The molecular landscape and associated clinical experience in infant medulloblastoma: prognostic significance of second-generation subtypes.

AIMS: Biomarker-driven therapies have not been developed for infant medulloblastoma (iMB). We sought to robustly sub-classify iMB, and proffer strategies for personalized, risk-adapted therapies. METHODS: We characterized the iMB molecular landscape, including second-generation subtyping, and the associated retrospective clinical experience, using large independent discovery/validation cohorts (n = 387). RESULTS: iMBGrp3 (42%) and iMBSHH (40%) subgroups predominated. iMBGrp3 harboured second-generation subtypes II/III/IV. Subtype II strongly associated with large-cell/anaplastic pathology (LCA; 23%) and MYC amplification (19%), defining a very-high-risk group (0% 10yr overall survival (OS)), which progressed rapidly on all therapies; novel approaches are urgently required. Subtype VII (predominant within iMBGrp4 ) and subtype IV tumours were standard risk (80% OS) using upfront CSI-based therapies; randomized-controlled trials of upfront radiation-sparing and/or second-line radiotherapy should be considered. Seventy-five per cent of iMBSHH showed DN/MBEN histopathology in discovery and validation cohorts (P < 0.0001); central pathology review determined diagnosis of histological variants to WHO standards. In multivariable models, non-DN/MBEN pathology was associated significantly with worse outcomes within iMBSHH . iMBSHH harboured two distinct subtypes (iMBSHH-I/II ). Within the discriminated favourable-risk iMBSHH DN/MBEN patient group, iMBSHH-II had significantly better progression-free survival than iMBSHH-I , offering opportunities for risk-adapted stratification of upfront therapies. Both iMBSHH-I and iMBSHH-II showed notable rescue rates (56% combined post-relapse survival), further supporting delay of irradiation. Survival models and risk factors described were reproducible in independent cohorts, strongly supporting their further investigation and development. CONCLUSIONS: Investigations of large, retrospective cohorts have enabled the comprehensive and robust characterization of molecular heterogeneity within iMB. Novel subtypes are clinically significant and subgroup-dependent survival models highlight opportunities for biomarker-directed therapies.

Ethical tradeoffs in trial design: case study of an HPV vaccine trial in HIV-infected adolescent girls in lower income settings.

The Declaration of Helsinki and the Council of the International Organization of Medical Sciences provide guidance on standards of care and prevention in clinical trials. In the current and increasingly challenging research environment, the ethical status of a trial design depends not only on protection of participants, but also on social value, feasibility, and scientific validity. Using the example of a study assessing efficacy of a vaccine to prevent human papilloma virus in HIV-1 infected adolescent girls in low resource countries without access to the vaccine, we compare several trial designs which rank lower on some criteria and higher on others, giving rise to difficult trade-offs. This case demonstrates the need for developing more nuanced guidance documents to help researchers balance these often conflicting criteria.

Minimal methylation classifier (MIMIC): A novel method for derivation and rapid diagnostic detection of disease-associated DNA methylation signatures.

Rapid and reliable detection of disease-associated DNA methylation patterns has major potential to advance molecular diagnostics and underpin research investigations. We describe the development and validation of minimal methylation classifier (MIMIC), combining CpG signature design from genome-wide datasets, multiplex-PCR and detection by single-base extension and MALDI-TOF mass spectrometry, in a novel method to assess multi-locus DNA methylation profiles within routine clinically-applicable assays. We illustrate the application of MIMIC to successfully identify the methylation-dependent diagnostic molecular subgroups of medulloblastoma (the most common malignant childhood brain tumour), using scant/low-quality samples remaining from the most recently completed pan-European medulloblastoma clinical trial, refractory to analysis by conventional genome-wide DNA methylation analysis. Using this approach, we identify critical DNA methylation patterns from previously inaccessible cohorts, and reveal novel survival differences between the medulloblastoma disease subgroups with significant potential for clinical exploitation.

Slow replication of palindrome-containing DNA.

Lambda red gam phage carrying a 571 base-pair palindrome are unviable in wild-type Escherichia coli hosts. By using de-methylation to study the fate of DNA strands introduced into E. coli, we have demonstrated that a decrease in the yield of palindrome-containing molecules with two newly synthesized strands can occur without any concomitant loss of replicated molecules containing input strands. This implies that the palindrome-containing DNA is not being destroyed even as a consequence of replication, but rather that its replication rate is reduced. These results demonstrate that a palindrome can mediate unviability without directing cleavage of its carrier replicon.

Mutation analysis of the spastin gene (SPG4) in patients with hereditary spastic paraparesis.

BACKGROUND: Hereditary spastic paraparesis is a genetically heterogeneous condition. Recently, mutations in the spastin gene were reported in families linked to the common SPG4 locus on chromosome 2p21-22. OBJECTIVES: To study a population of patients with hereditary spastic paraparesis for mutations in the spastin gene (SPG4) on chromosome 2p21-22. METHODS: DNA from 32 patients (12 from families known to be linked to SPG4) was analysed for mutations in the spastin gene by single strand conformational polymorphism analysis and sequencing. All patients were also examined clinically. RESULTS: Thirteen SPG4 mutations were identified, 11 of which are novel. These mutations include missense, nonsense, frameshift, and splice site mutations, the majority of which affect the AAA cassette. We also describe a nucleotide substitution outside this conserved region which appears to behave as a recessive mutation. CONCLUSIONS: Recurrent mutations in the spastin gene are uncommon. This reduces the ease of mutation detection as a part of the diagnostic work up of patients with hereditary spastic paraparesis. Our findings have important implications for the presumed function of spastin and schemes for mutation detection in HSP patients.

Cross-species epigenetics identifies a critical role for VAV1 in SHH subgroup medulloblastoma maintenance.

The identification of key tumorigenic events in Sonic Hedgehog (SHH) subgroup medulloblastomas (MBSHH) will be essential for the development of individualized therapies and improved outcomes. However, beyond confirmation of characteristic SHH pathway mutations, recent genome-wide sequencing studies have not revealed commonly mutated genes with widespread relevance as potential therapeutic targets. We therefore examined any role for epigenetic DNA methylation events in MBSHH using a cross-species approach to candidate identification, prioritization and validation. MBSHH-associated DNA methylation events were first identified in 216 subgrouped human medulloblastomas (50 MBSHH, 28 Wnt/Wingless, 44 Group 3 and 94 Group 4) and their conservation then assessed in tumors arising from four independent murine models of Shh medulloblastoma, alongside any role in tumorigenesis using functional assessments in mouse and human models. This strategy identified widespread regional CpG hypo-methylation of VAV1, leading to its elevated expression, as a conserved aberrant epigenetic event, which characterizes the majority of MBSHH tumors in both species, and is associated with a poor outcome in MBSHH patients. Moreover, direct modulation of VAV1 in mouse and human models revealed a critical role in tumor maintenance, and its abrogation markedly reduced medulloblastoma growth. Further, Vav1 activity regulated granule neuron precursor germinal zone exit and migration initiation in an ex vivo model of early postnatal cerebellar development. These findings establish VAV1 as a critical epigenetically regulated oncogene with a key role in MBSHH maintenance, and highlight its potential as a validated therapeutic target and prognostic biomarker for the improved therapy of medulloblastoma.

Paraplegin gene analysis in hereditary spastic paraparesis (HSP) pedigrees in northeast England.

OBJECTIVE: To identify the frequency and characterize the phenotype of paraplegin mutations in the hereditary spastic paraparesis (HSP) population in the northeast of England. BACKGROUND: HSP is a disorder that shows both clinical and genetic heterogeneity. To date, 13 loci have been associated with an HSP phenotype, with the causative gene having been identified in four of these. Two autosomal genes have been identified, paraplegin and spastin, and two X-linked genes have been identified, L1CAM (cell adhesion molecule) and proteolipid protein. METHODS: Thirty HSP pedigrees from the northeast of England were analyzed for mutation in each of the 17 exons of the paraplegin gene. RESULTS: A single family with a paraplegin mutation was identified in which the paraplegin mutation co-segregates with an HSP phenotype in an apparent dominant manner. The authors also describe frequent polymorphism in the paraplegin gene in both the HSP and control populations. CONCLUSION: Mutations in the paraplegin gene are not a common cause of HSP in the northeast of England. The phenotype of the paraplegin-related HSP family described had several striking features including amyotrophy, raised creatine kinase, sensorimotor peripheral neuropathy, and oxidative phosphorylation defect on muscle biopsy.

A comparison of continuous- and discrete- time three-state models for rodent tumorigenicity experiments.

The three-state illness-death model provides a useful way to characterize data from a rodent tumorigenicity experiment. Most parametrizations proposed recently in the literature assume discrete time for the death process and either discrete or continuous time for the tumor onset process. We compare these approaches with a third alternative that uses a piecewise continuous model on the hazards for tumor onset and death. All three models assume proportional hazards to characterize tumor lethality and the effect of dose on tumor onset and death rate. All of the models can easily be fitted using an Expectation Maximization (EM) algorithm. The piecewise continuous model is particularly appealing in this context because the complete data likelihood corresponds to a standard piecewise exponential model with tumor presence as a time-varying covariate. It can be shown analytically that differences between the parameter estimates given by each model are explained by varying assumptions about when tumor onsets, deaths, and sacrifices occur within intervals. The mixed-time model is seen to be an extension of the grouped data proportional hazards model [Mutat. Res. 24:267-278 (1981)]. We argue that the continuous-time model is preferable to the discrete- and mixed-time models because it gives reasonable estimates with relatively few intervals while still making full use of the available information. Data from the ED01 experiment illustrate the results.

Correlates of opportunistic infections in children infected with the human immunodeficiency virus managed before highly active antiretroviral therapy.

BACKGROUND: Opportunistic infections (OIs) are an important cause of morbidity and mortality in children infected with HIV. However, few data are available regarding the overall prevalence, incidence and immunologic correlates associated with these diseases in the pediatric HIV population. The Pediatric AIDS Clinical Trials Group (PACTG) has conducted multicenter studies in HIV-infected children since 1988 and through these studies has collected prospective data on the immunologic and virologic status of study participants and recorded complications, including infectious diseases, related to HIV infection and its treatments. Therefore data were analyzed from across 13 PACTG studies, performed before treatment with highly active antiretroviral therapy was given, to determine the rates of various infectious complications and the immunologic correlates, specifically CD4 cell counts, associated with these diseases. RESULTS: OIs were tabulated from 3331 HIV-infected children who participated in 13 clinic trials undertaken before highly effective antiretroviral therapy was available. Five OIs occurred at event rates of >1.0 per 100 patient years (person years): serious bacterial infections, 15.1; herpes zoster, 2.9; disseminated Mycobacterium avium complex (DMAC), 1.8; Pneumocystis carinii pneumonia, 1.3; and tracheobronchial and esophageal candidiasis, 1.2. Six other OIs evaluated, cytomegalovirus (CMV) disease, cryptosporidiosis, tuberculosis, systemic fungal infections, toxoplasmosis and progressive multifocal leukoencephalopathy, occurred at event rates of <1.0 per 100 person years. Pneumonia (11.1 per 100 person years) and bacteremia (3.3 per 100 person years) were the most common bacterial infections. An AIDS-defining OI before entry was a risk factor for the development of a new OI during a trial. Bacterial infections, herpes zoster and tuberculosis occurred frequently at all stages of HIV infection; whereas DMAC, P. carinii pneumonia, CMV and other OIs occurred primarily in children with severe immunosuppression. CONCLUSIONS: The frequency of OIs in HIV-infected children in the pre-highly active antiretroviral therapy era varies with age, pathogen, prior OI and immunologic status. Analysis of CD4 counts at the time of DMAC, CMV and PCP provide validation for current prophylaxis guidelines in children > or =2 years old. This information on infectious complications of pediatric HIV will be especially valuable for contemporary management of HIV infection that is poorly responsive to highly active antiretroviral therapy.

Intrapolation and extrapolation of age-equivalent scores for the Bayley II: a comparison of two methods of estimation.

The Bayley Scales of Infant Development II (1) is a well established standardized test for assessing the mental ability of infants and young children. It provides an age-adjusted standard score as a summary measure, but for very low (or very high) functioning children the raw scores on this test may not allow the calculation of a standard score. The manual provides for the transformation of raw scores into age-equivalents but this translation is not unique and results in a step function. The availability of a unique and continuous transformation of raw scores to age-equivalents is critical when evaluating longitudinal mental development, particularly in the environment of controlled clinical trials or natural history studies. We compared two methods for deriving unique age equivalents: a local regression method, with estimates restricted to age-equivalents within the age range of the test, and a linear method, which also allows extrapolation outside the age range of the test. The linear method was found to be most useful and the values, which are provided in table format, can be used for assigning age equivalent scores to individual children. They are also useful in clinical trials which use the Bayley to assess the safety and efficacy of treatments with potential cognitive effects, when conducted in populations where the children are likely to record scaled scores below the limits of the test.

Methodological issues in analyzing psychological test scores in pediatric clinical trials.

Clinical trials to address drug dosing, safety, and efficacy issues in the pediatric population are becoming more common. In some studies, tests of mental ability are administered at regular intervals in drug trials for treatment of children with HIV, certain types of cancer, sickle cell anemia, and diabetes. The test scores are used to examine differences between treatments in efficacy and safety over time. In addition to the well-known problems of analyzing repeated measures with incomplete data profiles, the analyses of these data are complicated by a number of unique features, including that children can be so ill that their raw scores cannot be mapped to a normed scaled score, and that children may be in the studies long enough that they transition between the age-appropriate instruments. These issues are often ignored in data analyses and can potentially cause incorrect conclusions regarding treatment efficacy and safety. This article describes these issues and their possible consequences. A simple approach to determine their impact on the statistical analysis of a particular clinical trial is suggested. The approach is illustrated with data from a Phase III trial in HIV-infected children.

Interpreting treatment differences when patients drop out of a clinical trial.

Clinical trials are the standard for identifying new drugs for the treatment of disease, but results are dependent on patient compliance. The success of treatments for HIV disease in particular may be judged in part by their effect on immunologic, virologic, or clinical measures collected on patients at regular predefined intervals. If patients drop out of a trial before study completion, the analysis of the repeatedly collected parameters needs to be undertaken and interpreted with care. The authors recommend using graphic techniques to assess the impact of the missing data on the profiles of the parameters over time. To assess treatment differences, a variety of simple tests are proposed that allow different assumptions to be made regarding the reasons for the incomplete data. A case study is presented providing an analysis of CD4 data from the Pediatric Aids Clinical Trials Group (PACTG) Protocol 051, in which only 52% of the patients completed the study while remaining on treatment; younger patients with lower CD4 counts were more likely to stop treatment earlier. This type of systematic missing data can lead to incorrect conclusions regarding different treatment effects on CD4 counts. With the data of PACTG 051, however, regardless of the methodology used, no treatment differences were found. Inconsistent conclusions would have indicated the need for more sophisticated statistical techniques to adequately test for treatment differences.

Serologic examination of hepatitis B infection and immunization in HIV-positive youth and associated risks. The Pediatric AIDS Clinical Trials Group Protocol 220 Team.

This seroprevalence report examines serologic evidence of hepatitis B immunization or infection and associated demographic/behavioral factors in adolescent (aged 12-20) subjects enrolled in a nontherapeutic clinical trial at 43 Pediatric AIDS Clinical Trials Group (PACTG) clinical centers. Subjects (n = 94) infected with the human immunodeficiency virus (HIV) through sexual activity were categorized as hepatitis B virus (HBV)-immunized, HBV-infected, or nonimmune by hepatitis B serology performed on specimens collected within the subject's first 48 weeks on study (1993-1995). Sixteen percent of the 94 serologically classified subjects were immunized; 19% HBV-infected; 65% nonimmune. Of the three risk factor scores examined (sociodemographic, sexual, and substance abuse), substance use alone demonstrated a significant difference among groups (despite virtually no reported injecting drug behavior), with the sexual risk score exhibiting marginally significant differences. Logistic regression analysis (restricted to nonimmunized subjects) showed that male-male sexual activity raised the odds of HBV infection by a factor of 5.14 (95% confidence interval [CI]: 1.45-18. 23) relative to heterosexual activity; and that for every one point increase on the substance abuse risk scale the odds of infection increased 5% (95% CI: 0.99-1.10). The HBV infection rate in PACTG 220 HIV-positive females is twice United States population-based rates; the rate in PACTG 220 HIV-positive males is nearly seven times higher. Past immunization efforts in this population appear to have been based on sexual activity volume without regard to injecting-drug use in sex partners.

Abacavir pharmacokinetics during chronic therapy in HIV-1-infected adolescents and young adults.

The pharmacokinetics of abacavir and its metabolites were investigated in 30 human immunodeficiency virus (HIV)-infected adolescents and young adults 13-25 years of age, equally divided into two groups: <18 years of age and >or=18 years of age. All the subjects received the recommended adult dose of 300 mg twice daily. The area under the plasma concentration-time curve (AUC) and half-life of abacavir did not differ significantly between the age groups or by gender or race, and there were only modest associations of age with apparent abacavir clearance and with volume of distribution. There were no significant correlations of carboxylate or glucuronide metabolite levels with age or gender, although glucuronide AUC was higher in Hispanic subjects than in African-American subjects. Zidovudine and lamivudine concentration profiles were also similar in the two age groups. A novel aspect of the study included an assessment of intracellular carbovir, zidovudine, and lamivudine triphosphate levels, and these were found to be similar in the two age-based groups. Overall, these findings suggest that current recommendations relating to adult dosages are appropriate for adolescents and young adults.

Alcohol disorders among Asian Americans: associations with unfair treatment, racial/ethnic discrimination, and ethnic identification (the national Latino and Asian Americans study, 2002-2003).

STUDY OBJECTIVE: To examine history of alcohol abuse/dependence disorder in relation to unfair treatment, racial/ethnic discrimination, and ethnic identification among Asian Americans. DESIGN: Weighted multivariate analyses of cross-sectional national survey data predicting lifetime history of alcohol abuse/dependence disorders. SETTING: USA, Asian Americans. PARTICIPANTS: 2007 Asian American adults recruited to the National Latino and Asian American Study (NLAAS; 2002-2003). RESULTS: Controlling for sociodemographic characteristics, Asian Americans who reported experiencing unfair treatment had higher odds of history of alcohol abuse/dependence disorder (OR 5.26, 95% CI 1.90 to 14.56). Participants who reported high levels of ethnic identification had lower odds of history of alcohol abuse/dependence disorders (OR 0.46, 95% CI 0.23 to 0.90). Ethnic identification moderated the influence of racial/ethnic discrimination (p = 0.097). Among participants with low levels of ethnic identification, racial/ethnic discrimination was associated with greater odds of having a history of alcohol disorder compared with those with high levels of ethnic identification. CONCLUSIONS: Social hazards such as unfair treatment and racial/ethnic discrimination should be considered in the development of programmes addressing alcohol disorders among Asian Americans. Interventions that promote ethnic identification in this population may be particularly relevant in mitigating the negative influence of racial/ethnic discrimination on alcohol disorders.

Epigenetic deregulation of multiple S100 gene family members by differential hypomethylation and hypermethylation events in medulloblastoma.

Deregulated expression of genes encoding members of the S100 family of calcium-binding proteins has been associated with the malignant progression of multiple tumour types. Using a pharmacological expression reactivation approach, we screened 16 S100 genes for evidence of epigenetic regulation in medulloblastoma, the most common malignant brain tumour of childhood. Four family members (S100A2, S100A4, S100A6 and S100A10) demonstrated evidence of upregulated expression in multiple medulloblastoma cell lines, following treatment with the DNA methyltransferase inhibitor, 5'-aza-2'-deoxycytidine. Subsequent analysis revealed methylation of critical CpG sites located within these four genes in an extended cell line panel. Assessment of these genes in the non-neoplastic cerebellum (from which medulloblastomas develop) revealed strong somatic methylation affecting S100A2 and S100A4, whereas S100A6 and S100A10 were unmethylated. Assessed against these normal tissue-specific methylation states, S100A6 and S100A10 demonstrated tumour-specific hypermethylation in medulloblastoma primary tumours (5 out of 40 and 4 out of 35, respectively, both 12%) and cell lines (both 7 out of 9, 78%), which was associated with their transcriptional silencing. Moreover, S100A6 hypermethylation was significantly associated with the aggressive large cell/anaplastic morphophenotype (P=0.026). In contrast, pro-metastatic S100A4 displayed evidence of hypomethylation relative to the normal cerebellum in a significant proportion primary tumours (7 out of 41, 17%) and cell lines (3 out of 9, 33%), which was associated with its elevated expression. In summary, these data characterise complex patterns of somatic methylation affecting S100 genes in the normal cerebellum and demonstrate their disruption causing epigenetic deregulation of multiple S100 family members in medulloblastoma development. Epigenetic events affecting S100 genes have potential clinical utility and merit further investigation as molecular biomarkers for this disease.

Issues in the design of clinical trials for safety in HIV-infected children.

The use of newly approved drugs for human immunodeficiency virus (HIV)-infected adults is limited in children until child-specific pharmacokinetic and safety data can be submitted to the Food and Drug Administration (FDA) to fulfill labeling requirements. Design of a clinical trial to assess drug safety in children requires a different set of issues from standard Phase II and III efficacy trials in adults. For example, Phase II trials in adults are done to collect preliminary efficacy information. In children, efficacy of the drug is assumed and only safety needs to be shown. As a result, control groups may not be required and it may not be necessary to show superiority of the new drug over a control. This paper describes these issues in some detail and gives examples of designs appropriate in different scenarios.

Tutorial in biostatistics methods for interval-censored data.

In standard time-to-event or survival analysis, occurrence times of the event of interest are observed exactly or are right-censored, meaning that it is only known that the event occurred after the last observation time. There are numerous methods available for estimating the survival curve and for testing and estimation of the effects of covariates in this context. In some situations, however, the times of the events of interest may only be known to have occurred within an interval of time. In clinical trials, for example, patients are often seen at pre-scheduled visits but the event of interest may occur in between visits. These data are interval-censored. Owing to the lack of well-known statistical methodology and available software, a common ad hoc approach is to assume that the event occurred at the end (or beginning or midpoint) of each interval, and then apply methods for standard time-to-event data. However, this approach can lead to invalid inferences, and in particular will tend to underestimate the standard errors of the estimated parameters. The purpose of this tutorial is to illustrate and compare available methods which correctly treat the data as being interval-censored. It is not meant to be a full review of all existing methods, but only those which are available in standard statistical software, or which can be easily programmed. All approaches will be illustrated on two data sets and compared with methods which ignore the interval-censored nature of the data. We hope this tutorial will allow those familiar with the application of standard survival analysis techniques the option of applying appropriate methods when presented with interval-censored data.

Multi-state Markov models for analysing incomplete disease history data with illustrations for HIV disease.

Multi-state Markov models can be useful in analysing disease history data. We apply the general estimation methods of Kalbfleisch and Lawless to panel data in which individuals are viewed over only a portion of their life history and complete information about transition times between states is unavailable. Methods to assess goodness-of-fit are proposed. To illustrate the methods, we consider models of HIV disease relating important immunological marker measurements to the onset of AIDS.

Local EM estimation of the hazard function for interval-censored data.

We propose a smooth hazard estimator for interval-censored survival data using the method of local likelihood. The model is fit using a local EM algorithm. The estimator is more descriptive than traditional empirical estimates in regions of concentrated information and takes on a parametric flavor in regions of sparse information. We derive two different standard error estimates for the smooth curve, one based on asymptotic theory and the other on the bootstrap. We illustrate the local EM method for times to breast cosmesis deterioration (Finkelstein, 1986, Biometrics 42, 845-854) and for times to HIV-1 infection for individuals with hemophilia (Kroner et al., 1994, Journal of AIDS 7, 279-286). Our hazard estimates for each of these data sets show interesting structures that would not be found using a standard parametric hazard model or empirical survivorship estimates.