1,187 research outputs found
Achieving behaviour change for detection of Lynch syndrome using the Theoretical Domains Framework Implementation (TDFI) approach: A study protocol
© 2016 Taylor et al. Background: Lynch syndrome is an inherited disorder associated with a range of cancers, and found in 2-5 % of colorectal cancers. Lynch syndrome is diagnosed through a combination of significant family and clinical history and pathology. The definitive diagnostic germline test requires formal patient consent after genetic counselling. If diagnosed early, carriers of Lynch syndrome can undergo increased surveillance for cancers, which in turn can prevent late stage cancers, optimise treatment and decrease mortality for themselves and their relatives. However, over the past decade, international studies have reported that only a small proportion of individuals with suspected Lynch syndrome were referred for genetic consultation and possible genetic testing. The aim of this project is to use behaviour change theory and implementation science approaches to increase the number and speed of healthcare professional referrals of colorectal cancer patients with a high-likelihood risk of Lynch syndrome to appropriate genetic counselling services. Methods: The six-step Theoretical Domains Framework Implementation (TDFI) approach will be used at two large, metropolitan hospitals treating colorectal cancer patients. Steps are: 1) form local multidisciplinary teams to map current referral processes; 2) identify target behaviours that may lead to increased referrals using discussion supported by a retrospective audit; 3) identify barriers to those behaviours using the validated Influences on Patient Safety Behaviours Questionnaire and TDFI guided focus groups; 4) co-design interventions to address barriers using focus groups; 5) co-implement interventions; and 6) evaluate intervention impact. Chi square analysis will be used to test the difference in the proportion of high-likelihood risk Lynch syndrome patients being referred for genetic testing before and after intervention implementation. A paired t-test will be used to assess the mean time from the pathology test results to referral for high-likelihood Lynch syndrome patients pre-post intervention. Run charts will be used to continuously monitor change in referrals over time, based on scheduled monthly audits. Discussion: This project is based on a tested and refined implementation strategy (TDFI approach). Enhancing the process of identifying and referring people at high-likelihood risk of Lynch syndrome for genetic counselling will improve outcomes for patients and their relatives, and potentially save public money
Increased entropy of signal transduction in the cancer metastasis phenotype
Studies into the statistical properties of biological networks have led to
important biological insights, such as the presence of hubs and hierarchical
modularity. There is also a growing interest in studying the statistical
properties of networks in the context of cancer genomics. However, relatively
little is known as to what network features differ between the cancer and
normal cell physiologies, or between different cancer cell phenotypes. Based on
the observation that frequent genomic alterations underlie a more aggressive
cancer phenotype, we asked if such an effect could be detectable as an increase
in the randomness of local gene expression patterns. Using a breast cancer gene
expression data set and a model network of protein interactions we derive
constrained weighted networks defined by a stochastic information flux matrix
reflecting expression correlations between interacting proteins. Based on this
stochastic matrix we propose and compute an entropy measure that quantifies the
degree of randomness in the local pattern of information flux around single
genes. By comparing the local entropies in the non-metastatic versus metastatic
breast cancer networks, we here show that breast cancers that metastasize are
characterised by a small yet significant increase in the degree of randomness
of local expression patterns. We validate this result in three additional
breast cancer expression data sets and demonstrate that local entropy better
characterises the metastatic phenotype than other non-entropy based measures.
We show that increases in entropy can be used to identify genes and signalling
pathways implicated in breast cancer metastasis. Further exploration of such
integrated cancer expression and protein interaction networks will therefore be
a fruitful endeavour.Comment: 5 figures, 2 Supplementary Figures and Table
A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer
Recently, several classifiers that combine primary tumor data, like gene
expression data, and secondary data sources, such as protein-protein
interaction networks, have been proposed for predicting outcome in breast
cancer. In these approaches, new composite features are typically constructed
by aggregating the expression levels of several genes. The secondary data
sources are employed to guide this aggregation. Although many studies claim
that these approaches improve classification performance over single gene
classifiers, the gain in performance is difficult to assess. This stems mainly
from the fact that different breast cancer data sets and validation procedures
are employed to assess the performance. Here we address these issues by
employing a large cohort of six breast cancer data sets as benchmark set and by
performing an unbiased evaluation of the classification accuracies of the
different approaches. Contrary to previous claims, we find that composite
feature classifiers do not outperform simple single gene classifiers. We
investigate the effect of (1) the number of selected features; (2) the specific
gene set from which features are selected; (3) the size of the training set and
(4) the heterogeneity of the data set on the performance of composite feature
and single gene classifiers. Strikingly, we find that randomization of
secondary data sources, which destroys all biological information in these
sources, does not result in a deterioration in performance of composite feature
classifiers. Finally, we show that when a proper correction for gene set size
is performed, the stability of single gene sets is similar to the stability of
composite feature sets. Based on these results there is currently no reason to
prefer prognostic classifiers based on composite features over single gene
classifiers for predicting outcome in breast cancer
The breast cancer somatic 'muta-ome': tackling the complexity
Acquired somatic mutations are responsible for approximately 90% of breast tumours. However, only one somatic aberration, amplification of the HER2 locus, is currently used to define a clinical subtype, one that accounts for approximately 10% to 15% of breast tumours. In recent years, a number of mutational profiling studies have attempted to further identify clinically relevant mutations. While these studies have confirmed the oncogenic or tumour suppressor role of many known suspects, they have exposed complexity as a main feature of the breast cancer mutational landscape (the 'muta-ome'). The two defining features of this complexity are (a) a surprising richness of low-frequency mutants contrasting with the relative rarity of high-frequency events and (b) the relatively large number of somatic genomic aberrations (approximately 20 to 50) driving an average tumour. Structural features of this complex landscape have begun to emerge from follow-up studies that have tackled the complexity by integrating the spectrum of genomic mutations with a variety of complementary biological knowledge databases. Among these structural features are the growing links between somatic gene disruptions and those conferring breast cancer risk, mutually exclusive coexistence and synergistic mutational patterns, and a clearly non-random distribution of mutations implicating specific molecular pathways in breast tumour initiation and progression. Recognising that a shift from a gene-centric to a pathway-centric approach is necessary, we envisage that further progress in identifying clinically relevant genomic aberration patterns and associated breast cancer subtypes will require not only multi-dimensional integrative analyses that combine mutational and functional profiles, but also larger profiling studies that use second- and third-generation sequencing technologies in order to fill out the important gaps in the current mutational landscape
The need for co-ordinated studies for obesity-related problems like diabetes mellitus in Libyan population
Case report: hypoglycemia due to a novel activating glucokinase variant in an adult – a molecular approach
We present a case of an obese 22-year-old man with activating GCK variant who had neonatal hypoglycemia, re-emerging with hypoglycemia later in life. We investigated him for asymptomatic hypoglycemia with a family history of hypoglycemia. Genetic testing yielded a novel GCK missense class 3 variant that was subsequently found in his mother, sister and nephew and reclassified as a class 4 likely pathogenic variant. Glucokinase enables phosphorylation of glucose, the rate-limiting step of glycolysis in the liver and pancreatic β cells. It plays a crucial role in the regulation of insulin secretion. Inactivating variants in GCK cause hyperglycemia and activating variants cause hypoglycemia. Spleen-preserving distal pancreatectomy revealed diffuse hyperplastic islets, nuclear pleomorphism and periductular islets. Glucose stimulated insulin secretion revealed increased insulin secretion in response to glucose. Cytoplasmic calcium, which triggers exocytosis of insulin-containing granules, revealed normal basal but increased glucose-stimulated level. Unbiased gene expression analysis using 10X single cell sequencing revealed upregulated INS and CKB genes and downregulated DLK1 and NPY genes in β-cells. Further studies are required to see if alteration in expression of these genes plays a role in the metabolic and histological phenotype associated with glucokinase pathogenic variant. There were more large islets in the patient’s pancreas than in control subjects but there was no difference in the proportion of β cells in the islets. His hypoglycemia was persistent after pancreatectomy, was refractory to diazoxide and improved with pasireotide. This case highlights the variable phenotype of GCK mutations. In-depth molecular analyses in the islets have revealed possible mechanisms for hyperplastic islets and insulin hypersecretion
Imaging and impact of myocardial fibrosis in aortic stenosis
Aortic stenosis is characterized both by progressive valve narrowing and the left ventricular remodeling response that ensues. The only effective treatment is aortic valve replacement, which is usually recommended in patients with severe
stenosis and evidence of left ventricular decompensation. At present, left ventricular decompensation is most frequently identified by the development of typical symptoms or a marked reduction in left ventricular ejection fraction <50%. However, there is growing interest in using the assessment of myocardial fibrosis as an earlier and more objective marker
of left ventricular decompensation, particularly in asymptomatic patients, where guidelines currently rely on non- randomized data and expert consensus. Myocardial fibrosis has major functional consequences, is the key pathological process driving left ventricular decompensation, and can be divided into 2 categories. Replacement fibrosis is irreversible and identified using late gadolinium enhancement on cardiac magnetic resonance, while diffuse fibrosis occurs earlier, is potentially reversible, and can be quantified with cardiac magnetic resonance T1 mapping techniques. There is a substantial body of observational data in this field, but there is now a need for randomized clinical trials of myocardial imaging in aortic stenosis to optimize patient management. This review will discuss the role that myocardial fibrosis plays in aortic stenosis, how it can be imaged, and how these approaches might be used to track myocardial health and improve the timing of aortic valve replacement
Determining Frequent Patterns of Copy Number Alterations in Cancer
Cancer progression is often driven by an accumulation of genetic changes but also accompanied by increasing genomic instability. These processes lead to a complicated landscape of copy number alterations (CNAs) within individual tumors and great diversity across tumor samples. High resolution array-based comparative genomic hybridization (aCGH) is being used to profile CNAs of ever larger tumor collections, and better computational methods for processing these data sets and identifying potential driver CNAs are needed. Typical studies of aCGH data sets take a pipeline approach, starting with segmentation of profiles, calls of gains and losses, and finally determination of frequent CNAs across samples. A drawback of pipelines is that choices at each step may produce different results, and biases are propagated forward. We present a mathematically robust new method that exploits probe-level correlations in aCGH data to discover subsets of samples that display common CNAs. Our algorithm is related to recent work on maximum-margin clustering. It does not require pre-segmentation of the data and also provides grouping of recurrent CNAs into clusters. We tested our approach on a large cohort of glioblastoma aCGH samples from The Cancer Genome Atlas and recovered almost all CNAs reported in the initial study. We also found additional significant CNAs missed by the original analysis but supported by earlier studies, and we identified significant correlations between CNAs
Search for Gravitational Waves Associated with 39 Gamma-Ray Bursts Using Data from the Second, Third, and Fourth LIGO Runs
We present the results of a search for short-duration gravitational-wave
bursts associated with 39 gamma-ray bursts (GRBs) detected by gamma-ray
satellite experiments during LIGO's S2, S3, and S4 science runs. The search
involves calculating the crosscorrelation between two interferometer data
streams surrounding the GRB trigger time. We search for associated
gravitational radiation from single GRBs, and also apply statistical tests to
search for a gravitational-wave signature associated with the whole sample. For
the sample examined, we find no evidence for the association of gravitational
radiation with GRBs, either on a single-GRB basis or on a statistical basis.
Simulating gravitational-wave bursts with sine-gaussian waveforms, we set upper
limits on the root-sum-square of the gravitational-wave strain amplitude of
such waveforms at the times of the GRB triggers. We also demonstrate how a
sample of several GRBs can be used collectively to set constraints on
population models. The small number of GRBs and the significant change in
sensitivity of the detectors over the three runs, however, limits the
usefulness of a population study for the S2, S3, and S4 runs. Finally, we
discuss prospects for the search sensitivity for the ongoing S5 run, and beyond
for the next generation of detectors.Comment: 24 pages, 10 figures, 14 tables; minor changes to text and Fig. 2;
accepted by Phys. Rev.
Search for gravitational waves from binary inspirals in S3 and S4 LIGO data
We report on a search for gravitational waves from the coalescence of compact
binaries during the third and fourth LIGO science runs. The search focused on
gravitational waves generated during the inspiral phase of the binary
evolution. In our analysis, we considered three categories of compact binary
systems, ordered by mass: (i) primordial black hole binaries with masses in the
range 0.35 M(sun) < m1, m2 < 1.0 M(sun), (ii) binary neutron stars with masses
in the range 1.0 M(sun) < m1, m2 < 3.0 M(sun), and (iii) binary black holes
with masses in the range 3.0 M(sun)< m1, m2 < m_(max) with the additional
constraint m1+ m2 < m_(max), where m_(max) was set to 40.0 M(sun) and 80.0
M(sun) in the third and fourth science runs, respectively. Although the
detectors could probe to distances as far as tens of Mpc, no gravitational-wave
signals were identified in the 1364 hours of data we analyzed. Assuming a
binary population with a Gaussian distribution around 0.75-0.75 M(sun), 1.4-1.4
M(sun), and 5.0-5.0 M(sun), we derived 90%-confidence upper limit rates of 4.9
yr^(-1) L10^(-1) for primordial black hole binaries, 1.2 yr^(-1) L10^(-1) for
binary neutron stars, and 0.5 yr^(-1) L10^(-1) for stellar mass binary black
holes, where L10 is 10^(10) times the blue light luminosity of the Sun.Comment: 12 pages, 11 figure
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