses mentalizing as a salve for prejudice. Although these studies report optimistic conclusions, we identify troubling indications of publication bias that may exaggerate effects. Furthermore, landmark studies often find limited effects, which suggests the need for further theoretical innovation or synergies with other kinds of psychological or structural interventions. We conclude that much research effort is theoretically and empirically ill-suited to provide actionable, evidence-based recommendations for reducing prejudice.

Molecular genetic profiling reveals novel association between FLT3 mutation and survival in glioma.

INTRODUCTION: Recent molecular characterization of gliomas has uncovered somatic gene variation and DNA methylation changes that are associated with etiology, prognosis, and therapeutic response. Here we describe genomic profiling of gliomas assessed for associations between genetic mutations and patient outcomes, including overall survival (OS) and recurrence-free survival (RFS). METHODS: Mutations in a 50-gene cancer panel, 1p19q co-deletion, and MGMT promoter methylation (MGMT methylation) status were obtained from tumor tissue of 293 glioma patients. Multivariable regression models for overall survival (OS) and recurrence-free survival (RFS) were constructed for MGMT methylation, 1p19q co-deletion, and gene mutations controlling for age, treatment status, and WHO grade. RESULTS: Mutational profiles of gliomas significantly differed based on WHO Grade, such as high prevalence of BRAF V600E, IDH1, and PTEN mutations in WHO Grade I, II/III, and IV tumors, respectively. In multivariate regression analysis, MGMT methylation and IDH1 mutations were significantly associated with improved OS (HR = 0.44, p = 0.0004 and HR = 0.21, p = 0.007, respectively), while FLT3 and TP53 mutations were significantly associated with poorer OS (HR = 19.46, p < 0.0001 and HR = 1.67, p = 0.014, respectively). MGMT methylation and IDH1 mutations were the only significant alterations associated with improved RFS in the model (HR = 0.42, p < 0.0001 and HR = 0.37, p = 0.002, respectively). These factors were then included in a combined model, which significantly exceeded the predictive value of the base model alone (age, surgery, radiation, chemo, grade) (likelihood ratio test OS p = 1.64 × 10-8 and RFS p = 3.80 × 10-7). CONCLUSIONS: This study highlights the genomic landscape of gliomas in a single-institution cohort and identifies a novel association between FLT3 mutation and OS in gliomas.