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Background: A 15-gene expression profiling (GEP) test is widely used for prognostication of metastatic risk in uveal melanoma (UM) patients. Because the amount of tumor tissue that can be safely obtained by biopsy from UM is limited, it is critical to obtain as much individualized genomic information as possible from each biopsy sample. Mutational profiling of UM tumors using next generation sequencing (NGS) in combination with GEP allows for analysis of both DNA and RNA from a single tumor sample, offers additional prognostic value, and can potentially inform therapy selection. This study evaluated the analytical performance of a targeted custom NGS panel for mutational profiling of the seven genes known to be commonly mutated in primary UM.Methods: 105 primary UM samples were analyzed, including 37 formalin-fixed paraffin embedded (FFPE) specimens and 68 fine needle aspiration biopsy (FNAB) specimens obtained with a 25- or 27-gauge needle. Sequencing was performed on the Ion GeneStudio S5 platform to an average read depth of greater than 500X per region of interest in a clinical laboratory accredited by the College of American Pathologists (CAP) and certified under the Clinical Laboratory Improvement Amendments (CLIA).Results: The 7-gene panel assay achieved a positive percent agreement (PPA) of 100% for detection of both single nucleotide variants (SNVs) and insertions/deletions (INDELs), with a technical positive predictive value (TPPV) of 99.4% and 100%, respectively. Intra-assay and inter-assay concordance studies confirmed the reproducibility and repeatability of the assay. The limit of detection was determined to be 5% variant allele frequency (VAF) for both SNVs and INDELs, with a minimum DNA input requirement of 1.5ng for FNAB and 5ng for FFPE samples.Conclusions: The 7-gene panel is a robust, highly accurate NGS test that can be successfully performed, along with GEP, from a single small gauge needle biopsy sample.

Purpose: The development of a genetic signature for the identification of high-risk cutaneous melanoma tumors would provide a valuable prognostic tool with value for stage I and II patients who represent a remarkably heterogeneous group with a 3% to 55% chance of disease progression and death 5 years from diagnosis. Experimental Design: A prognostic 28-gene signature was identified by analysis of microarray expression data. Primary cutaneous melanoma tumor tissue was evaluated by RT-PCR for expression of the signature, and radial basis machine (RBM) modeling was performed to predict risk of metastasis. Results: RBM analysis of cutaneous melanoma tumor gene expression reports low risk (class 1) or high risk (class 2) of metastasis. Metastatic risk was predicted with high accuracy in development (ROC = 0.93) and validation (ROC = 0.91) cohorts of primary cutaneous melanoma tumor tissue. Kaplan–Meier analysis indicated that the 5-year disease-free survival (DFS) rates in the development set were 100% and 38% for predicted classes 1 and 2 cases, respectively (P < 0.0001). DFS rates for the validation set were 97% and 31% for predicted classes 1 and 2 cases, respectively (P < 0.0001). Gene expression profile (GEP), American Joint Committee on Cancer stage, Breslow thickness, ulceration, and age were independent predictors of metastatic risk according to Cox regression analysis. Conclusions: The GEP signature accurately predicts metastasis risk in a multicenter cohort of primary cutaneous melanoma tumors. Preliminary Cox regression analysis indicates that the signature is an independent predictor of metastasis risk in the cohort presented. Clin Cancer Res; 21(1); 175–83. ©2015 AACR.

// Matthew G. Field 1 , Michael A. Durante 1 , Christina L. Decatur 1 , Bercin Tarlan 1 , Kristen M. Oelschlager 2 , John F. Stone 2 , Jeffim Kuznetsov 1 , Anne M. Bowcock 3 , Stefan Kurtenbach 1 , J. William Harbour 1 1 Bascom Palmer Eye Institute, Sylvester Comprehensive Cancer Center and Interdisciplinary Stem Cell Institute, University of Miami Miller School of Medicine, Miami, FL, USA 2 Castle Biosciences, Inc., Friendswood, TX, USA 3 National Heart and Lung Institute, Imperial College London, London, UK Correspondence to: J. William Harbour, email: harbour@miami.edu Keywords: PRAME, preferentially expressed antigen in melanoma, uveal melanoma, DNA methylation, chromosomal instability Received: June 07, 2016 Accepted: July 13, 2016 Published: July 30, 2016 ABSTRACT Background: We previously identified PRAME as a biomarker for metastatic risk in Class 1 uveal melanomas. In this study, we sought to define a threshold value for positive PRAME expression (PRAME+) in a large dataset, identify factors associated with PRAME expression, evaluate the prognostic value of PRAME in Class 2 uveal melanomas, and determine whether PRAME expression is associated with aberrant hypomethylation of the PRAME promoter. Results: Among 678 samples analyzed by qPCR, 498 (73.5%) were PRAME- and 180 (26.5%) were PRAME+. Class 1 tumors were more likely to be PRAME-, whereas Class 2 tumors were more likely to be PRAME+ ( P < 0.0001). PRAME expression was associated with shorter time to metastasis and melanoma specific mortality in Class 2 tumors ( P = 0.01 and P = 0.02, respectively). In Class 1 tumors, PRAME expression was directly associated with SF3B1 mutations ( P < 0.0001) and inversely associated with EIF1AX mutations ( P = 0.004). PRAME expression was strongly associated with hypomethylation at 12 CpG sites near the PRAME promoter. Materials and methods: Analyses included PRAME mRNA expression, Class 1 versus Class 2 status, chromosomal copy number, mutation status of BAP1 , EIF1AX , GNA11 , GNAQ and SF3B1 , and genomic DNA methylation status. Analyses were performed on 555 de-identified samples from Castle Biosciences, 123 samples from our center, and 80 samples from the TCGA. Conclusions: PRAME is aberrantly hypomethylated and activated in Class 1 and Class 2 uveal melanomas and is associated with increased metastatic risk in both classes. Since PRAME has been successfully targeted for immunotherapy, it may prove to be a companion prognostic biomarker.

A molecular test performed using fresh-frozen tissue was proposed for use in the prognosis of patients with pleural mesothelioma. The accuracy of the test and its properties was assessed under Clinical Laboratory Improvement Amendments–approved guidelines using FFPE tissue from an independent multicenter patient cohort. Concordance studies were performed using matched frozen and FFPE mesothelioma samples. The prognostic value of the test was evaluated in an independent validation cohort of 73 mesothelioma patients who underwent surgical resection. FFPE-based classification demonstrated overall high concordance (83%) with the matched frozen specimens, on removal of cases with low confidence scores, showing sensitivity and specificity in predicting type B classification (poor outcome) of 43% and 98%, respectively. Concordance between research and clinical methods increased to 87% on removal of low confidence cases. Median survival times in the validation cohort were 18 and 7 months in type A and type B cases, respectively (P = 0.002). Multivariate classification adding pathologic staging information to the gene expression score resulted in significant stratification of risk groups. The median survival times were 52 and 14 months in the low-risk (class 1) and intermediate-risk (class 2) groups, respectively. The prognostic molecular test for mesothelioma can be performed on FFPE tissues to predict survival, and can provide an orthogonal tool, in combination with established pathologic parameters, for risk evaluation.

In a preliminary effort to stem a steep decline in graduate enrollments, a regional comprehensive university began a search for its perceived market advantages. Using the tenets of Bormann's (1985) Symbolic Convergence Theory, the investigation identified fantasy types involved in student decisions to enroll and, after surveying new students (N = 739) over a four year period, isolated two emergent rhetorical visions ∼ “Better Program, Quality University,” and “Small Campus, Big Opportunity”‐that were shared, to differing degrees, by students in professionally diverse academic programs. Results are discussed in terms of what they suggest about promoting professional master's degree programs generally, and communication programs specifically, and what they reveal about the saliency of rhetorical visions.

Not AvailableStudy supported by Castle Biosciences.

A gene expression profile (GEP) test able to accurately identify risk of metastasis for patients with cutaneous melanoma has been clinically validated.We aimed for assessment of the prognostic accuracy of GEP and sentinel lymph node biopsy (SLNB) tests, independently and in combination, in a multicenter cohort of 217 patients.Reverse transcription polymerase chain reaction (RT-PCR) was performed to assess the expression of 31 genes from primary melanoma tumors, and SLNB outcome was determined from clinical data. Prognostic accuracy of each test was determined using Kaplan-Meier and Cox regression analysis of disease-free, distant metastasis-free, and overall survivals.GEP outcome was a more significant and better predictor of each end point in univariate and multivariate regression analysis, compared with SLNB (P.0001 for all). In combination with SLNB, GEP improved prognostication. For patients with a GEP high-risk outcome and a negative SLNB result, Kaplan-Meier 5-year disease-free, distant metastasis-free, and overall survivals were 35%, 49%, and 54%, respectively.Within the SLNB-negative cohort of patients, overall risk of metastatic events was higher (∼30%) than commonly found in the general population of patients with melanoma.In this study cohort, GEP was an objective tool that accurately predicted metastatic risk in SLNB-eligible patients.

We present the case of a 12-year-old boy admitted with the diagnosis of acute leukemia, but found to have an infiltration of the marrow by an alveolar rhabdomyosarcoma (RMS) as determined by the cytogenetic demonstration of a t(2;13)(q25;q14). A primary tumor could not be found. With this case as a basis, we have tabulated features of all similar cases in the literature and discuss the possible optimal approaches to establishing the correct diagnosis in such patients.

Pancreatic adenocarcinoma is a highly lethal malignant tumor that is increasing in frequency, now ranking fifth in the United States as a cause of death attributed to cancer. Patients with pancreatic carcinoma have one of the poorest prognoses of all cancer patients, with the number of deaths being approximately 75% of the total number of cases. The use of comparative genomic hybridization (CGH) has gained widespread use in the study of some types of solid tumors, and it seems to be a very good approach in pancreatic adenocarcinomas, in which just a few cases have been studied cytogenetically, mostly owing to the fact that these tumors are very difficult to grow in culture. Fourteen pancreatic cancer lines were examined with CGH. In 11 of these lines, we found an amplicon at 1q31, not previously reported in pancreatic cancer. More studies need to be done in primary tumors to determine the involvement of 1q31 in this type of tumor.

Three cases of acute nonlymphocytic leukemia with a Philadelphia chromosome (Ph) as a secondary abnormality are reported. The Ph was late-appearing in one patient and appeared as an additional anomaly in the other two patients. Fluorescence in situ hybridization studies of the first patient identified the presence of a minor BCR/ABL rearrangement. The findings of these cases support the conclusion that the Ph plays a role not only in leukemogenesis, but also in disease progression. An overview of the literature dealing with similar cases is also presented.

We report on a solid and cystic papillary epithelial neoplasm of the pancreas containing the unbalanced chromosome translocation der(17)t(13;17)(q14;p11), resulting in loss of 13q14-->qter and 17p11-->pter. Although the clinical and pathologic characteristics of this case are largely typical of this uncommon pancreatic neoplasm, the presence of cellular pleomorphism, tumor giant cells, and a DNA tetraploid tumor population suggest that this tumor may have an increased metastatic potential. The unbalanced translocation between chromosomes 13 and 17 and the genes flanking the breakpoints may prove to be markers for solid and cystic papillary epithelial neoplasm of the pancreas and provide insight into its histogenesis.

Pleural and ascitic fluids (PAF) are complications of both nonmalignant and malignant conditions, such as congestive heart failure and chronic infections, as well as neoplasias, such as mesothelioma, lymphoma, and adenocarcinomas of the lung, ovary, endometrium, breast, colon, stomach, and pancreas. Differentiation between malignant and nonmalignant PAF is not always easy to assess on the basis of clinical, cytologic, and other criteria. A review of the chromosomal anomalies in neoplasms which can cause PAF revealed aneusomies of chromosomes 1, 3, 7, 8, 10, and 11 in about 40% to 80% of these malignancies. We performed FISH using centromere-specific probes for chromosomes 1, 3, 7, 8, 10, and 11 and chromosomal analysis on PAF cells from 21 patients, including 3 with ovarian cancer, 2 with lymphoma, 5 with adenocarcinoma of unknown origin, 1 with breast cancer, and 10 with atypical lymphocytosis of unknown cause. The results indicate a) a high correspondence between FISH and the clinical diagnosis (9 of the 11 cases of malignant fluid showing FISH abnormalities); b) that FISH is more sensitive than cytogenetics in detecting abnormal clones (10 vs. 6); and c) that FISH is a valuable adjunct to cytology in the interpretation of atypical lymphocytosis (3 of the 10 cases were shown to be abnormal by FISH). Thus, the FISH technique can be a very useful adjunct to conventional cytogenetics in yielding crucial information on the origin of PAF.

Loss of an X chromosome in females and of the Y chromosome in males are phenomena associated with aging. X chromosome loss occurs in and may be limited to PHA stimulated peripheral lymphocytes. In males, the loss of the Y is most evident in bone marrow cells, but also occurs to a lesser extent in PHA stimulated peripheral lymphocytes. X chromosome loss is associated with premature centromere division leading to anaphase lag and elimination in micronuclei. The mechanism of Y chromosome loss has not been elucidated. No pathological consequence of either X or Y chromosome loss has been convincingly demonstrated. With the advent of FISH technology, measurement of sex chromosome aneuploidy may prove to be a convenient assay for cellular senecence and aging.

Stomatal activity of leaves can be related to factors under producer control, including row spacing and orientation. In both grain sorghum [Sorghum bicolor (L.) Moench] and peanut (Arachis hypogaea L.), evapotranspiration has been reduced with narrow north-south row. Under high evaporative demand, this row pattern also resulted in a more efficient plant energy budget for peanut. The trigger was stomatal action (i.e., the tendency for stomates in narrow-row plots to close earlier in the day than in wide-row plots), with no effect from leaf water potential or soil water content. To see if high evaporative demand causes stomatal action in narrow-row grain sorghum, two plots were planted at 0.40- and 1.22-m row spacing and used through six growing seasons. Treatments were randomly assigned to plots each year. Stomatal resistance and leaf water potential were measured at half-hour intervals ; soil water content was monitored weekly, prior to irrigation. Sixty-five days of data were classified as to evaporative demand and stomatal activity based on stomatal resistance behavior throughout the day. On 14 d, stomatal resistance was consistently higher in the narrow-row than the wide-row plots. Generally, these 14 d had high evaporative demand. Another 11 d showed intermediate differences, and the 40 remaining days (which included some high-demand days) showed no significant differences. The narrow-row stomatal closure effect was most likely to occur on days that accumulated >6 MJ m -2 of advected energy between 0730 and 1330 h apparent solar time. As with peanut, the stomatal action effect appeared to be insensitive to leaf water potential and soil water content. Narrow north-south planting of these crops may offer some control of evapotranspiration through stomatal action. Given the similarity of stomatal action effects in the dissimilar species of peanut and sorghum, studies of row spacing and orientation vs. stomatal activity in other species seem merited.

Due to some empiric reasons, bone marrow (BM) has never been emphasized and appreciated as a valuable alternative source for metaphases of tumor nature. In the present study, we report the cytogenetic and fluorescence in situ hybridization (FISH) studies of BM in 172 patients with various tumors. Our results indicate that cytogenetic and FISH analyses of BM provide a valuable biologic approach concerning the diagnosis of tumors, evaluation of metastasis, and assessment of secondary hematologic malignancies. Thus, we suggest strongly that these studies become a standard part of clinical pathologic investigations in dealing with clinical oncology.

A hibernoma studied cytogenetically had the karyotype 46,XY,t(9;10;11)(q34;q22;q13),t(17;19) (q21.3;q13). The findings are discussed and compared with those of the previous case described in the literature.

This essay extends the tradition of organically explicating dialectical conflict in feature film. The author creates the Motivational/Metaphysical Model to analyze Platoon—exploring not only how the filmic and narrative elements function to channel viewers into the “Vietnam experience,” but also how the mythic conflict between humane and destructive impulses of war is symbolically resolved. What results is an interpretation of the film that suggest the presence of a previously unidentified pattern of conflict resolution the author refers to as dialectical centering. It is this new pattern, the essay concludes, that permits the film to move beyond providing a unifying homage to those who served in Vietnam to a point where it prescriptively outlines a message with foreign policy implications.

In the present study, three chronic myelogenous leukemia (CML) patients with variant Philadelphia (Ph) chromosomes (complex types), two CML patients with a masked Ph, one case with Ph positive acute lymphocytic leukemia (ALL), and one with Ph positive acute myelocytic leukemia (AML) were analyzed by standard cytogenetic techniques (G-banding), Southern blot studies, and fluorescence in situ hybridization (FISH) procedures using probes from portions of the bcr and abl genes. It has been previously shown that this FISH approach could detect the bcr/abl fusion event in CML patients with classic or variant (simple type) Ph. Our results demonstrate that this FISH assay can also detect the bcr/abl fusion status in CML patients with masked or variant (complex type) Ph chromosomes and in some patients with Ph positive ALL or AML.

Research has shown that wide-spaced furrow irrigation can often produce acceptable yields of crops with less water than every-furrow irrigation. In some seasons wide-spaced will result in less yield because too little water may be applied, particularly if the season has low rainfall and high evaporative demand. Seven years of production studies with different seasonal amounts and timing of irrigation produced well fit functions relating yield and irrigation water for wide-spaced and every-furrow. Results showed that wide-spaced was 15% more efficient than every-furrow. They also showed that at the highest yield levels noted, the wide-spaced treatment would require 38% less water for the same yield of cotton. Also, a given water recharge of the soil produced a 48% greater yield if the water were applied as wide-spaced furrow irrigation than as every-furrow irrigation.

Purpose Selective tumor cell cytotoxicity can be achieved through a synthetic lethal strategy using poly(ADP)-ribose polymerase (PARP) inhibitor therapy in BRCA1/2 mutation carriers in whom tumor cells have defective homologous recombination (HR) DNA repair. Platinum-based chemotherapy responses correlate with HR DNA repair capacity. Olaparib is a potent, oral PARP inhibitor that is well tolerated, with antitumor activity in BRCA1/2 mutation carriers. Patients and Methods Patients with BRCA1/2-mutated ovarian cancer were treated with olaparib within a dose-escalation and single-stage expansion of a phase I trial. Antitumor activity was subsequently correlated with platinum sensitivity. Results Fifty patients were treated: 48 had germline BRCA1/2 mutations; one had a BRCA2 germline sequence change of unknown significance, and another had a strong family history of BRCA1/2-associated cancers who declined mutation testing. Of the 50 patients, 13 had platinum-sensitive disease, 24 had platinum-resistant disease, and 13 had platinum-refractory disease (according to platinum-free interval). Twenty (40%; 95% CI, 26% to 55%) achieved Response Evaluation Criteria in Solid Tumors (RECIST) complete or partial responses and/or tumor marker (CA125) responses, and three (6.0%) maintained RECIST disease stabilization for more than 4 months, giving an overall clinical benefit rate of 46% (95% CI, 32% to 61%). Median response duration was 28 weeks. There was a significant association between the clinical benefit rate and platinum-free interval across the platinum-sensitive, resistant, and refractory subgroups (69%, 45%, and 23%, respectively). Post hoc analyses indicated associations between platinum sensitivity and extent of olaparib response (radiologic change, P = .001; CA125 change, P = .002). Conclusion Olaparib has antitumor activity in BRCA1/2 mutation ovarian cancer, which is associated with platinum sensitivity.

We report a case of idic(X)(q13),r(X)(p22q13), and del(X)(:p11-->cen-->q11:) in a 71-year-old female patient with de novo acute nonlymphocytic leukemia (ANLL), FAB-M4. The abnormal X chromosomes of this patient were identified cytogenetically by G-banding technique and were further confirmed by fluorescence in situ hybridization (FISH) using an alpha-satellite probe to chromosome X centromere. The features of this are compared with other cases reported in the literature.

We present the case of a patient with true hermaphroditism and partial duplication of chromosome 22. Cytogenetic evaluation showed no evidence of a Y chromosome in blood, skin, or gonadal tissue. Additional investigations using molecular probes showed no evidence of SRY. We conclude that there are genes on chromosome 22 that are involved in sex determination.

Soil water from plots containing cotton, devil's- claw, cotton with devil's-claw, and bare soil was measured throughout the growing season using a neutron probe and related to weed interference with the crop. Volumetric water content throughout the soil profile to a depth of 180 cm did not differ among treatments before the 5th or 6th week after cotton emergence. Greater water depletion occurred early in the season in plots containing devil's- claw which corresponded to a period of rapid weed growth. In plots containing only cotton, the largest reduction in water content occurred later in the season during peak bloom and early boll formation. Soil water content at depths greater than 105 cm remained un- changed in all plots throughout the season. Interference from devil's-claw reduced cotton lint yield 96% in 1986 and 46% in 1987. Higher rainfall and reduced weed populations in 1987 reduced the impact of weed interfer- ence on cotton lint yield. Nomenclature: Devil's-claw, Proboscidea louisianica (Mill.) Thellung #3 PROLO; cotton, Gossypium hirsutum L. 'Paymaster 145'. Additional index words. Neutron probe, volumetric water content, soil water depletion, competition, unicorn-plant

e15011 Background: Approximately 25% of patients with locoregional esophageal adenocarcinoma (EC) are resistant (marked by minimal tumor regression; TRG 3) to preoperative chemoradiation, including...

Cosmid probes specific for the major BCR/ABL rearrangement (commercially available probes) were employed by us to evaluate 134 patients with the clinical diagnosis of chronic myelocytic leukemia (CML). The following represent our main observations: 1) No significant statistical difference regarding a false positive fusion signal was seen in the distribution pattern between the Ph negative (-) cases (110) and the normal controls (3.23 +/- 1.97 vs 2.8 +/- 1.92, respectively). 2) The mean percentage of cells with a positive fusion signal in the Ph positive (+) CML cases at presentation was 70 +/- 12.3 in bone marrow samples (12 cases) and 45 +/- 12.4 in blood samples (3 cases). 3) A significant discrepancy was seen between the interphase FISH and cytogenetics data in the monitoring of four out of eight patients post-therapy. The clinical significance of this observation needs to be clarified. 4) Three Ph(-) patients with significant leukocytosis had closely adjacent but not fused signals (20%, 16%, and 20% of cells, respectively, vs. the control: 4%). This may indicate a temporal and spatial association between chromosomes 9 and 22 prior to the BCR/ABL rearrangement (Ph chromosome formation).

9022 Background: We recently validated a GEP test that provides accurate prediction of metastatic risk for CM cases. The GEP of 31 genes provides a binary outcome of Class 1 (low risk of metastasis...

We report a case of an intramuscular lipoma with the following karyotype: 46,XY,t(12;14) (q14–15;q24). To our knowledge, this is the third report of a t(12;14) as a sole abnormality in a lipoma.

Female pseudohermaphroditism with caudal dysplasia is a clinical entity in which normal-appearing male genitalia may occur in the apparent absence of testosterone or the sex-determining gene (SR Y). We have extended observations of two previously reported cases, and report a third case, which strongly suggests multiple etiologies. The first case was one of identical twins. The other identical twin did not show female pseudohermaphroditism with caudal dysplasia, but both patients had the rare birth defect of neonatal cataracts. We have explored skewed X-inactivation as a possible difference between the two twins, with a negative result. The second case had a deletion at 10q25.3-->ter. This is near the location of PAX2, and we searched for mutations in PAX2 in both this and the first case, with negative results. Neither patient had a scrotal raphe, suggesting that a failure of division of the cloacal membrane was an important step in their development of female pseudohermaphroditism. The final case is newly described and differed from the above two in the presence of a scrotal raphe and an elevated testosterone level. Although no source for the testosterone was found, this case suggests that the etiology in this patient was different and that the presence of a scrotal raphe can be used to distinguish between at least two etiologies.

PurposeThymoma represents one of the rarest of all malignancies. Stage and completeness of resection have been used to ascertain postoperative therapeutic strategies albeit with limited prognostic accuracy. A molecular classifier would be useful to improve the assessment of metastatic behaviour and optimize patient management.MethodsqRT-PCR assay for 23 genes (19 test and four reference genes) was performed on multi-institutional archival primary thymomas (n = 36). Gene expression levels were used to compute a signature, classifying tumors into classes 1 and 2, corresponding to low or high likelihood for metastases. The signature was validated in an independent multi-institutional cohort of patients (n = 75).ResultsA nine-gene signature that can predict metastatic behavior of thymomas was developed and validated. Using radial basis machine modeling in the training set, 5-year and 10-year metastasis-free survival rates were 77% and 26% for predicted low (class 1) and high (class 2) risk of metastasis (P = 0.0047, log-rank), respectively. For the validation set, 5-year metastasis-free survival rates were 97% and 30% for predicted low- and high-risk patients (P = 0.0004, log-rank), respectively. The 5-year metastasis-free survival rates for the validation set were 49% and 41% for Masaoka stages I/II and III/IV (P = 0.0537, log-rank), respectively. In univariate and multivariate Cox models evaluating common prognostic factors for thymoma metastasis, the nine-gene signature was the only independent indicator of metastases (P = 0.036).ConclusionA nine-gene signature was established and validated which predicts the likelihood of metastasis more accurately than traditional staging. This further underscores the biologic determinants of the clinical course of thymoma and may improve patient management.

7605 Background: Thymomas and thymic carcinomas (TC) are rare epithelial tumors derived from the thymic gland in the anterior mediastinum. Although all histological types of thymomas, albeit with different frequencies, can give rise to metastases, TC have a more aggressive behavior and metastasize earlier and more frequently than thymomas. We previously developed a prognostic gene signature able to accurately determine metastatic behavior of thymomas (Gökmen-Polar et al. ASCO 2012). The signature is currently used in clinical practice to identify patients at high or low risk for metastatic disease. In the current study, we sought to evaluate the utility of this signature for determining risk from TC tumors. Methods: FFPE tissue sections were macrodissected from 35 primary TC. RNA was isolated and RT-PCR was performed to assess the expression of 23 genes (19 test and four reference genes). Predictive modeling was performed using Radial Basis Machine (RBM) software from JMP Genomics (SAS), and survival analysis was done using the Kaplan-Meier method. Results: Samples from the TC cohort ranged from stage II through IVB, with a median age of 54 years. 26 samples had evidence of metastatic progression, while nine samples did not. Prediction of metastasis, based upon comparison to the previously developed thymoma training set and using a 19-gene signature, yielded an ROC = 0.66. Independent analysis of the TC cohort with the thymoma 19-gene signature resulted in a predictive model with an ROC = 0.97 (overall accuracy = 87%, sensitivity = 73% and specificity=100%). Further modeling and gene set reduction revealed a separate ten-gene signature able to segregate metastatic from non-metastatic cases with 100% accuracy. All the cases classified as high risk (n= 26) developed metastasis within 5 years while none of the cases categorized as low-risk (n= 9) had any events at 5 years of follow-up. Conclusions: A ten-gene signature was established that appears to predict metastatic behavior of TC with a high degree of accuracy; however, validation in an independent cohort is necessary. Our data suggests that the biologic determinants of the clinical course of TC maybe distinct from thymoma and could be used to improve patient management.

9022 Background: Wide variability exists in metastatic rates of primary cutaneous melanoma (CM), even within TNM stage groupings. We developed an RT-PCR based gene expression profile (GEP) test to predict distant metastases in early stage CM. Methods: RNA was isolated from formalin-fixed, paraffin embedded biopsies or wide excisions of primary CM from patients with stage 1-4 CM (87% stage 1-2) converted to cDNA and analyzed using RT-PCR. All analyses were done using JMP Genomics and WinSTAT. Radial Basis Machine (RBM) modeling was used to predict metastasis-free survival (MFS) for the training set of 149 samples. Independent validation was performed on an additional 107 CM samples. RBM reports a binary Class 1 (low risk) and Class 2 (high risk). Results: Analysis of the training set resulted in a model with 85% receiver operating characteristic (ROC) and sensitivity of 82%. Prediction of metastatic risk for the validation set resulted in a 90% ROC and sensitivity of 89%. 30 of 33 stage 1-3 cases with a known metastatic event were accurately called Class 2. Kaplan-Meier analysis showed 5-year MFS rates of 88% and 25% for predicted Class 1 and Class 2, respectively, in the training set (p

We report a patient with extramedullary acute promyelocytic leukemia (APL) occurring after radiation therapy for carcinoma of the prostate. To the authors' knowledge, this patient represents the first case of cytogenetically and fluorescence in situ hybridization (FISH) confirmed therapy-related extramedullary APL. In contrast to the majority of previously reported t-APL, this case underwent a very unfavorable course.

A male patient with Turner-like hydrops in the newborn period (Bonnevie-Ullrich syndrome) was studied. The karyotype was 46, X, t(Y;16)(q11.2;q24) in 100 cells. Chromosome painting with the heterochromatic Y chromosome-specific long arm repeat DYZ2 disclosed that all the hybridization was on the derivative 16. This was confirmed by chromosome painting with DYZ1, the other major Y long arm heterochromatic repeat, and DYZ3, the Y alphoid, centromeric repeat which showed chromosomal separation of the 2 stained regions. To further localize the breakpoint, FISH was performed using individual YACs from a Y-YAC contig (Foote et al., 1992). This disclosed two YACs (yOX111 and yOX123) which hybridized to both the Y and der16 chromosomes. The YACS spanning the translocation breakpoint region were located just proximal to the Y heterochromatin boundary. The recent discovery of a candidate gene for the azoospermia factor (AZF) in this region (Ma et al., 1993) suggests the possibility that there are several Y-expressed genes adjacent to the heterochromatin boundary (as there are near the pseudoautosomal boundary) which may include a gene involved with lymphedema which is disrupted by the translocation in this patient.

Fluorescence in situ hybridization (FISH) provides a sensitive and effective approach in identifying the RAR-α/PML fusion event in acute promyelocytic leukemia (APL) with the t(15;17). In the present study we describe the use of this assay for the identification of the RAR-α/PML fusion in bone marrow (BM) cells from three APL patients with complex t(15;17) translocations.

We observed three cases of acute leukemia with trisomy 10 (+10) as the sole abnormality, two were adult patients with ANLL (subtype M0 and M1 respectively), and the third that of a child with ALL. The literature describes nine additional cases, four with ALL (all of whom were children) and five with ANLL (all of whom were adults). Cell marker studies on the ANLL cases showed a common positivity for CD7 and CD33 in our two cases, as well as in four of the previously reported cases, whereas in ALL the only two informative cases were classified as early pre-B ALL. There appears to be an age-related pattern in the specificity of the leukemic lineage. Trisomy 10 appears to be associated exclusively with ALL in children and with ANLL (usually M0-M1) in adults. The prognosis appears to be also divided between the two groups, being good in the pediatric group and moderate in the adult group.

Random chromosome abnormality is an important issue in clinical cytogenetics, especially in cancer cytogenetics. The significance of random abnormalities needs to be well defined. In the present study, ten patients with malignant hematologic disorders were analyzed by classical cytogenetic techniques and fluorescence in situ hybridization (FISH) procedures. Cytogenetic studies showed all ten patients to have a single cell with trisomy, i.e., +8, +8 (5 cases), +12, +15, +18, +20, and +21, respectively. FISH necessitated revision of the cytogenetic diagnosis and confirmed the clonality of these “random” abnormalities.

The Julian Day is used by astronomers to record periodic events. It is a reckoning of the number of days from 12 noon, January 1, 4713 B.C. Some biological scientists have used this pre-empted term to describe the calendar day of the year. Examples of its use for astronomical and biological applications have been noted. The term ‘day of the year’ would seem to be adequate for biological cases noted in the literature where calendricity needs to be preserved on the time base. Current misuse of the term Julian Day by biologists is not justified and should be abandoned.

Furrow irrigation studies comparing water applications to narrow and wide-spaced furrows were conducted on three crops at thee locations in Oklahoma over eight growing seasons. Wide-spaced-furrow irrigation usually required about half the water of narrow spacing. In 9 of 11 studies, no yield reductions were noted. In the seasons where yield reductions were noted, the atmospheric evaporative demand was high. A simple test was devised to indicate if a season in progress shows high atmospheric demand. The evaporative demand test involves measurement of rainfall and daily wind movement. Using standard National Weather Service instruments, daily average of rain > 1.6 mm between 15 July and 31 Aug. combined with daily wind movement < 155 km in August caused no yield reduction in wide-spaced-furrow irrigation. Wind was measured at the standard height of a “Class A” evaporation pan (51 cm). Conservation of water from wide-spaced-furrow irrigation should be possible on medium to fine textured soils in many semiarid regions of the world.

Both irrigated and nonirrigated conditions were imposed on various populations for three years using the peanut (Arachis hypogaea L.) cultivar Argentine. Row spacings were 0.25, 0.5, 0.75 and 1 m. Within-row plant spacings ranged between 2 and 27 plants/m. The dependent variables of yield (kg/ha and g/plant), other kernels (%) and net return ($/ha) were fitted with a surface response equation Y = β1 + β2X1 + β3X12+ β4X2 + β5X22+ β6X1X2, with X1 spacing between rows and X2 spacing between plants within the row. This model fitted all dependent variables very well for both irrigated and nonirrigated conditions. Resulting interpolation of the data using the above equation indicated that the 0.25 m row spacing gave the highest yield of unshelled peanuts for both irrigated and nonirrigated conditions. Approximately 15 plants/m was the optimal plant spacing (in all row spacings) for maximum yield and quality. Integrating yield and quality in terms of net returns, the 0.25 m row spacing was optimal for production of Argentine peanuts. Computations based on the above equation and evaluated at constant population density (plants/ha) showed yield was still increased to the narrowest row spacing in the study. Subsequently, row spacing vs. yield studies with Starr and Comet cultivars were conducted over seven growing seasons at a spacing in the row of about 10 plants/m. Row spacing varied from 0.15 to 1 m. In every year, the narrow spacings outyielded the wider spacings.

Characteristics of crop yield and water use in wide-spaced furrow irrigation (W) were compared to every furrow irrigation (E). The study was conducted at Goodwell, Oklahoma on a clay loam soil with grain sorghum (Sorghum bicolor (L.) Moench). E furrows were 1.42 m apart and W applied water to alternate furrows, making a 2.84 m spacing. W treatments caused no greater yield variation down the furrow than the E treatment, although about 1 2 the water was applied to the W plots as for E. In the W treatments not all furrows were irrigated at any one time and, on occasion, the dry furrows were noted to crack. Subsequent irrigation to cracked dry furrows showed significantly greater penetration of water into the profile than the E treatments. Soil water tended to be depleted to greater degree in the W treatments than the E treatment over the growing season, but seasonal evapotranspiration was lesser in the W plots.

Studies of wide-spaced furrow irrigation were conducted at Goodwell, OK. Wide-spaced furrow irrigation applies water to the root zone while maintaining a relatively dry soil surface. This condition reduced evapotranspiration losses and can reduce water requirements by 20 to 50%. Probability of a yield reduction with this water conservation method is lessened by either: (a) abandoning the wide-spaced furrow irrigation method on 1 August of a high water-stress season; or (b) alternating the dry furrows in an alternate-furrow scheme. A high stress season is defined as one in which the August wind velocity averages greater than 1.8 m/s and less than 7.5 cm of rain falls between 15 July and 1 September (in the temperate northern hemisphere). The test for high stress conditions consists of measuring rain and wind velocity beginning on 15 July. The averages are examined on 1 August. If rainfall average is less than 1.6 mm/day and wind average is more than 1.8 m/s then normal irrigation is practiced on subsequent irrigations. Studies were conducted in 60 m plots and in field scale research with 0.8 km rows.

Characteristics of water flow in wide-spaced furrow irrigation (W), 2.84 m spacing, were compared to every furrow irrigation (E), 1.42 m spacing. The study was conducted at Goodwell, Oklahoma on a clay loam soil with grain sorghum. Water was applied at a constant 0.75 L s−1 rate to all furrows. Because W prevents meeting of wetting fronts from adjacent furrows, it was expected that water would advance more slowly in the W than in E due to the continual lateral wetting in W. Rate of advance of water down the furrow in the E treatment ranged from 1.23 to 1.48 times greater than in the W depending upon soil type and slope. Logarithm of distance of advance of furrow stream varied closely with logarithm of time for each furrow indicating that measurements made relatively early in the irrigation of a furrow could predict rate of advance while irrigating. Advance rates of the W treatment were no more variable than the E. W could be adjusted by trial and error to advance at the same rate as E by making needed adjustments to furrow inflow rate to W early in the irrigation. One would merely need to have several adjacent E furrows in the field close by for comparison.

The effects of hogpotato interference on cotton and of the crop on the weed were measured under field conditions in four environments. Full-season interference from 105 ± 21 hogpotato plants/m2reduced cotton plant height by 14 to 44%. Conversely, weed dry weight was reduced 54% through full-season interference from cotton. Lint yield reductions in cotton ranged from 31 to 98% following full-season weed interference. Interference during the first 7 weeks of crop growth reduced lint yield by approximately 40%; however, interference after 7 weeks of weed-free maintenance did not affect lint yield. Interference reduced boll size in 3 of 4 yr, lint percent in 2 of 4, and boll number in the only year it was measured. Cotton fiber length, uniformity index, and micronaire were reduced by full-season interference in 1 of 2 yr; however, fiber strength was not affected in either year. Significant use of soil water by hogpotato occurred at 120 cm and deeper in the soil while cotton used water primarily in the upper 75 cm.