TCGASpliceSeq a compendium of alternative mRNA splicing in cancer

TCGA's RNASeq data represent one of the largest collections of cancer transcriptomes ever assembled. RNASeq technology, combined with computational tools like our SpliceSeq package, provides a comprehensive, detailed view of alternative mRNA splicing. Aberrant splicing patterns in cancers have been implicated in such processes as carcinogenesis, de-differentiation and metastasis. TCGA SpliceSeq (http://bioinformatics.mdanderson.org/TCGASpliceSeq) is a web-based resource that provides a quick, user-friendly, highly visual interface for exploring the alternative splicing patterns of TCGA tumors. Percent Spliced In (PSI) values for splice events on samples from 33 different tumor types, including available adjacent normal samples, have been loaded into TCGA SpliceSeq. Investigators can interrogate genes of interest, search for the genes that show the strongest variation between or among selected tumor types, or explore splicing pattern changes between tumor and adjacent normal samples. The interface presents intuitive graphical representations of splicing patterns, read counts and various statistical summaries, including percent spliced in. Splicing data can also be downloaded for inclusion in integrative analyses. TCGA SpliceSeq is freely available for academic, government or commercial use.

Inter-laboratory study of human in vitro toxicogenomics-based tests as alternative methods for evaluating chemical carcinogenicity: a bioinformatics perspective

The assessment of the carcinogenic potential of chemicals with alternative, human-based in vitro systems has become a major goal of toxicogenomics. The central read-out of these assays is the transcriptome, and while many studies exist that explored the gene expression responses of such systems, reports on robustness and reproducibility, when testing them independently in different laboratories, are still uncommon. Furthermore, there is limited knowledge about variability induced by the data analysis protocols. We have conducted an inter-laboratory study for testing chemical carcinogenicity evaluating two human in vitro assays: hepatoma-derived cells and hTERT-immortalized renal proximal tubule epithelial cells, representing liver and kidney as major target organs. Cellular systems were initially challenged with thirty compounds, genome-wide gene expression was measured with microarrays, and hazard classifiers were built from this training set. Subsequently, each system was independently established in three different laboratories, and gene expression measurements were conducted using anonymized compounds. Data analysis was performed independently by two separate groups applying different protocols for the assessment of inter-laboratory reproducibility and for the prediction of carcinogenic hazard. As a result, both workflows came to very similar conclusions with respect to (1) identification of experimental outliers, (2) overall assessment of robustness and inter-laboratory reproducibility and (3) re-classification of the unknown compounds to the respective toxicity classes. In summary, the developed bioinformatics workflows deliver accurate measures for inter-laboratory comparison studies, and the study can be used as guidance for validation of future carcinogenicity assays in order to implement testing of human in vitro alternatives to animal testing.

Assessing the Pathogenicity of Insertion and Deletion Variants with the Variant Effect Scoring Tool (VEST-Indel)

Insertion/deletion variants (indels) alter protein sequence and length, yet are highly prevalent in healthy populations, presenting a challenge to bioinformatics classifiers. Commonly used features—DNA and protein sequence conservation, indel length, and occurrence in repeat regions—are useful for inference of protein damage. However, these features can cause false positives when predicting the impact of indels on disease. Existing methods for indel classification suffer from low specificities, severely limiting clinical utility. Here, we further develop our variant effect scoring tool (VEST) to include the classification of in‐frame and frameshift indels (VEST‐indel) as pathogenic or benign. We apply 24 features, including a new “PubMed” feature, to estimate a gene's importance in human disease. When compared with four existing indel classifiers, our method achieves a drastically reduced false‐positive rate, improving specificity by as much as 90%. This approach of estimating gene importance might be generally applicable to missense and other bioinformatics pathogenicity predictors, which often fail to achieve high specificity. Finally, we tested all possible meta‐predictors that can be obtained from combining the four different indel classifiers using Boolean conjunctions and disjunctions, and derived a meta‐predictor with improved performance over any individual method.

The Multimodal Brain Tumor Image Segmentation Benchmark (BRATS)

In this paper we report the set-up and results of the Multimodal Brain Tumor Image Segmentation Benchmark (BRATS) organized in conjunction with the MICCAI 2012 and 2013 conferences. Twenty state-of-the-art tumor segmentation algorithms were applied to a set of 65 multi-contrast MR scans of low- and high-grade glioma patients-manually annotated by up to four raters-and to 65 comparable scans generated using tumor image simulation software. Quantitative evaluations revealed considerable disagreement between the human raters in segmenting various tumor sub-regions (Dice scores in the range 74%-85%), illustrating the difficulty of this task. We found that different algorithms worked best for different sub-regions (reaching performance comparable to human inter-rater variability), but that no single algorithm ranked in the top for all sub-regions simultaneously. Fusing several good algorithms using a hierarchical majority vote yielded segmentations that consistently ranked above all individual algorithms, indicating remaining opportunities for further methodological improvements. The BRATS image data and manual annotations continue to be publicly available through an online evaluation system as an ongoing benchmarking resource.

The DNA repair endonuclease Mus81 facilitates fast DNA replication in the absence of exogenous damage

The Mus81 endonuclease resolves recombination intermediates and mediates cellular responses to exogenous replicative stress. Here, we show that Mus81 also regulates the rate of DNA replication during normal growth by promoting replication fork progression while reducing the frequency of replication initiation events. In the absence of Mus81 endonuclease activity, DNA synthesis is slowed and replication initiation events are more frequent. In addition, Mus81-deficient cells fail to recover from exposure to low doses of replication inhibitors and cell viability is dependent on the XPF endonuclease. Despite an increase in replication initiation frequency, cells lacking Mus81 use the same pool of replication origins as Mus81-expressing cells. Therefore, decelerated DNA replication in Mus81-deficient cells does not initiate from cryptic or latent origins not used during normal growth. These results indicate that Mus81 plays a key role in determining the rate of DNA replication without activating a novel group of replication origins.

Diagnosis and treatment of sleep related breathing disorders in children: 2007 to 2011

Sleep related breathing disorders (SRBD) have historically been under-recognised and under-treated. Obstructive sleep apnoea (OSA) affects approximately 3% of children. In line with the increased recognition of SRBD there has been an increase in demand for diagnostic services. We determined the awareness of SRBD amongst Irish paediatricians, examined the provision of sleep services to children throughout the country between 2007 and 2011 and audited diagnostic sleep services in a tertiary centre in 2011. Amongst respondents there was an awareness of SRBD but a poor understanding of diagnostic evaluation with 31/46 (67) referring to inappropriate services. There has been a sharp increase in both diagnostic sleep tests (433-1793 [414]) and in the use of non-invasive ventilation (NIV) (31-186 [627]) for treatment of SRBD between 2007 and 2011. Paediatric sleep services are organized in an ad-hoc manner nationally with significant service variation. The use of domiciliary overnight oximetry reduced the requirement for more formal polysomnography by 70%.

Comparison of primary percutaneous coronary intervention in patients with ST-elevation myocardial infarction during and prior to availability of an in-house STEMI system: early experience and intermediate outcomes of the HARRT program for achieving routine D2B times <60 minutes

BACKGROUND

Over the last decade, significant advances in ST-elevation myocardial infarction (STEMI) workflow have resulted in most hospitals reporting door-to-balloon (D2B) times within the 90 min standard. Few programs have been enacted to systematically attempt to achieve routine D2B within 60 min. We sought to determine whether 24-hr in-house catheterization laboratory coverage via an In-House Interventional Team Program (IHIT) could achieve D2B times below 60 min for STEMI and to compare the results to the standard primary percutaneous coronary intervention (PCI) approach.

METHODS

An IHIT program was established consisting of an attending interventional cardiologist, and a catheterization laboratory team present in-hospital 24 hr/day. For all consecutive STEMI patients, we compared the standard primary PCI approach during the two years prior to the program (group A) to the initial 20 months of the IHIT program (group B), and repeated this analysis for only CMS-reportable patients. The D2B process was analyzed by calculating workflow intervals. The primary endpoint was D2B process times, and secondary endpoints included in-hospital and 6-month cardiovascular outcomes and resource utilization.

RESULTS

An IHIT program for STEMI resulted in significant reductions across all treatment intervals with an overall 57% reduction in D2B time, and an absolute reduction in mean D2B time of 71 min. There were no differences pre- and post-program implementation in regard to individual or composite components of in-hospital cardiovascular outcomes; however at 6 months, there was a reduction in cardiovascular rehospitalization after program implementation (30 vs. 5%, P < 0.01). The IHIT program resulted in a significant reduction in length-of-stay (LOS) (90 ± 102 vs. 197 ± 303 hr, P = 0.02), and critical care time (54 ± 97 vs. 149 ± 299 hr, P = 0.02).

CONCLUSIONS

Availability of an in-house 24-hr STEMI team significantly decreased reperfusion time and led to improved clinical outcomes and a shorter LOS for PCI-treated STEMI patients.

A qualitative investigation of patients' understanding of carbohydrate in the clinical management of type 2 diabetes

BACKGROUND

A healthy diet is the cornerstone of type 2 diabetes (T2DM) self-management. Carbohydrate is of particular interest as the nutrient with the greatest direct effect on blood glucose (BG) levels. The present study aimed to explore T2DM patients' understanding of carbohydrate and beliefs around the role of carbohydrate in T2DM management.

METHODS

Fifteen semi-structured interviews were conducted with T2DM patients. Interviews were audio-recorded and transcribed, and a deductive thematic approach to analysis was employed using the Framework method.

RESULTS

Four significant themes emerged: (i) a naïve conceptual understanding of carbohydrate and sugar-centric specificity to dietary behaviours; (ii) a narrow focus on BG management to the neglect of overall dietary balance; (iii) positive reception of moderate dietary advice focused on portion control from healthcare professionals (HCPs); and (iv) the impact of external moderators of dietary choices, including the influence of significant others, emotional and opportunistic eating and budgetary constraints.

CONCLUSIONS

Participants' beliefs and understanding of carbohydrate led to an overemphasis on sugar restriction for blood glucose control to the neglect of their overall dietary balance. Diabetes educators need to place greater emphasis on the role of various types of carbohydrate foods for glycaemic control, as well as on concepts of wider metabolic health, during T2DM dietary education. Participants placed a high level of trust and value on practical, moderate portion control advice from HCPs regarding carbohydrate foods. However, HCPs need to be cognisant of external moderators of behaviour, such as the influence of family and friends, budgetary constraints and environmental eating triggers.

Mapping replication origin sequences in eukaryotic chromosomes

Recent advances in genome-sequencing technology have led to the complete mapping of DNA replication initiation sites in the human genome. This thorough origin mapping facilitates understanding of the relationship between replication initiation events, transcription, and chromatin modifications, and allows the characterization of consensus sequences of potential replication origins. This unit provides a detailed protocol for isolation and sequence analysis of nascent DNA strands. Two variations of the protocol based on non-overlapping assumptions are described below, addressing potential bias issues for whole-genome analyses.

A comparison of medication adherence/persistence for asthma and chronic obstructive pulmonary disease in the United Kingdom

AIM

To describe and compare adherence and persistence with maintenance therapies in patients with asthma or chronic obstructive pulmonary disease (COPD) in the United Kingdom (UK).

METHODS

A retrospective prescribing database cohort was obtained from 44 general practitioner surgeries in National Health Service Forth Valley Scotland. Patients with physician-diagnosed asthma or COPD who received maintenance therapy between January 2008 and December 2009 were included. Five classes of therapy were assessed: inhaled corticosteroids, long-acting beta-agonists, combination therapy inhalers, theophyllines and long-acting muscarinic antagonists. Adherence was calculated using the medication possession ratio (MPR) and persistence was determined using Kaplan-Meier survival analysis for the time to discontinuation (TTD) over 1 year. Two step-wise logistic regressions were performed to assess the contribution of diagnosis to adherence/persistence.

RESULTS

A total of 13,322 patients were included in the analysis: 10,521 patients with asthma and 2801 patients with COPD. 25.2% of medication episodes for asthma and 45.6% of medication episodes for COPD were classified as having an adequate medication supply (MPR of 80-120%). The overall median TTD was 92 days (IQR, interquartile range: 50-186 days) for patients with asthma and 116 days (IQR: 58-259 days, comparison p < 0.001) for patients with COPD. Patients with COPD were found to be more likely to achieve an MPR of at least 80% (OR: 1.27, 95% CI: 1.15-1.40), but had a similar likelihood of persistence at 1 year to patients with asthma.

CONCLUSION

Adherence and persistence with respiratory therapies in the UK is relatively low. There is suggestion that patients with COPD may display more adherent behaviours than patients with asthma.

Follow-up arrangements for breast cancer patients; is it appropriate to transfer surveillance to general practitioners?

The aim of this study was to examine the evidence for hospital follow up of breast cancer survivors and to identify patient preferences for hospital or community follow-up. We surveyed General Practitioner attitudes towards community follow-up and quantified the incidence of new or recurrent cancers within a patient cohort to identify their primary symptoms and thus cancer detection in the community. A 22 item questionnaire was distributed to 101 breast cancer survivors from a cohort of 921 treated patients. A 9 item questionnaire was distributed to 81 General Practitioners. Patients are reassured by hospital outpatient appointments, n=63 (74%) but have high levels of confidence in General Practitioner follow-up, n=57 (67%). General Practitioners are equally divided regarding their support for the transfer of follow-up (51%, 49%). Ten of the 14 new cancer episodes were associated with obvious clinical signs (p < 0.05). The proposed transfer of follow-up for patients to general practice by the national cancer control programme is appropriate.

Best practices for mapping replication origins in eukaryotic chromosomes

Understanding the regulatory principles ensuring complete DNA replication in each cell division is critical for deciphering the mechanisms that maintain genomic stability. Recent advances in genome sequencing technology facilitated complete mapping of DNA replication sites and helped move the field from observing replication patterns at a handful of single loci to analyzing replication patterns genome-wide. These advances address issues, such as the relationship between replication initiation events, transcription, and chromatin modifications, and identify potential replication origin consensus sequences. This unit summarizes the technological and fundamental aspects of replication profiling and briefly discusses novel insights emerging from mining large datasets, published in the last 3 years, and also describes DNA replication dynamics on a whole-genome scale.

Evaluating the potential for a Helicobacter pylori drinking water guideline

Helicobacter pylori is a microaerophilic, gram-negative bacterium that is linked to adverse health effects including ulcers and gastrointestinal cancers. The goal of this analysis is to develop the necessary inputs for a quantitative microbial risk assessment (QMRA) needed to develop a potential guideline for drinking water at the point of ingestion (e.g., a maximum contaminant level, or MCL) that would be protective of human health to an acceptable level of risk while considering sources of uncertainty. Using infection and gastric cancer as two discrete endpoints, and calculating dose-response relationships from experimental data on humans and monkeys, we perform both a forward and reverse risk assessment to determine the risk from current reported surface water concentrations of H. pylori and an acceptable concentration of H. pylori at the point of ingestion. This approach represents a synthesis of available information on human exposure to H. pylori via drinking water. A lifetime risk of cancer model suggests that a MCL be set at <1 organism/L given a 5-log removal treatment because we cannot exclude the possibility that current levels of H. pylori in environmental source waters pose a potential public health risk. Research gaps include pathogen occurrence in source and finished water, treatment removal rates, and determination of H. pylori risks from other water sources such as groundwater and recreational water.

Ledipasvir and sofosbuvir for 8 or 12 weeks for chronic HCV without cirrhosis

BACKGROUND

High rates of sustained virologic response were observed among patients with hepatitis C virus (HCV) infection who received 12 weeks of treatment with the nucleotide polymerase inhibitor sofosbuvir combined with the NS5A inhibitor ledipasvir. This study examined 8 weeks of treatment with this regimen.

METHODS

In this phase 3, open-label study, we randomly assigned 647 previously untreated patients with HCV genotype 1 infection without cirrhosis to receive ledipasvir and sofosbuvir (ledipasvir-sofosbuvir) for 8 weeks, ledipasvir-sofosbuvir plus ribavirin for 8 weeks, or ledipasvir-sofosbuvir for 12 weeks. The primary end point was sustained virologic response at 12 weeks after the end of therapy.

RESULTS

The rate of sustained virologic response was 94% (95% confidence interval [CI], 90 to 97) with 8 weeks of ledipasvir-sofosbuvir, 93% (95% CI, 89 to 96) with 8 weeks of ledipasvir-sofosbuvir plus ribavirin, and 95% (95% CI, 92 to 98) with 12 weeks of ledipasvir-sofosbuvir. As compared with the rate of sustained virologic response in the group that received 8 weeks of ledipasvir-sofosbuvir, the rate in the 12-week group was 1 percentage point higher (97.5% CI, -4 to 6) and the rate in the group that received 8 weeks of ledipasvir-sofosbuvir with ribavirin was 1 percentage point lower (95% CI, -6 to 4); these results indicated noninferiority of the 8-week ledipasvir-sofosbuvir regimen, on the basis of a noninferiority margin of 12 percentage points. Adverse events were more common in the group that received ribavirin than in the other two groups. No patient who received 8 weeks of only ledipasvir-sofosbuvir discontinued treatment owing to adverse events.

CONCLUSIONS

Ledipasvir-sofosbuvir for 8 weeks was associated with a high rate of sustained virologic response among previously untreated patients with HCV genotype 1 infection without cirrhosis. No additional benefit was associated with the inclusion of ribavirin in the regimen or with extension of the duration of treatment to 12 weeks. (Funded by Gilead Sciences; ION-3 ClinicalTrials.gov number, NCT01851330.).

Allele-specific genome-wide profiling in human primary erythroblasts reveal replication program organization

We have developed a new approach to characterize allele-specific timing of DNA replication genome-wide in human primary basophilic erythroblasts. We show that the two chromosome homologs replicate at the same time in about 88% of the genome and that large structural variants are preferentially associated with asynchronous replication. We identified about 600 megabase-sized asynchronously replicated domains in two tested individuals. The longest asynchronously replicated domains are enriched in imprinted genes suggesting that structural variants and parental imprinting are two causes of replication asynchrony in the human genome. Biased chromosome X inactivation in one of the two individuals tested was another source of detectable replication asynchrony. Analysis of high-resolution TimEX profiles revealed small variations termed timing ripples, which were undetected in previous, lower resolution analyses. Timing ripples reflect highly reproducible, variations of the timing of replication in the 100 kb-range that exist within the well-characterized megabase-sized replication timing domains. These ripples correspond to clusters of origins of replication that we detected using novel nascent strands DNA profiling methods. Analysis of the distribution of replication origins revealed dramatic differences in initiation of replication frequencies during S phase and a strong association, in both synchronous and asynchronous regions, between origins of replication and three genomic features: G-quadruplexes, CpG Islands and transcription start sites. The frequency of initiation in asynchronous regions was similar in the two homologs. Asynchronous regions were richer in origins of replication than synchronous regions.

DNA replication in mammalian cells proceeds according to a distinct order. Genes that are expressed tend to replicate before genes that are not expressed. We report here that we have developed a method to measure the timing of replication of the maternal and paternal chromosomes separately. We found that the paternal and maternal chromosomes replicate at exactly the same time in the large majority of the genome and that the 12% of the genome that replicated asynchronously was enriched in imprinted genes and in structural variants. Previous experiments have shown that chromosomes could be divided into replication timing domains that are a few hundred thousand to a few megabases in size. We show here that these domains can be divided into sub-domains defined by ripples in the timing profile. These ripples corresponded to clusters of origins of replication. Finally, we show that the frequency of initiation in asynchronous regions was similar in the two homologs.

Public opinion of drug treatment policy: exploring the public's attitudes, knowledge, experience and willingness to pay for drug treatment strategies

BACKGROUND

Research evidence is strong for opiate replacement treatment (ORT). However, public opinion (attitudes) can be at odds with evidence. This study explored the relationships between, attitudes, knowledge of drugs and a range of socio-demographic variables that potentially influence attitude. This is relevant in the current policy arena in which a major shift from harm reduction to, rehabilitation is underway.

METHODS

A cross sectional postal questionnaire survey in Scotland was conducted where the drug, treatment strategy has changed from harm-reduction to recovery-based. A random sample (N=3000), of the general public, >18 years, and on the electoral register was used. The questionnaire was largely structured with tick box format but included two open questions for qualitative responses. Valuation was measured using the economic willingness-to-pay (WTP) method.

RESULTS

The response rate was 38.1% (1067/2803). Less than 10% had personal experience of drug, misuse but 16.7% had experience of drug misuse via a friend/acquaintance. Regression modelling revealed more positive attitudes towards drug users in those with personal experience of drug misuse, (p<0.001), better knowledge of drugs (p=0.001) and higher income (those earning >£50,000 per, annum compared to <£15K; p=0.01). Over half of respondents were not willing to pay anything for drug treatment indicating they did not value these treatments at all. Respondents were willing-to-pay most for community rehabilitation and least for methadone maintenance treatment. Qualitative analysis of open responses indicated many strong negative attitudes, doubts over the efficacy of methadone and consideration of addiction as self-inflicted. There was ambivalence with respondents weighing up negative feelings towards treatment against societal benefit.

CONCLUSIONS

There is a gap between public attitudes and evidence regarding drug treatment. Findings suggest a way forward might be to develop and evaluate treatment that integrates ORT with a community rehabilitative approach. Evaluation of public engagement/education to improve knowledge of drug treatment effectiveness is recommended.

First metatarsal base osteotomies for hallux abducto valgus deformities

Proximal first metatarsal osteotomies have historically been associated with and limited to treatment of severe hallux valgus deformities. These procedures are powerful in deformity correction and overall realignment of first ray function because of their ability to correct closer to the deformity's origin. When considering all factors in bunion correction, they are good options for correction of a wide range of hallux abducto valgus deformities. This article discusses the use of proximal metatarsal osteotomies for correction of hallux valgus deformity, techniques to facilitate optimal outcome, and common complications of these osteotomies.

Secondary demyelination disorders and destruction of white matter

Demyelinating disorders of the central nervous system are characterized by the breakdown of myelin, with or without preservation of the associated axons. Primary demyelinating diseases typically involve loss of myelin with relative sparing of axons. Secondary demyelinating disorders represent a spectrum of white matter disease characterized by damage to neurons or axons with the resultant breakdown of myelin. The pathologic changes seen in secondary demyelinating disorders are varied, ranging from pure demyelination to necrosis with subsequent demyelination. Secondary demyelinating diseases are associated with a wide variety of conditions, including infections/vaccinations, nutritional/vitamin deficiencies, chemical agents, genetic abnormalities, and vascular insult.

Reduction in interval cancer rates following the introduction of two-view mammography in the UK breast screening programme

BACKGROUND

The introduction of two-view mammography at incident (subsequent) screens in the National Health Service Breast Screening Programme (NHSBSP) has led to an increased number of cancers detected at screen. However, the effect of two-view mammography on interval cancer rates has yet to be assessed.

METHODS

Routine screening and interval cancer data were collated from all screening programmes in the United Kingdom for women aged 50-64, screened between 1 April 2003 and 31 March 2005. Interval cancer rates were compared based on whether two-view mammography was in use at the last routine screen.

RESULTS

The reduction in interval cancers following screening using two-view mammography compared with one view was 0.68 per 1,000 women screened. Overall, this suggests the introduction of two-view mammography at incident screen was accompanied by a 15-20% reduction in interval cancer rates in the NHSBSP.

CONCLUSION

The introduction of two-view mammography at incident screens is associated with a reduction in incidence of interval cancers. This is consistent with previous publications on a contemporaneous increase in screen-detected cancers. The results provide further evidence of the benefit of the use of two-view mammography at incident screens.