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1.
Artículo en Inglés | MEDLINE | ID: mdl-38493480

RESUMEN

BACKGROUND: Congenital adrenal hyperplasia (CAH) encompasses a rare group of autosomal recessive disorders, characterised by enzymatic defects in steroidogenesis. Heterogeneity in management practices has been observed internationally. The International Congenital Adrenal Hyperplasia registry (I-CAH, https://sdmregistries.org/) was established to enable insights into CAH management and outcomes, yet its global adoption by endocrine centres remains unclear. DESIGN: We sought (1) to assess current practices amongst clinicians managing patients with CAH in the United Kingdom and Ireland, with a focus on choice of glucocorticoid, monitoring practices and screening for associated co-morbidities, and (2) to assess use of the I-CAH registry. MEASUREMENTS: We designed and distributed an anonymised online survey disseminated to members of the Society for Endocrinology and Irish Endocrine Society to capture management practices in the care of patients with CAH. RESULTS: Marked variability was found in CAH management, with differences between general endocrinology and subspecialist settings, particularly in glucocorticoid use, biochemical monitoring and comorbidity screening, with significant disparities in reproductive health monitoring, notably in testicular adrenal rest tumours (TARTs) screening (p = .002), sperm banking (p = .0004) and partner testing for CAH (p < .0001). Adoption of the I-CAH registry was universally low. CONCLUSIONS: Differences in current management of CAH continue to exist. It appears crucial to objectify if different approaches result in different long-term outcomes. New studies such as CaHASE2, incorporating standardised minimum datasets including replacement therapies and monitoring strategies as well as longitudinal data collection, are now needed to define best-practice and standardise care.

2.
Horm Res Paediatr ; 2024 Mar 12.
Artículo en Inglés | MEDLINE | ID: mdl-38471495

RESUMEN

INTRODUCTION: Quantifying differences in service provision for children and young people (CYP) living with Congenital Adrenal Hyperplasia (CAH) across the United Kingdom. METHODS: A national service evaluation using online questionnaires circulated to patients and clinicians from secondary and tertiary UK centres managing CYP with CAH, and via the "Living with CAH" support group mailing list. RESULTS: Total of 195 responses relating to patients aged 0-20 years attending 33 clinics (43 patients, 152 carers), as well as 34 clinicians from 18 trusts working across the 33 clinics. Only 12% of clinicians were 'completely satisfied' with the service provided, compared to 68% of carers and 76% of patients. Whilst 94% of clinicians reported providing formal training to families with CAH, over 80% of both patients and carers reported not attending what they considered formal training. Appetite for further training was higher in carers (86%) than patients (55%), although further 'unsure' responses suggested formal training sessions would likely be well attended. Access to psychological services was difficult for 44% of clinicians. Biochemical monitoring of treatment was broadly in keeping with international guidelines, with 67% of clinicians reporting regular use of dried blood spots, and 12% regular urinary steroid metabolites. CONCLUSION: While there is overall good satisfaction with care provision among patients and carers with CAH in the UK, extra resources addressing the psychological and educational needs about the disease and its management would benefit patients and carers. Improved access to allied health professionals and psychologists will help support families and improve patient outcomes.

3.
J Endocr Soc ; 7(12): bvad127, 2023 Nov 02.
Artículo en Inglés | MEDLINE | ID: mdl-37942292

RESUMEN

Context: The adrenocorticotropin hormone stimulation test (AST) is used to diagnose adrenal insufficiency, and is often repeated in patients when monitoring recovery of the hypothalamo-pituitary-adrenal axis. Objective: To develop and validate a prediction model that uses previous AST results with new baseline cortisol to predict the result of a new AST. Methods: This was a retrospective, longitudinal cohort study in patients who had undergone at least 2 ASTs, using polynomial regression with backwards variable selection, at a Tertiary UK adult endocrinology center. Model was developed from 258 paired ASTs over 5 years in 175 adults (mean age 52.4 years, SD 16.4), then validated on data from 111 patients over 1 year (51.8, 17.5) from the same center, data collected after model development. Candidate prediction variables included previous test baseline adrenocorticotropin hormone (ACTH), previous test baseline and 30-minute cortisol, days between tests, and new baseline ACTH and cortisol used with calculated cortisol/ACTH ratios to assess 8 candidate predictors. The main outcome measure was a new test cortisol measured 30 minutes after Synacthen administration. Results: Using 258 sequential ASTs from 175 patients for model development and 111 patient tests for model validation, previous baseline cortisol, previous 30-minute cortisol and new baseline cortisol were superior at predicting new 30-minute cortisol (R2 = 0.71 [0.49-0.93], area under the curve [AUC] = 0.97 [0.94-1.0]) than new baseline cortisol alone (R2 = 0.53 [0.22-0.84], AUC = 0.88 [0.81-0.95]). Conclusion: Results of a previous AST can be objectively combined with new early-morning cortisol to predict the results of a new AST better than new early-morning cortisol alone. An online calculator is available at https://endocrinology.shinyapps.io/sheffield_sst_calculator/ for external validation.

4.
Artículo en Inglés | MEDLINE | ID: mdl-37608608

RESUMEN

Monitoring of hormone replacement therapy represents a major challenge in the management of congenital adrenal hyperplasia (CAH). In the absence of clear guidance and standardised monitoring strategies, there is no consensus among clinicians regarding the relevance of various biochemical markers used in practice, leading to wide variability in their application and interpretation. In this review, we summarise the published evidence on biochemical monitoring of CAH. We discuss temporal variations of the most commonly measured biomarkers throughout the day, the interrelationship between different biomarkers, as well as their relationship with different glucocorticoid and mineralocorticoid treatment regimens and clinical outcomes. Our review highlights significant heterogeneity across studies in both aims and methodology. However, we identified key messages for the management of patients with CAH. The approach to hormone replacement therapy should be individualised, based on the individual hormonal profile throughout the day in relation to medication. There are limitations to using 17-hydroxyprogesterone, androstenedione and testosterone, and the role of additional biomarkers such 11-oxygenated androgens which are more disease specific should be further established. Noninvasive monitoring via salivary and urinary steroid measurements is becoming increasingly available and should be considered, especially in the management of children with CAH. Additionally, this review indicates the need for large scale longitudinal studies analysing the interrelation between different monitoring strategies used in clinical practice and health outcomes in children and adults with CAH.

5.
Horm Res Paediatr ; 2023 Aug 23.
Artículo en Inglés | MEDLINE | ID: mdl-37611560

RESUMEN

Congenital adrenal hyperplasia (CAH) due to 21-hydroxylase deficiency (21OHD) leads to impaired glucocorticoid and mineralocorticoid synthesis with excess production of androgens. Replication of the normal circadian cortisol secretion is challenging and supraphysiological doses of glucocorticoids are often required. Most patients experience transient episodes of hyper- and hypocortisolaemia during the day leading to adverse metabolic outcomes such as insulin resistance, visceral adiposity and cardiovascular morbidity, including hypertension. These health problems are commonly diagnosed in adolescence and adulthood. Herein, we review the published data on the variation in blood pressure in CAH due to 21OHD and the interrelation with disease and treatment factors.

6.
Pediatr Allergy Immunol Pulmonol ; 36(3): 94-103, 2023 09.
Artículo en Inglés | MEDLINE | ID: mdl-37433192

RESUMEN

Background: Pediatric inflammatory multisystem syndrome temporarily associated with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection (PIMS-TS) is an acute complication of previous SARS-CoV-2 exposure. The relationship between inflammatory markers and anti-inflammatory medication in PIMS-TS is unknown. We retrospectively investigated the relationship between demographics, biomarkers, treatment, and length of stay (LOS) in this novel disease. Methods: We reviewed the case notes and blood tests of all patients who met the Royal College of Paediatrics and Child Health diagnostic criteria for PIMS-TS at a large tertiary center in the United Kingdom. Biomarker trajectories were modeled using log linear mixed effects, and factors affecting LOS in hospital were evaluated using multiple regression. Results: Between March 2020 and May 2022, a total of 56 patients attended Sheffield Children's Hospital with PIMS-TS, 70% male. Mean age was 7.4 ± 3.7 years and mean LOS 8.7 ± 4.5 days with 50% requiring intensive care and 20% requiring inotropes. Older males had shorter LOS than younger males (P = 0.04), not seen in females. Treatment included intravenous glucocorticoids in 93%, intravenous immunoglobulins (IVIG) in 77%, Anakinra in 11%, and infliximab in 1.8%. Biomarkers correlated poorly with trajectories that peaked at different times. C-reactive protein peaked first after median 1.3 days postadmission; while LFT's and neutrophils peaked after 3 days. Age had a large effect on some biomarkers, with older children having larger troponin and ferritin, and lower lymphocytes and platelets. Cumulative dose of glucocorticoids and IVIG had a statistically significant effect on some biomarkers, but effect size was small. Conclusions: The heterogenous nature of PIMS-TS highlights the importance of a multidisciplinary approach. Worse inflammatory markers in older children within our cohort may be an indication of a different disease process occurring at different ages. Future work to investigate the association between age and troponin and ferritin in hyperinflammatory states is warranted.


Asunto(s)
COVID-19 , Femenino , Humanos , Masculino , Niño , Adolescente , Preescolar , Glucocorticoides , Inmunoglobulinas Intravenosas , Estudios Retrospectivos , SARS-CoV-2 , Antiinflamatorios , Biomarcadores , Ferritinas , Hospitales Pediátricos
7.
J Clin Endocrinol Metab ; 109(1): e336-e346, 2023 Dec 21.
Artículo en Inglés | MEDLINE | ID: mdl-37439248

RESUMEN

CONTEXT: Quality of life (QoL) has been inconsistently reported in children and young people (CYP) with congenital adrenal hyperplasia (CAH). OBJECTIVE: Assess QoL in CYP with CAH in the UK alongside biometric and androgen profiles. DESIGN: To define the evidence base for health care delivery, we conducted a cross-sectional study in CYP with CAH in the UK. Questionnaire results were compared with normative data and between groups, and modelled for association with sex, height, weight, body mass index, or steroid biomarkers of CAH control. SETTING: Tertiary care in 14 UK centers. PATIENTS: Results from 104 patients, 55% female, mean age 12.7 years (SD 3.0), paired responses from parents. INTERVENTIONS: Strengths and Difficulties questionnaire (SDQ) and pediatric QoL questionnaire. MAIN OUTCOME MEASURE: Total QoL scores as assessed by SDQ and a pediatric QoL questionnaire in comparison to normative data. RESULTS: Total scores were worse in parents than normative data, but similar in patients. Patient QoL was rated better in social functioning but worse in emotional, school, and peer domains by patients, and worse in total scores and domains of peer problems, and psychosocial, emotional, and school functioning by parents. Parents consistently scored QoL of their children lower than their child. Larger height-SD score and lower weight-SD score were associated with better QoL. Girls with lower steroid biomarkers had worse SDQ scores. CONCLUSIONS: In CYP with CAH, reduced height, increased weight, and hormonal biomarkers consistent with overtreatment were associated with worse QoL; addressing these problems should be prioritized in clinical management.Clinical Trials Registration Number: SCH/15/088.


Asunto(s)
Hiperplasia Suprarrenal Congénita , Niño , Humanos , Femenino , Adolescente , Masculino , Hiperplasia Suprarrenal Congénita/tratamiento farmacológico , Calidad de Vida/psicología , Estudios Transversales , Biomarcadores , Esteroides , Reino Unido/epidemiología
8.
J Endocr Soc ; 7(5): bvad026, 2023 Mar 06.
Artículo en Inglés | MEDLINE | ID: mdl-36936713

RESUMEN

Context: Growth hormone (GH) therapy can increase linear growth in patients with growth hormone deficiency (GHD), Turner syndrome (TS), Noonan syndrome (NS), and Prader-Willi syndrome (PWS), although outcomes vary by disease state. Objective: To assess growth and identify factors associated with growth response with long-term GH therapy. Methods: Data from pediatric patients with GHD, TS, NS, and PWS obtained at GH treatment initiation (baseline) and annually for 5 years in the ANSWER Program and NordiNet® IOS were analyzed retrospectively. Height standard deviation score (HSDS) was assessed over time, and multivariate analyses determined variables with significant positive effects on growth outcomes in each patient cohort. Results: Data from patients with GHD (n = 12 683), TS (n = 1307), NS (n = 203), and PWS (n = 102) were analyzed. HSDS increased over time during GH treatment in all cohorts. Factors with significant positive effects on ΔHSDS were younger age at GH initiation and lower HSDS at baseline (all cohorts) and higher GH dose (GHD and TS only); sex had no effect in any cohort. The modeling analysis showed that ΔHSDS was greatest in year 1 and attenuated over consecutive years through year 5. Estimated least-squares mean ΔHSDS values at year 5 by cohort were 1.702 (females) and 1.586 (males) in GHD, 1.033 in TS, 1.153 in NS, and 1.392 in PWS. Conclusion: Long-term GH therapy results in large increases in HSDS in patients with GHD, TS, NS, and PWS. Greater gains in HSDS can be obtained with higher GH doses and earlier initiation of treatment.

10.
Eur J Endocrinol ; 187(4): 543-553, 2022 Oct 01.
Artículo en Inglés | MEDLINE | ID: mdl-36001026

RESUMEN

Objective: There is limited knowledge on the onset of comorbidities in congenital adrenal hyperplasia (CAH) during childhood. We aimed to establish the health status of children with CAH in the UK. Design and methods: This cross-sectional multicentre study involved 14 tertiary endocrine UK units, recruiting 101 patients aged 8-18 years with classic 21-hydroxylase deficiency and 83 controls. We analysed demographic, clinical and metabolic data, as well as psychological questionnaires (Strengths and Difficulties (SDQ), Paediatric Quality of Life (PedsQL)). Results: Patient height SDS in relation to mid-parental height decreased with age, indicating the discrepancy between height achieved and genetic potential height. Bone age was advanced in 40.5% patients, with a mean difference from the chronological age of 1.8 (±2.3) years. Patients were more frequently overweight (27%) or obese (22%) compared to controls (10.8% and 10.8%, respectively, P < 0.001). No consistent relationship between glucocorticoid dose and anthropometric measurements or hormonal biomarkers was detected. A small number of patients had raised total cholesterol (3.0%), low HDL (3.0%), raised LDL (7.0%) and triglycerides (5.0%). SDQ scores were within the 'high' and 'very high' categories of concern for 16.3% of patients. 'School functioning' was the lowest PedsQL scoring dimension with a median (interquartile range) of 70 (55-80), followed by 'emotional functioning' with a median of 75 (65-85). Conclusions: Our results show an increased prevalence of problems with growth and weight gain in CAH children and suggest reduced quality of life. This highlights the urgent need to optimise management and monitoring strategies to improve long-term health outcomes.


Asunto(s)
Hiperplasia Suprarrenal Congénita , Hiperplasia Suprarrenal Congénita/epidemiología , Hiperplasia Suprarrenal Congénita/metabolismo , Biomarcadores , Niño , Colesterol , Estudios Transversales , Glucocorticoides , Estado de Salud , Humanos , Calidad de Vida , Triglicéridos , Reino Unido/epidemiología
11.
Clin Endocrinol (Oxf) ; 97(5): 551-561, 2022 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-35781728

RESUMEN

OBJECTIVE: Congenital adrenal hyperplasia (CAH) requires exogenous steroid replacement. Treatment is commonly monitored by measuring 17-OH progesterone (17OHP) and androstenedione (D4). DESIGN: Retrospective cohort study using real-world data to evaluate 17OHP and D4 in relation to hydrocortisone (HC) dose in CAH patients treated in 14 countries. PATIENTS: Pseudonymized data from children with 21-hydroxylase deficiency (21OHD) recorded in the International CAH Registry. MEASUREMENTS: Assessments between January 2000 and October 2020 in patients prescribed HC were reviewed to summarise biomarkers 17OHP and D4 and HC dose. Longitudinal assessment of measures was carried out using linear mixed-effects models (LMEM). RESULTS: Cohort of 345 patients, 52.2% female, median age 4.3 years (interquartile range: 3.1-9.2) were taking a median 11.3 mg/m2 /day (8.6-14.4) of HC. Median 17OHP was 35.7 nmol/l (3.0-104.0). Median D4 under 12 years was 0 nmol/L (0-2.0) and above 12 years was 10.5 nmol/L (3.9-21.0). There were significant differences in biomarker values between centres (p < 0.05). Correlation between D4 and 17OHP was good in multiple regression with age (p < 0.001, R2 = 0.29). In longitudinal assessment, 17OHP levels did not change with age, whereas D4 levels increased with age (p < 0.001, R2 = 0.08). Neither biomarker varied directly with dose or weight (p > 0.05). Multivariate LMEM showed HC dose decreasing by 1.0 mg/m2 /day for every 1 point increase in weight standard deviation score. DISCUSSION: Registry data show large variability in 17OHP and D4 between centres. 17OHP correlates with D4 well when accounting for age. Prescribed HC dose per body surface area decreased with weight gain.


Asunto(s)
Hiperplasia Suprarrenal Congénita , 17-alfa-Hidroxiprogesterona , Hiperplasia Suprarrenal Congénita/tratamiento farmacológico , Androstenodiona , Niño , Preescolar , Femenino , Humanos , Hidrocortisona/uso terapéutico , Masculino , Progesterona , Sistema de Registros , Estudios Retrospectivos
12.
Entropy (Basel) ; 23(9)2021 Aug 31.
Artículo en Inglés | MEDLINE | ID: mdl-34573759

RESUMEN

The Schrödinger bridge problem (SBP) finds the most likely stochastic evolution between two probability distributions given a prior stochastic evolution. As well as applications in the natural sciences, problems of this kind have important applications in machine learning such as dataset alignment and hypothesis testing. Whilst the theory behind this problem is relatively mature, scalable numerical recipes to estimate the Schrödinger bridge remain an active area of research. Our main contribution is the proof of equivalence between solving the SBP and an autoregressive maximum likelihood estimation objective. This formulation circumvents many of the challenges of density estimation and enables direct application of successful machine learning techniques. We propose a numerical procedure to estimate SBPs using Gaussian process and demonstrate the practical usage of our approach in numerical simulations and experiments.

13.
Signif (Oxf) ; 17(6): 12, 2020 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-33362874

RESUMEN

In emergency situations like the coronavirus pandemic, decisions must be made quickly, with only partial information. But good decisions are still possible using risk-benefit analysis. By Peter J. Diggle, Tim Gowers, Frank Kelly and Neil Lawrence.

15.
Clin Endocrinol (Oxf) ; 91(3): 417-423, 2019 09.
Artículo en Inglés | MEDLINE | ID: mdl-31179554

RESUMEN

OBJECTIVE: We aimed to document current practice in the medical management of paediatric hyperthyroidism in the UK and compare to international recommendations. DESIGN: A 27-question online survey distributed via an electronic newsletter in August 2018. PARTICIPANTS: Responses from 48 members (11%) of the British Society for Paediatric Endocrinology and Diabetes. MEASUREMENTS: Information about antithyroid drug (ATD) preference, treatment duration, monitoring of full blood count (FBC), management of neutropaenia, agranulocytosis screening and patient education. RESULTS: Carbimazole is favoured by 98% of respondents and a "dose titration" regimen preferred over "block and replace" (65% vs 29%). TRAbs (thyroid-stimulating hormone receptor antibodies) are used for diagnostic purposes by 85% and by 33% to look for evidence of disease remission. The majority (81%) treat for a minimum of 2 years before considering a trial off ATD. All respondents reported that they "always/usually" warn their patients about the risk of agranulocytosis before starting ATD, but written information is "rarely/never" provided by 63%. Sore throat (98%) and fever (92%) are the most commonly cited symptoms used to alert a patient to possible agranulocytosis. FBC is measured prior to treatment by 65% and measured periodically during treatment by 70%. CONCLUSIONS: The management of paediatric hyperthyroidism with ATDs in the UK is not consistent with all international recommendations because a block and replace ATD regimen remains widely used. TRAbs are utilized at presentation, but underused for detecting disease remission. National consensus guidelines and written patient information may refine the management of paediatric patients on ATDs.


Asunto(s)
Antitiroideos/uso terapéutico , Pediatras , Pautas de la Práctica en Medicina , Agranulocitosis/inducido químicamente , Antitiroideos/efectos adversos , Monitoreo de Drogas/métodos , Humanos , Hipertiroidismo/complicaciones , Hipertiroidismo/tratamiento farmacológico , Guías de Práctica Clínica como Asunto , Encuestas y Cuestionarios
16.
Philos Trans R Soc Lond B Biol Sci ; 374(1771): 20180025, 2019 04 29.
Artículo en Inglés | MEDLINE | ID: mdl-30852998

RESUMEN

From neuroscience, brain imaging and the psychology of memory, we are beginning to assemble an integrated theory of the brain subsystems and pathways that allow the compression, storage and reconstruction of memories for past events and their use in contextualizing the present and reasoning about the future-mental time travel (MTT). Using computational models, embedded in humanoid robots, we are seeking to test the sufficiency of this theoretical account and to evaluate the usefulness of brain-inspired memory systems for social robots. In this contribution, we describe the use of machine learning techniques-Gaussian process latent variable models-to build a multimodal memory system for the iCub humanoid robot and summarize results of the deployment of this system for human-robot interaction. We also outline the further steps required to create a more complete robotic implementation of human-like autobiographical memory and MTT. We propose that generative memory models, such as those that form the core of our robot memory system, can provide a solution to the symbol grounding problem in embodied artificial intelligence. This article is part of the theme issue 'From social brains to social robots: applying neurocognitive insights to human-robot interaction'.


Asunto(s)
Cognición , Aprendizaje Automático , Memoria Episódica , Robótica , Humanos , Modelos Teóricos , Conducta Social , Factores de Tiempo , Viaje
17.
Cogn Sci ; 42 Suppl 3: 809-832, 2018 06.
Artículo en Inglés | MEDLINE | ID: mdl-29315735

RESUMEN

Both scientists and children make important structural discoveries, yet their computational underpinnings are not well understood. Structure discovery has previously been formalized as probabilistic inference about the right structural form-where form could be a tree, ring, chain, grid, etc. (Kemp & Tenenbaum, 2008). Although this approach can learn intuitive organizations, including a tree for animals and a ring for the color circle, it assumes a strong inductive bias that considers only these particular forms, and each form is explicitly provided as initial knowledge. Here we introduce a new computational model of how organizing structure can be discovered, utilizing a broad hypothesis space with a preference for sparse connectivity. Given that the inductive bias is more general, the model's initial knowledge shows little qualitative resemblance to some of the discoveries it supports. As a consequence, the model can also learn complex structures for domains that lack intuitive description, as well as predict human property induction judgments without explicit structural forms. By allowing form to emerge from sparsity, our approach clarifies how both the richness and flexibility of human conceptual organization can coexist.


Asunto(s)
Formación de Concepto , Modelos Teóricos , Algoritmos , Animales , Conjuntos de Datos como Asunto , Humanos , Juicio
18.
Future Healthc J ; 5(3): 207-212, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31098568

RESUMEN

In contrast to secondary care, where handwritten records remain widespread, electronic patient records have long been a key feature of UK general practice. By 1996, 96% of general practices were computerised and now almost every primary care consultation in the UK is recorded on a computerised clinical system. Consequently, we now have a vast repository of patient health data that spans decades, which could be used to address a range of important research questions. Unfortunately, accessing primary care data for health researchers can be a burdensome, confusing and time-consuming process. Understanding the way in which primary care data are recorded and 'coded' is not intuitive to those unfamiliar with general practice. The requirements of information governance mean that some data, or data presented in particular ways, are not available at all. This review provides a practical overview of the types of data recorded in primary care, the bodies responsible for them and how they can be accessed.

19.
Future Healthc J ; 5(3): 229-230, 2018 Oct.
Artículo en Inglés | MEDLINE | ID: mdl-31098572

RESUMEN

The potential promise of 'big data' in the NHS has not been overhyped. However, cyber security and linkage attacks remain ongoing concerns, and previously damaging projects, such as care.data and the Royal Free's collaboration with google DeepMind, have raised concern among patient groups. We must use technology itself to minimise these risks, while publicising the good news stories and the positive case for using patient data in research. '#Datasaveslives' is a national campaign, launched by the Farr Institute in 2014, that aims to spread the importance of our duty to share patient data for the benefits of health outcomes. 2018 is an incredibly important year for the future of data sharing. We urge our colleagues to join the campaign by sharing stories online with #Datasaveslives to promote how learning from patient data helps improve healthcare for us all.

20.
Bioinformatics ; 33(23): 3776-3783, 2017 Dec 01.
Artículo en Inglés | MEDLINE | ID: mdl-28961802

RESUMEN

MOTIVATION: Regulation of gene expression in prokaryotes involves complex co-regulatory mechanisms involving large numbers of transcriptional regulatory proteins and their target genes. Uncovering these genome-scale interactions constitutes a major bottleneck in systems biology. Sparse latent factor models, assuming activity of transcription factors (TFs) as unobserved, provide a biologically interpretable modelling framework, integrating gene expression and genome-wide binding data, but at the same time pose a hard computational inference problem. Existing probabilistic inference methods for such models rely on subjective filtering and suffer from scalability issues, thus are not well-suited for realistic genome-scale applications. RESULTS: We present a fast Bayesian sparse factor model, which takes input gene expression and binding sites data, either from ChIP-seq experiments or motif predictions, and outputs active TF-gene links as well as latent TF activities. Our method employs an efficient variational Bayes scheme for model inference enabling its application to large datasets which was not feasible with existing MCMC-based inference methods for such models. We validate our method on synthetic data against a similar model in the literature, employing MCMC for inference, and obtain comparable results with a small fraction of the computational time. We also apply our method to large-scale data from Mycobacterium tuberculosis involving ChIP-seq data on 113 TFs and matched gene expression data for 3863 putative target genes. We evaluate our predictions using an independent transcriptomics experiment involving over-expression of TFs. AVAILABILITY AND IMPLEMENTATION: An easy-to-use Jupyter notebook demo of our method with data is available at https://github.com/zhenwendai/SITAR. CONTACT: mudassar.iqbal@manchester.ac.uk. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.


Asunto(s)
Sitios de Unión , Inmunoprecipitación de Cromatina/métodos , Perfilación de la Expresión Génica/métodos , Regulación Bacteriana de la Expresión Génica , Modelos Biológicos , Mycobacterium tuberculosis/genética , Factores de Transcripción/metabolismo , Teorema de Bayes , Biología Computacional/métodos , Transcripción Genética
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