ClonEvol: clonal ordering and visualization in cancer sequencing.

BACKGROUND: Reconstruction of clonal evolution is critical for understanding tumor progression and implementing personalized therapies. This is often done by clustering somatic variants based on their cellular prevalence estimated via bulk tumor sequencing of multiple samples. The clusters, consisting of the clonal marker variants, are then ordered based on their estimated cellular prevalence to reconstruct clonal evolution trees, a process referred to as 'clonal ordering'. However, cellular prevalence estimate is confounded by statistical variability and errors in sequencing/data analysis, and therefore inhibits accurate reconstruction of the clonal evolution. This problem is further complicated by intra- and inter-tumor heterogeneity. Furthermore, the field lacks a comprehensive visualization tool to facilitate the interpretation of complex clonal relationships. To address these challenges we developed ClonEvol, a unified software tool for clonal ordering, visualization, and interpretation. MATERIALS AND METHODS: ClonEvol uses a bootstrap resampling technique to estimate the cellular fraction of the clones and probabilistically models the clonal ordering constraints to account for statistical variability. The bootstrapping allows identification of the sample founding- and sub-clones, thus enabling interpretation of clonal seeding. ClonEvol automates the generation of multiple widely used visualizations for reconstructing and interpreting clonal evolution. RESULTS: ClonEvol outperformed three of the state of the art tools (LICHeE, Canopy and PhyloWGS) for clonal evolution inference, showing more robust error tolerance and producing more accurate trees in a simulation. Building upon multiple recent publications that utilized ClonEvol to study metastasis and drug resistance in solid cancers, here we show that ClonEvol rediscovered relapsed subclones in two published acute myeloid leukemia patients. Furthermore, we demonstrated that through noninvasive monitoring ClonEvol recapitulated the emerging subclones throughout metastatic progression observed in the tumors of a published breast cancer patient. CONCLUSIONS: ClonEvol has broad applicability for longitudinal monitoring of clonal populations in tumor biopsies, or noninvasively, to guide precision medicine. AVAILABILITY: ClonEvol is written in R and is available at https://github.com/ChrisMaherLab/ClonEvol.

A genomic case study of mixed fibrolamellar hepatocellular carcinoma.

BACKGROUND: Mixed fibrolamellar hepatocellular carcinoma (mFL-HCC) is a rare liver tumor defined by the presence of both pure FL-HCC and conventional HCC components, represents up to 25% of cases of FL-HCC, and has been associated with worse prognosis. Recent genomic characterization of pure FL-HCC identified a highly recurrent transcript fusion (DNAJB1:PRKACA) not found in conventional HCC. PATIENTS AND METHODS: We performed exome and transcriptome sequencing of a case of mFL-HCC. A novel BAC-capture approach was developed to identify a 400 kb deletion as the underlying genomic mechanism for a DNAJB1:PRKACA fusion in this case. A sensitive Nanostring Elements assay was used to screen for this transcript fusion in a second case of mFL-HCC, 112 additional HCC samples and 44 adjacent non-tumor liver samples. RESULTS: We report the first comprehensive genomic analysis of a case of mFL-HCC. No common HCC-associated mutations were identified. The very low mutation rate of this case, large number of mostly single-copy, long-range copy number variants, and high expression of ERBB2 were more consistent with previous reports of pure FL-HCC than conventional HCC. In particular, the DNAJB1:PRKACA fusion transcript specifically associated with pure FL-HCC was detected at very high expression levels. Subsequent analysis revealed the presence of this fusion in all primary and metastatic samples, including those with mixed or conventional HCC pathology. A second case of mFL-HCC confirmed our finding that the fusion was detectable in conventional components. An expanded screen identified a third case of fusion-positive HCC, which upon review, also had both conventional and fibrolamellar features. This screen confirmed the absence of the fusion in all conventional HCC and adjacent non-tumor liver samples. CONCLUSION: These results indicate that mFL-HCC is similar to pure FL-HCC at the genomic level and the DNAJB1:PRKACA fusion can be used as a diagnostic tool for both pure and mFL-HCC.

NFATc1 promotes prostate tumorigenesis and overcomes PTEN loss-induced senescence.

Despite recent insights into prostate cancer (PCa)-associated genetic changes, full understanding of prostate tumorigenesis remains elusive owing to complexity of interactions among various cell types and soluble factors present in prostate tissue. We found the upregulation of nuclear factor of activated T cells c1 (NFATc1) in human PCa and cultured PCa cells, but not in normal prostates and non-tumorigenic prostate cells. To understand the role of NFATc1 in prostate tumorigenesis in situ, we temporally and spatially controlled the activation of NFATc1 in mouse prostate and showed that such activation resulted in prostatic adenocarcinoma with features similar to those seen in human PCa. Our results indicate that the activation of a single transcription factor, NFATc1 in prostatic luminal epithelium to PCa can affect expression of diverse factors in both cells harboring the genetic changes and in neighboring cells through microenvironmental alterations. In addition to the activation of oncogenes c-MYC and STAT3 in tumor cells, a number of cytokines and growth factors, such as IL1ß, IL6 and SPP1 (osteopontin, a key biomarker for PCa), were upregulated in NFATc1-induced PCa, establishing a tumorigenic microenvironment involving both NFATc1 positive and negative cells for prostate tumorigenesis. To further characterize interactions between genes involved in prostate tumorigenesis, we generated mice with both NFATc1 activation and Pten inactivation in prostate. We showed that NFATc1 activation led to acceleration of Pten null-driven prostate tumorigenesis by overcoming the PTEN loss-induced cellular senescence through inhibition of p21 activation. This study provides direct in vivo evidence of an oncogenic role of NFATc1 in prostate tumorigenesis and reveals multiple functions of NFATc1 in activating oncogenes, in inducing proinflammatory cytokines, in oncogene addiction, and in overcoming cellular senescence, which suggests calcineurin-NFAT signaling as a potential target in preventing PCa.

Sleep duration or bedtime? Exploring the association between sleep timing behaviour, diet and BMI in children and adolescents.

OBJECTIVE: To determine whether sleep timing behaviour is associated with energy intake and diet quality in children and adolescents. DESIGN: Cross-sectional analysis of nationally representative survey data. SAMPLE: A total of 2200 participants of the 2007 Australian National Children's Nutrition and Physical Activity Survey aged 9-16 years with 2 days of food intake data, 4 days of use of time data and complete anthropometry. Participants were grouped into one of four sleep-wake behaviour categories: early bed-early rise (EE); early bed-late rise (EL); late bed-early rise (LE) and late bed-late rise (LL). The four categories were compared for body mass index (BMI) z-score, energy intake and diet quality assessed using the Dietary Guideline Index for Children and Adolescents. Analyses were adjusted for survey design, sociodemographic characteristics, sleep duration and physical activity level (PAL). RESULTS: In adjusted multivariate regression models with sleep timing behaviour group as the independent variable, the 'LL' category compared with the 'EE' category had a higher BMI z-score (ß=0.20, 95% confidence interval (CI) 0.06 to 0.34, P=0.007), and lower diet quality (ß=-4.0, 95% CI -5.7 to -2.3, P<0.001). Children and adolescents who went to bed late also had a higher intake of extra foods (that is, energy-dense, nutrient-poor foods) while those whom went to bed early consumed more fruit and vegetables. Energy intake was associated with sleep duration (ß=-4.5 kJ, 95% CI -6.7 to -2.4, P<0.001), but not sleep timing behaviour. CONCLUSION: Late bedtimes and late wake up times are associated with poorer diet quality, independent of sleep duration, PAL and child and sociodemographic characteristics.

Minutes, MET minutes, and METs: unpacking socio-economic gradients in physical activity in adolescents.

BACKGROUND: There is conflicting evidence regarding the relationship between socio-economic position (SEP) and physical activity in adolescents. The aim of this study was to investigate associations between SEP and characteristics of physical activity in Australian adolescents using a high-resolution use-of-time tool. METHOD: Use-of-time and pedometer data were collected on a random sample of 2071 9-16-year-old Australian children. Use-of-time was recorded using a computerised 24-h use-of-time recall, the Multimedia Activity Recall for Children and Adults. Reported household income was used as a marker of SEP. RESULTS: There were no differences in self-reported minutes of moderate to vigorous physical activity (MVPA) across the income bands and only very small differences in the number of daily steps. However, the mix of MVPA components varied across income bands, with adolescents from low-SEP families experiencing less sport but more active transport. Because the mean rate of energy expenditure was greater in sport than in other forms of MVPA (play, active transport or chores), there were significant differences in MVPA-related and total daily energy expenditure across income bands, with the lower bands having significantly lower values. Differences in total daily energy expenditure were almost entirely explained by differences in energy expenditure associated with sport. CONCLUSION: Physical activity patterns vary across SEP bands in Australian adolescents, with sport being the major locus of differences. Instruments which do not account for the energy costs of various activities may fail to detect important relationships.

Trends in the prevalence of childhood overweight and obesity in Australia between 1985 and 2008.

BACKGROUND: Popular media, health experts and researchers talk about a paediatric 'obesity epidemic' with exponentially increasing rates of obesity and overweight. However, some recent reports suggest that prevalence may have plateaued. This study examined trends in the prevalence of Australian childhood overweight and obesity since 1985. Specifically, it aimed to determine whether there have been (a) overall increases in average body mass index (BMI), (b) differential patterns of change within age groups and (c) increases in BMI within each weight-status category. METHOD: Forty-one Australian studies of childhood weight status conducted between 1985 and 2008 were reviewed. The studies included data on 264 905 Australians aged 2-18 years, with raw data being available on 70 758 children (27%). Children were classified as overweight or obese based on BMI using the criteria of Cole et al. (BMJ, 2000). The prevalence estimates were adjusted for age and sex, and plotted against measurement year using Lowess plots and two-linear-segment models. Where raw data were available, BMI z-scores (UK 1990 standard) were plotted against measurement year for all children and children in various age groups. Lowess plots and two-linear-segment models were used to assess secular trends in BMI z-scores pre- and post-1996 within age, gender and weight-status categories. RESULTS: There has been a plateau, or only slight increase, in the percentage of boys and girls classified as overweight or obese, with almost no change over the last 10 years. In boys and girls, prevalence rates have settled around 21-25% for overweight and obesity together, and 5-6% for obesity alone. Similar trends were found for BMI z-scores. These patterns were fairly consistent across the age span. Within each weight-status category, average BMI has not increased. CONCLUSIONS: Although levels of Australian paediatric overweight remain high, the prevalence of overweight and obesity seems to have flattened and has not followed the anticipated exponential trajectory.

A systems approach to managing conflict in orthopaedic nursing.

Conflict management is considered from a psychologic perspective. Therein, a systems approach to managing conflict is described with particular reference to orthopaedic nursing practice. Within that context, conflict management is portrayed as a process that is applied by orthopaedic nurses to particular conflict situations by means of separate, yet interrelated phases: clarification of the conflict situation; design of a conflict resolution plan; implementation of the plan; and evaluation of the extent to which conflict has been resolved. Application of this systems approach by orthopaedic nursing managers or by staff nurses may be valuable in focusing their attention and that of other health care providers on important behaviors, tasks, and accomplishments rather than on personality constructs and other noncontrollable correlates of managing conflict effectively. Directions for empirical inquiry relating to conflict management in orthopaedic nursing are briefly considered.

On considering the unintended impact of evaluation: reactive distortions in program goals and activities.

The relationship between program planning and evaluation can be viewed as bidirectional; that is, evaluation methods, procedures, instruments, and criteria not only are determined by, but also influence, program goals and activities. Within the human services context, several factors or sources of reactivity between evaluation and program planning can be identified. These involve (a) quantification of goals and activities, (b) preferences by different audiences for various kinds of evaluation data, (c) values and evaluation criteria, and (d) evaluation requirements and resource availability. Effects of these reactive features are discussed and illustrated with examples drawn from mental health evaluation and accountability practices. It is argued that for evaluation to be a credible and useful practice, evaluators should plan their efforts and assess their own effectiveness within the larger context of human service systems.

An evaluation system for school-community prevention programs.

A management-oriented system for the evaluation of school-community prevention programs is described and examples of how the system has been applied to serve program management decisions with primary, secondary, and tertiary prevention programs are provided. The approach, termed "Program Analysis and Review System (PARS)," emphasizes a cooperative relationship between a program evaluator and prevention program manager in order that informed judgments can be made about program development and improvement. PARS, which was developed by the author in response to a perceived need for management-oriented approaches to prevention program evaluation, has been field tested with school-community prevention programs in Bergenfield, New Jersey, and Somerville, New Jersey, and has been adapted for use in other communities. PARS consists of three interrelated steps: Program Specification, Program Documentation, and Program Outcome Determination.