Population Genome Sequencing of the Scab Fungal Species Venturia inaequalis, Venturia pirina, Venturia aucupariae and Venturia asperata.

The Venturia genus comprises fungal species that are pathogens on Rosaceae host plants, including V. inaequalis and V. asperata on apple, V. aucupariae on sorbus and V. pirina on pear. Although the genetic structure of V. inaequalis populations has been investigated in detail, genomic features underlying these subdivisions remain poorly understood. Here, we report whole genome sequencing of 87 Venturia strains that represent each species and each population within V. inaequalis We present a PacBio genome assembly for the V. inaequalis EU-B04 reference isolate. The size of selected genomes was determined by flow cytometry, and varied from 45 to 93 Mb. Genome assemblies of V. inaequalis and V. aucupariae contain a high content of transposable elements (TEs), most of which belong to the Gypsy or Copia LTR superfamilies and have been inactivated by Repeat-Induced Point mutations. The reference assembly of V. inaequalis presents a mosaic structure of GC-equilibrated regions that mainly contain predicted genes and AT-rich regions, mainly composed of TEs. Six pairs of strains were identified as clones. Single-Nucleotide Polymorphism (SNP) analysis between these clones revealed a high number of SNPs that are mostly located in AT-rich regions due to misalignments and allowed determining a false discovery rate. The availability of these genome sequences is expected to stimulate genetics and population genomics research of Venturia pathogens. Especially, it will help understanding the evolutionary history of Venturia species that are pathogenic on different hosts, a history that has probably been substantially influenced by TEs.

The components of progression as explanatory variables for overall survival in the Response Evaluation Criteria in Solid Tumours 1.1 database.

PURPOSE: Progressive disease (PD) per Response Evaluation Criteria in Solid Tumours (RECIST) 1.1 is defined as growth of measurable target lesions, presence of new lesions or unequivocal progression of non-target disease. In this manuscript we explored whether a more refined categorisation of tumour response and/or these components of progression, varying over time, can improve prediction of overall survival (OS) in the RECIST database. METHODS: Data were randomly selected from 13 randomised clinical trials (3758 patients with breast, lung or colorectal cancer). A maximum of five target lesions contributed to the sum of longest diameters. At each measurement time we determined: best target response as best % improvement from baseline; tumour growth of target lesions as worst % change and worst rate of increase (mm/week) from nadir; presence of new lesions and occurrence of non-target PD. OS was analysed by tumour type using Cox regression, adjusting for baseline sum and including these parameters as time-dependent covariates. RESULTS: 36% of patients had new lesions, 28% non-target PD and 49% experienced target lesion growth (median strongest growth 1.5mm/week). Regardless of tumour type, presence of new lesions (hazard ratio (HR) ranging 1.5-2.3) and non-target PD (HR 1.5-2.0) were strongly associated with worse OS. The explanatory value of tumour growth for OS was low compared to the other components. CONCLUSION: Modelling target lesion tumour growth did not show a marked improvement in OS prediction over and above the other components. These analyses enable a better understanding of the role of each component in PD evaluation. Work is ongoing to incorporate this information into an updated version of RECIST with enhanced prediction of subsequent survival.

Adjuvant chemotherapy for resected stage II and III colon cancer: comparison of two widely used prognostic calculators.

Two Web-based prognostic calculators (Adjuvant! and Numeracy) are widely used to individualize decisions regarding adjuvant therapy among patients with resected stage II and III colon cancer. However, these tools have not been directly compared. Hypothetical scenarios were formulated for the Numeracy calculator based on all potential combinations of age, lymph nodes status, tumor stage, and grade of tumor. These were then applied to three postsurgical therapy choices: observation, 5-fluorouracil (5-FU), or FOLFOX (5-FU, leucovorin, and oxaliplatin chemotherapy) to obtain the predicted 5-year disease-free survival (DFS) and overall survival (OS). Wilcoxon signed rank tests were used to compare the numerical predictions between the Adjuvant! and Numeracy calculators for each combination. A total of 192 hypothetical patient scenarios were obtained. For these patients, DFS and OS predictions from Adjuvant! were statistically significantly different than Numeracy (P <.05), except for four of 144 categories. While the estimated benefit in DFS and OS for 5-FU compared to surgery obtained from Adjuvant! and Numeracy were similar, the benefit in DFS and OS for FOLFOX over 5-FU, obtained from the Adjuvant! tool was slightly lower than that estimated from Numeracy. Among patients with resected stage II and III colon cancer, the DFS and OS estimates obtained from Numeracy and Adjuvant!, regarding the benefit of 5-FU over surgery, are similar, but the benefits of FOLFOX over 5-FU differ. Validation studies are needed to clarify the discrepancy and to assess the accuracy of these tools for predicting actual patient outcomes.

Randomized phase II designs.

As the use of molecularly targeted agents, which are anticipated to increase overall survival (OS)and progression-free survival (PFS) but not necessarily tumor response, has increased in oncology, there has been a corresponding increase in the recommendation and use of randomized phase II designs. Such designs reduce the potential for bias, existent in comparisons with historical controls, but also substantially increase the sample size requirements. We review the principal statistical designs for historically controlled and randomized phase II trials, along with their advantages, disadvantages, and statistical design considerations. We review the arguments for and against the use of randomization in phase II studies, the situations in which the use of historical controls is preferred, and the situations in which the use of randomized designs is preferred. We review methods used to calculate predicted OS or PFS values from historical controls, adjusted so as to be appropriate for an experimental sample with particular prognostic characteristics. We show how adjustment of the type I and type II error bounds for randomized studies can facilitate the detection of appropriate target increases in median PFS or OS with sample sizes appropriate for phase II studies. Although there continue to be differences among investigators concerning the use of randomization versus historical controls in phase II trials, there is agreement that each approach will continue to be appropriate, and the optimal approach will depend upon the circumstances of the individual trial.

Individual patient data analysis to assess modifications to the RECIST criteria.

BACKGROUND: After the initial RECIST 1.0 were published in 2000, the criteria were widely implemented in the scientific oncology community. Since then, the RECIST working group has identified several issues to examine further. Two key issues that required careful, data-based assessment were the maximum number of lesions that should be assessed at each evaluation and the added value of requiring confirmation of response. METHODS: To address these questions, data were obtained from 16 clinical trials in metastatic cancer, with patients enrolled between 1993 and 2005. A total of 6512 patients were included in the primary analysis dataset, accounting for over 18,000 potential target lesions. Nine percent of the included patients (n=585) had six or more reported target lesions. The response and progression outcomes in the database were calculated using an adjusted RECIST methodology with a maximum of 5 (or 3) target lesions with/without confirmation and this was compared to the original RECIST version 1.0 which required up to 10 target lesions plus confirmation of response. RESULTS: Assessment of 5 lesions per patient led to a difference in best overall response assignment for an estimated 209 (3.2%) patients as compared to RECIST version 1.0. However, these changes did not affect the overall response rate. Progression-free survival was only minimally affected by measuring fewer lesions. In contrast, removing the requirement for response confirmation led to a significant increase in the numbers of patients classified as responders, resulting in a relative increase of approximately 19% in response rate. An algorithm using a maximum of three target lesions shows high concordance with the 10 lesions requirement in terms of response and TTP assignment. Concern that appropriate assessment of disease within an organ requires two lesions to be followed per organ suggests the approach of following two target lesions per organ, up to a maximum of five target lesions overall. Both strategies seem reasonable based on the data warehouse. The requirement of response confirmation in trials where this is a primary end-point is recommended to be maintained as its removal would substantially increase reported response rates.

Exploring and validating surrogate endpoints in colorectal cancer.

Sargent et al (J Clin Oncol 23: 8664-8670, 2005) concluded that 3-year disease-free survival (DFS) can be considered a valid surrogate (replacement) endpoint for 5-year overall survival (OS) in clinical trials of adjuvant chemotherapy for colorectal cancer. We address the question whether the conclusion holds for trials involving other classes of treatments than those considered by Sargent et al. Additionally, we assess if the 3-year cutpoint is an optimal one. To this aim, we investigate whether the results reported by Sargent et al. could have been used to predict treatment effects in three centrally randomized adjuvant colorectal cancer trials performed by the Japanese Foundation for Multidisciplinary Treatment for Cancer (JFMTC) (Sakamoto et al. J Clin Oncol 22:484-492, 2004). Our analysis supports the conclusion of Sargent et al. and shows that using DFS at 2 or 3 years would be the best option for the prediction of OS at 5 years.

Characterization of antigen processing machinery and Survivin expression in tonsillar squamous cell carcinoma.

BACKGROUND: There is a statistically significant association between human leukocyte antigen (HLA) Class I antigen expression and improved prognosis for some patients. This association reflects the control of tumor growth by HLA Class I antigen-restricted, tumor-associated antigen-specific cytolytic T cells. However, progression of other malignant diseases is not associated with the loss of HLA expression. These observations show that the poor prognosis of a subset of tumors, despite high HLA Class I antigen expression, may reflect the development of alternative mechanisms utilized by tumor cells to escape from immune recognition and destruction. METHODS: The authors evaluated the possible correlation between the expression of the antiapoptosis gene, Survivin, HLA Class I, and progression of tonsillar squamous cell carcinomas (TSCC) lesions. Tissue microarrays were constructed from primary TSCC, metastatically involved lymph nodes, adjacent normal mucosa, and tonsillar parenchyma excised for nonmalignant conditions. RESULTS: Immunoperoxidase staining of tissue sections demonstrated that Survivin expression is significantly higher (P < 0.001) in malignant tumors than in normal tissue samples. In addition, Survivin expression is significantly higher (P = 0.05) in metastatic than in primary lesions. Survivin expression in primary lesions correlated positively with delta (P = 0.025), tapasin (P = 0.028), and HLA Class I antigen (P = 0.006) expression. The expression patterns of delta, tapasin, HLA Class I antigen, beta-2-microglobulin, and Survivin did not demonstrate any significant association with the clinical course of disease. CONCLUSIONS: For TSCC that maintain the expression of HLA Class I antigen, overexpression of Survivin may provide an alternative explanation for tumor progression.

Swallow function in patients before and after intra-arterial chemoradiation.

OBJECTIVES/HYPOTHESIS: To prospectively evaluate swallow function in patients with advanced head and neck cancer before and after completion of intra-arterial chemoradiation therapy and planned neck dissection. STUDY DESIGN: Prospective nonrandomized study. METHODS Swallow function was evaluated in 11 patients with resectable T4 and selected T3 head and neck cancer before and, on average, 19 weeks after completion of treatment. RESULTS: The Performance Status Scale demonstrated worse scores for both eating in public (P =.004) and normalcy of diet (P =.004) after treatment. Patients who underwent neck dissections had significantly worse scores (P =.02) in normalcy of diet. A significant decline was noted in swallowing functional measures at the time of the repeat evaluation (P =.02). Videofluoroscopic swallow studies revealed altered swallow function in 9 of 11 patients before treatment, with aspiration seen in 3 patients. Following treatment, the incidence of aspiration increased to seven patients. Tongue base retraction, reduced laryngeal elevation, and increased laryngeal vestibule penetration of thick liquid were all statistically significantly worse after treatment. The overall score on the quality of life instrument was not significantly changed from before to after treatment. CONCLUSIONS: The majority of patients demonstrated significantly worse swallow function on all three methods of analysis at 19 weeks after completion of treatment. Continued detailed monitoring of patients' swallow function is critical in determining long-term effects of intra-arterial chemoradiation therapy and neck dissection.