Erratum: Bicritical states in temperature-modulated Rayleigh-Bénard convection [Phys. Rev. E 92, 013005 (2015)].

This corrects the article DOI: 10.1103/PhysRevE.92.013005.

Nonkeratinizing Nasopharyngeal Carcinoma, Undifferentiated Type With Trisomy 2: A Case Report and Short Review of Cytogenetic and Molecular Literature.

Carcinoma originating from the surface epithelium of the nasopharynx is classified by the World Health Organization (WHO) as nasopharyngeal carcinoma (NPC) and has 3 main types: keratinizing squamous cell carcinoma (WHO type 1) and nonkeratinizing carcinoma, differentiated (WHO type II), and undifferentiated (WHO type III). Nonkeratinizing NPC is strongly associated with prior Epstein-Barr virus (EBV) infection. These tumors may be divided into differentiated and undifferentiated carcinoma. Histologically, the tumor is characterized by syncytia of large malignant cells with vesicular nuclei, conspicuous nucleoli, and easily observed mitotic figures. We report a case of a 14-year-old boy diagnosed with EBV and human papillomavirus (HPV)-positive NPC (WHO type 3) with cytogenetics showing the presence of mosaic trisomy 2. This case report brings to light a rare cytogenetic aberration to our knowledge only reported once before in the literature in a xenograft model.

Bicritical states in a vertical layer of fluid under two-frequency temperature modulation.

In this paper, the effect of two-frequency modulation of boundary temperatures on the onset of natural convection in a layer of fluid (with Prandtl number <12.5) between two vertical parallel planes is considered. The ratio of the two forcing frequencies and the mixing angle for the amplitude of modulation provide an efficient way of controlling the underlying instability. At the onset of instability, the fluid layer executes harmonic and subharmonic oscillations. The transition between harmonic and subharmonic responses is found to occur through an intermediate bicritical state. In addition to bicritical states, the instability is found to exhibit an almost tricritical state for a particular combination of the modulation parameters. The onset of the instability depends upon the modulation parameters and Prandtl number of the fluid.

Rayleigh-Bénard convection with two-frequency temperature modulation.

The response of Rayleigh-Bénard convection in a horizontal fluid layer to time-periodic heating of its horizontal boundaries with a mixture of two frequencies is analyzed numerically. The ratio of the two forcing frequencies and the mixing angle of the amplitudes of modulation provide a control on the instability of the system. In addition to the existence of well-known harmonic and subharmonic instability responses under modulation, the time-periodic oscillation of the boundary temperatures of the fluid-layer with two frequencies results in more bicritical states in comparison to the single-frequency excitation. The onset of instability depends strongly on the modulation parameters and the Prandtl number of the fluid.

Bicritical states in temperature-modulated Rayleigh-Bénard convection.

We investigate the Rayleigh-Bénard convection under sinusoidally varying temperatures of the horizontal rigid planes bounding a laterally infinite fluid layer for the bicritical states. The problem is analogous to the well studied Faraday instability and Rayleigh-Bénard convection under gravity modulation. Under modulation, the neutral instability curve is found to alternate between the conventional harmonic and subharmonic tongues in the space of the dimensionless wave number of disturbance and the control parameter. The transition between harmonic and subharmonic critical instability responses is found to occur via a bicritical state, where the two instability responses coexist with different wave numbers. These bicritical states are found to depend upon the modulation parameters and the Prandtl number.

Comparison of Chromogenic In Situ Hybridization and Fluorescence In Situ Hybridization for the Evaluation of MDM2 Amplification in Adipocytic Tumors.

BACKGROUND: Atypical lipomatous tumor/well-differentiated liposarcoma (ALT-WDLPS) and dedifferentiated liposarcoma (DDLPS) are characterized cytogenetically by a 12q13-15 amplification involving the mouse double minute 2 (MDM2) oncogene. Fluorescence in situ hybridization (FISH) is used frequently to detect this amplification and aid with the diagnosis of these entities, which is difficult by morphology alone. Recently, bright-field in situ hybridization techniques such as chromogenic in situ hybridization (CISH) have been introduced for the determination of MDM2 amplification status. METHODS: The present study compared the results of FISH and CISH for detecting MDM2 amplification in 41 cases of adipocytic tumors. Amplification was defined in both techniques as a MDM2/CEN12 ratio of 2 or greater. RESULTS: Eleven cases showed amplification with both FISH and CISH, and 26 cases showed no amplification with both methods. Two cases had discordant results between CISH and FISH, and two cases were not interpretable by CISH. CONCLUSION: CISH is advantageous for allowing pathologists to evaluate the histologic and molecular alterations occurring simultaneously in a specimen. Moreover, CISH is found to be more cost- and time-efficient when used with automation, and the signals do not quench over time. CISH technique is a reliable alternative to FISH in the evaluation of adipocytic tumors for MDM2 amplification.

Validation of a next-generation-sequencing cancer panel for use in the clinical laboratory.

CONTEXT: Next-generation sequencing allows for high-throughput processing and sensitive variant detection in multiple genes from small samples. For many diseases, including cancer, a comprehensive mutational profile of a targeted list of genes can be used to simultaneously inform patient care, establish eligibility for ongoing clinical trials, and further research. OBJECTIVE: To validate a pan-cancer, next-generation-sequencing assay for use in the clinical laboratory. DESIGN: DNA was extracted from 68 clinical specimens (formalin-fixed, paraffin-embedded; fine-needle aspirates; peripheral blood; or bone marrow) and 5 normal controls. Sixty-four DNA samples (94%; 64 of 68) were successfully processed with the TruSeq Amplicon Cancer Panel (Illumina Inc, San Diego, California) and sequenced in 4 sequencing runs. The data were analyzed at 4 different filter settings for sequencing coverage and variant frequency cutoff. RESULTS: Libraries created from 40 specimens could be successfully sequenced in a single run and still yield sufficient coverage for robust data analysis of individual samples. Sensitivity for mutation detection down to 5% was demonstrated using dilutions of clinical specimens and control samples. The test was highly repeatable and reproducible and showed 100% concordance with clinically validated Sanger sequencing results. Comparison to an alternate next-generation sequencing technology was performed by also processing 9 of the specimens with the AmpliSeq Cancer Hotspot Panel (version 2; Life Technologies, Grand Island, New York). Thirty of the 31 (97%) TruSeq-detected variants covered by the designs of both panels were confirmed. CONCLUSIONS: A sensitive, high-throughput, pan-cancer mutation panel for sequencing of cancer hot-spot mutations in 42 genes was validated for routine use in clinical testing.

The utility of BRAF V600E mutation-specific antibody VE1 for the diagnosis of hairy cell leukemia.

OBJECTIVES: BRAF V600E mutation is characteristic of hairy cell leukemia (HCL). A V600E mutation-specific antibody, VE1, has been recently developed. We studied the diagnostic utility of this antibody in HCL and compared it with other B-cell neoplasms. METHODS: VE1 activity was assessed using immunohistochemistry in 90 mature B-cell neoplasms, including HCL (n = 17), HCL variant (n = 6), chronic lymphocytic leukemia (CLL) (n = 20), and 47 other B-cell lymphomas. Most (87/90) specimens were formalin-fixed, paraffin-embedded bone marrow (BM) biopsy specimens decalcified in either hydrochloric acid or formic acid. RESULTS: VE1 was positive in 15 (88%) cases of HCL and two (10%) cases of CLL and was negative in all other tumors assessed. The VE1-positive HCL cases showed uniform staining in all tumor cells, but intensity was variable. The two VE1-negative HCL cases had BRAF V600 mutations proven by molecular analysis. The two CLL cases positive with VE1 showed an atypical staining pattern with expression in a minority of lymphoma cells. Immunohistochemistry using the VE1 antibody had a sensitivity of 88% and a specificity of 97% for HCL. CONCLUSIONS: VE1 immunohistochemistry is a useful and convenient surrogate for detecting BRAF V600E mutation in BM biopsy specimens decalcified with hydrochloric or formic acid-based solutions.

Primary central nervous system Epstein-Barr virus-positive diffuse large B-cell lymphoma of the elderly: a clinicopathologic study of five cases.

We report five cases of primary central nervous system (CNS) Epstein-Barr virus (EBV)-positive lymphoma of the elderly. This represented an incidence of 4 % of primary CNS diffuse large B-cell lymphoma (DLBCL) after EBV screening in 134 cases. All five patients were 65 years or older with no previous history of congenital or iatrogenic immune deficiencies. The histologic morphology of all the cases was DLBCL, with variable amounts of necrosis. The cell of origin (COO) as determined by the Hans algorithm disclosed germinal center type in 2 cases and non-germinal center type in 3 cases. MYC translocation was not detected, and MYC overexpression was detected in only one case. Three patients died shortly after diagnosis, and the remaining 2 patients were in complete remission for 2 and 10 years, respectively. We conclude that EBV+ DLBCL among the elderly is uncommon in primary CNS lymphoma in the Eastern United States. The patients usually present with a single mass lesion with headache and sensorimotor symptoms. The histologic morphology is DLBCL, but clonal T-cell gene rearrangement may be detected. The outcome varies from case to case and appears to be unrelated to the COO or MYC status.

STAT5A/B gene locus undergoes amplification during human prostate cancer progression.

The molecular mechanisms underlying progression of prostate cancer (PCa) to castrate-resistant (CR) and metastatic disease are poorly understood. Our previous mechanistic work shows that inhibition of transcription factor Stat5 by multiple alternative methods induces extensive rapid apoptotic death of Stat5-positive PCa cells in vitro and inhibits PCa xenograft tumor growth in nude mice. Furthermore, STAT5A/B induces invasive behavior of PCa cells in vitro and in vivo, suggesting involvement of STAT5A/B in PCa progression. Nuclear STAT5A/B protein levels are increased in high-grade PCas, CR PCas, and distant metastases, and high nuclear STAT5A/B expression predicts early disease recurrence and PCa-specific death in clinical PCas. Based on these findings, STAT5A/B represents a therapeutic target protein for advanced PCa. The mechanisms underlying increased Stat5 protein levels in PCa are unclear. Herein, we demonstrate amplification at the STAT5A/B gene locus in a significant fraction of clinical PCa specimens. STAT5A/B gene amplification was more frequently found in PCas of high histologic grades and in CR distant metastases. Quantitative in situ analysis revealed that STAT5A/B gene amplification was associated with increased STAT5A/B protein expression in PCa. Functional studies showed that increased STAT5A/B copy numbers conferred growth advantage in PCa cells in vitro and as xenograft tumors in vivo. The work presented herein provides the first evidence of somatic STAT5A/B gene amplification in clinical PCas.

Bi-allelic deletions within 13q14 and transient trisomy 21 with absence of GATA1s in pediatric acute megakaryoblastic leukemia.

Oligonucleotide array comparative genomic hybridization, karyotype and fluorescence in situ hybridization analyses were employed to delineate the cytogenetic abnormalities in a case of pediatric acute megakaryoblastic leukemia. Here we present a unique genetic profile that includes bi-allelic deletions within 13q14, where the retinoblastoma tumor suppressor gene (RB1) resides, as well as isolated trisomy 21 without a concomitant mutation in the hematopoietic transcription factor GATA1s and translocation (17;22), that does not involve the megakaryoblastic leukemia 1 (MKL1) gene located on chromosome 22. Alteration of the RB1 gene is most likely the critical leukemogenic event in this patient.

Evidence-based genomic diagnosis characterized chromosomal and cryptic imbalances in 30 elderly patients with myelodysplastic syndrome and acute myeloid leukemia.

BACKGROUND: To evaluate the clinical validity of genome-wide oligonucleotide array comparative genomic hybridization (aCGH) for detecting somatic abnormalities, we have applied this genomic analysis to 30 cases (13 MDS and 17 AML) with clonal chromosomal abnormalities detected in more than 50% of analyzed metaphase cells. RESULTS: The aCGH detected all numerical chromosomal gains and losses from the mainline clones and 113 copy number alterations (CNAs) ranging from 0.257 to 102.519 megabases (Mb). Clinically significant recurrent deletions of 5q (involving the RPS14 gene), 12p12.3 (ETV6 gene), 17p13 (TP53 gene), 17q11.2 (NF1 gene) and 20q, double minutes containing the MYC gene and segmental amplification involving the MLL gene were further characterized with defined breakpoints and gene contents. Genomic features of microdeletions at 17q11.2 were confirmed by FISH using targeted BAC clones. The aCGH also defined break points in a derivative chromosome 6, der(6)t(3;6)(q21.3;p22.2), and an isodicentric X chromosome. However, chromosomally observed sideline clonal abnormalities in five cases were not detected by aCGH. CONCLUSIONS: Our data indicated that an integrated cytogenomic analysis will be a better diagnostic scheme to delineate genomic contents of chromosomal and cryptic abnormalities in patients with MDS and AML. An evidence-based approach to interpret somatic genomic findings was proposed.

Double-minute MYC amplification and deletion of MTAP, CDKN2A, CDKN2B, and ELAVL2 in an acute myeloid leukemia characterized by oligonucleotide-array comparative genomic hybridization.

Chromosomal analysis and fluorescence in situ hybridization (FISH) have been routinely used in detecting recurrent chromosomal abnormalities in patients with various hematological malignancies. However, the genomic imbalances underlying many recurrent abnormalities could not be delineated due to the low resolution of chromosome analysis. We have performed oligonucleotide-array comparative genomic hybridization (oaCGH) in an AML case with a 15p/17p translocation, a suspected 9p21 deletion, monosomies of chromosomes X and 9, and 2 to 60 double minutes. The oaCGH findings confirmed the chromosomal observations and further characterized a 21.338-Mb 17p deletion, a 3.916-Mb deletion at 9p21.3 containing the MTAP, CDKN2A, CDKN2B, and ELAVL2 genes, and a 3.981-Mb 8q24 double minute containing the TRIB1, FAM84B, MYC, and PVT1 genes, with an average of 30 double minutes in each cell. FISH using MYC probes and bacterial artificial chromosome clone probes confirmed the genomic findings and revealed a progressional pattern for the 9p21.3 deletion. These results demonstrate the potential of oaCGH as a powerful diagnostic tool for characterizing genomic imbalances for patients with hematological malignancies.