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1.
Genome Res ; 31(9): 1513-1518, 2021 09.
Artículo en Inglés | MEDLINE | ID: mdl-34301630

RESUMEN

The number of de novo mutations (DNMs) in the human germline is correlated with parental age at conception, but this explains only part of the observed variation. We investigated whether there is a family-specific contribution to the number of DNMs in offspring. The analysis of DNMs in 111 dizygotic twin pairs did not identify a substantial family-specific contribution. This result was corroborated by comparing DNMs of 1669 siblings to those of age-matched unrelated offspring following correction for parental age. In addition, by modeling DNM data from 1714 multi-offspring families, we estimated that the family-specific contribution explains ∼5.2% of the variation in DNM number. Furthermore, we found no substantial difference between the observed number of DNMs and those predicted by a stochastic Poisson process. We conclude that there is a small family-specific contribution to DNM number and that stochasticity explains a large proportion of variation in DNM counts.


Asunto(s)
Células Germinativas , Humanos , Mutación
2.
Stat Med ; 43(12): 2421-2438, 2024 May 30.
Artículo en Inglés | MEDLINE | ID: mdl-38589978

RESUMEN

Identifying predictive factors for an outcome of interest via a multivariable analysis is often difficult when the data set is small. Combining data from different medical centers into a single (larger) database would alleviate this problem, but is in practice challenging due to regulatory and logistic problems. Federated learning (FL) is a machine learning approach that aims to construct from local inferences in separate data centers what would have been inferred had the data sets been merged. It seeks to harvest the statistical power of larger data sets without actually creating them. The FL strategy is not always efficient and precise. Therefore, in this paper we refine and implement an alternative Bayesian federated inference (BFI) framework for multicenter data with the same aim as FL. The BFI framework is designed to cope with small data sets by inferring locally not only the optimal parameter values, but also additional features of the posterior parameter distribution, capturing information beyond what is used in FL. BFI has the additional benefit that a single inference cycle across the centers is sufficient, whereas FL needs multiple cycles. We quantify the performance of the proposed methodology on simulated and real life data.


Asunto(s)
Teorema de Bayes , Modelos Estadísticos , Estudios Multicéntricos como Asunto , Humanos , Aprendizaje Automático , Simulación por Computador , Interpretación Estadística de Datos , Análisis Multivariante
3.
Biom J ; 65(1): e2100123, 2023 01.
Artículo en Inglés | MEDLINE | ID: mdl-35818126

RESUMEN

Statistical methods to test for effects of single nucleotide polymorphisms (SNPs) on exon inclusion exist but often rely on testing of associations between multiple exon-SNP pairs, with sometimes subsequent summarization of results at the gene level. Such approaches require heavy multiple testing corrections and detect mostly events with large effect sizes. We propose here a test to find spliceQTL (splicing quantitative trait loci) effects that takes all exons and all SNPs into account simultaneously. For any chosen gene, this score-based test looks for an association between the set of exon expressions and the set of SNPs, via a random-effects model framework. It is efficient to compute and can be used if the number of SNPs is larger than the number of samples. In addition, the test is powerful in detecting effects that are relatively small for individual exon-SNP pairs but are observed for many pairs. Furthermore, test results are more often replicated across datasets than pairwise testing results. This makes our test more robust to exon-SNP pair-specific effects, which do not extend to multiple pairs within the same gene. We conclude that the test we propose here offers more power and better replicability in the search for spliceQTL effects.


Asunto(s)
Polimorfismo de Nucleótido Simple , Sitios de Carácter Cuantitativo , Estudio de Asociación del Genoma Completo/métodos
4.
Blood ; 135(14): 1161-1170, 2020 04 02.
Artículo en Inglés | MEDLINE | ID: mdl-32243522

RESUMEN

Anemia is a major and currently poorly understood clinical manifestation of hematopoietic aging. Upon aging, hematopoietic clones harboring acquired leukemia-associated mutations expand and become detectable, now referred to as clonal hematopoiesis (CH). To investigate the relationship between CH and anemia of the elderly, we explored the landscape and dynamics of CH in older individuals with anemia. From the prospective, population-based Lifelines cohort (n = 167 729), we selected all individuals at least 60 years old who have anemia according to World Health Organization criteria (n = 676) and 1:1 matched control participants. Peripheral blood of 1298 individuals was analyzed for acquired mutations at a variant allele frequency (VAF) of 1% or higher in 27 driver genes. To track clonal evolution over time, we included all available follow-up samples (n = 943). CH was more frequently detected in individuals with anemia (46.6%) compared with control individuals (39.1%; P = .007). Although no differences were observed regarding commonly detected DTA mutations (DNMT3A, TET2, ASXL1) in individuals with anemia compared with control individuals, other mutations were enriched in the anemia cohort, including TP53 and SF3B1. Unlike individuals with nutrient deficiency (P = .84), individuals with anemia of chronic inflammation and unexplained anemia revealed a higher prevalence of CH (P = .035 and P = .017, respectively) compared with their matched control individuals. Follow-up analyses revealed that clones may expand and decline, generally showing only a subtle increase in VAF (mean, 0.56%) over the course of 44 months, irrespective of the presence of anemia. Specific mutations were associated with different growth rates and propensities to acquire an additional hit. In contrast to smaller clones (<5% VAF), which did not affect overall survival, larger clones were associated with increased risk for death.


Asunto(s)
Anemia/genética , Hematopoyesis , Mutación , Factores de Edad , Anciano , Envejecimiento , Anemia/epidemiología , Femenino , Humanos , Estimación de Kaplan-Meier , Masculino , Persona de Mediana Edad , Estudios Prospectivos
5.
Pharm Stat ; 21(5): 879-894, 2022 09.
Artículo en Inglés | MEDLINE | ID: mdl-35191174

RESUMEN

In early phase clinical studies in oncology, Simon's two-stage designs are widely used. The trial design could be made more efficient by stopping early in the second stage when the required number of responses is reached, or when it has become clear that this target can no longer be met (a form of non-stochastic curtailment). Early stopping, however, will affect proper estimation of the response rate. We propose a uniformly minimum-variance unbiased estimator (UMVUE) for the response rate in this setting. The estimator is proven to be UMVUE using the Rao-Blackwell theorem. We evaluate the estimator's properties in terms of bias and mean squared error, both analytically and via simulations. We derive confidence intervals based on sample space orderings, and assess the coverage. For various design options, we evaluate the reduction in expected sample size as a function of the true response rate. Our method provides a solution for estimating response rates in case of a non-stochastic curtailment Simon's two-stage design.


Asunto(s)
Oncología Médica , Proyectos de Investigación , Sesgo , Humanos , Tamaño de la Muestra
6.
BMC Med Res Methodol ; 21(1): 17, 2021 01 11.
Artículo en Inglés | MEDLINE | ID: mdl-33430789

RESUMEN

INTRODUCTION: Recurrent episodes of pneumonia are frequently modeled using extensions of the Cox proportional hazards model with the underlying assumption of time-constant relative risks measured by the hazard ratio. We aim to relax this assumption in a study on the effect of factors on the evolution of pneumonia incidence over time based on data from a South African birth cohort study, the Drakenstein child health study. METHODS: We describe and apply two models: a time-constant and a time-varying relative effects model in a piece-wise exponential additive mixed model's framework for recurrent events. A more complex model that fits in the same framework is applied to study the continuously measured seasonal effects. RESULTS: We find that several risk factors (male sex, preterm birth, low birthweight, lower socioeconomic status, lower maternal education and maternal cigarette smoking) have strong relative effects that are persistent across time. When time-varying effects are allowed in the model, HIV exposure status (HIV exposed & uninfected versus HIV unexposed) shows a strong relative effect for younger children, but this effect weakens as children grow older, with a null effect reached from about 15 months. Weight-for-length at birth shows a time increasing relative effect. We also find that children born in the summer have a much higher risk of pneumonia in the 3-to-8-month age period compared with children born in winter. CONCLUSION: This work highlights the usefulness of flexible modelling tools in recurrent events models. It avoids stringent assumptions and allows estimation and visualization of absolute and relative risks over time of key factors associated with incidence of pneumonia in young children, providing new perspectives on the role of risk factors such HIV exposure.


Asunto(s)
Infecciones por VIH , Neumonía , Nacimiento Prematuro , Niño , Preescolar , Estudios de Cohortes , Femenino , Infecciones por VIH/epidemiología , Humanos , Incidencia , Lactante , Recién Nacido , Masculino , Neumonía/epidemiología , Neumonía/etiología , Embarazo , Factores de Riesgo , Sudáfrica/epidemiología
7.
BMC Cancer ; 20(1): 884, 2020 Sep 14.
Artículo en Inglés | MEDLINE | ID: mdl-32928177

RESUMEN

BACKGROUND: In recent years, there is increasing evidence showing a beneficial outcome (e.g. progression free survival; PFS) after metastases-directed therapy (MDT) with external beam radiotherapy (EBRT) or targeted surgery for oligometastatic hormone sensitive prostate cancer (oHSPC). However, many patients do not qualify for these treatments due to prior interventions or tumor location. Such oligometastatic patients could benefit from radioligand therapy (RLT) with 177Lu-PSMA; a novel tumor targeting therapy for end-stage metastatic castration-resistant prostate cancer (mCRPC). Especially because RLT could be more effective in low volume disease, such as the oligometastatic status, due to high uptake of radioligands in smaller lesions. To test the hypothesis that 177Lu-PSMA is an effective treatment in oHSPC to prolong PFS and postpone the need for androgen deprivation therapy (ADT), we initiated a multicenter randomized clinical trial. This is globally, the first prospective study using 177Lu-PSMA-I&T in a randomized multicenter setting. METHODS & DESIGN: This study compares 177Lu-PSMA-I&T MDT to the current standard of care (SOC); deferred ADT. Fifty-eight patients with oHSPC (≤5 metastases on PSMA PET) and high PSMA uptake (SUVmax > 15, partial volume corrected) on 18F-PSMA PET after prior surgery and/or EBRT and a PSA doubling time of < 6 months, will be randomized in a 1:1 ratio. The patients randomized to the interventional arm will be eligible for two cycles of 7.4GBq 177Lu-PSMA-I&T at a 6-week interval. After both cycles, patients are monitored every 3 weeks (including adverse events, QoL- and xerostomia questionnaires and laboratory testing) at the outpatient clinic. Twenty-four weeks after cycle two an end of study evaluation is planned together with another 18F-PSMA PET and (whole body) MRI. Patients in the SOC arm are eligible to receive 177Lu-PSMA-I&T after meeting the primary study objective, which is the fraction of patients who show disease progression during the study follow up. A second primary objective is the time to disease progression. Disease progression is defined as a 100% increase in PSA from baseline or clinical progression. DISCUSSION: This is the first prospective randomized clinical study assessing the therapeutic efficacy and toxicity of 177Lu-PSMA-I&T for patients with oHSPC. TRIAL REGISTRATION: Clinicaltrials.gov identifier: NCT04443062 .


Asunto(s)
Lutecio/administración & dosificación , Neoplasias Hormono-Dependientes/tratamiento farmacológico , Neoplasias de la Próstata Resistentes a la Castración/tratamiento farmacológico , Neoplasias de la Próstata/tratamiento farmacológico , Radioisótopos/administración & dosificación , Antagonistas de Andrógenos/administración & dosificación , Antagonistas de Andrógenos/efectos adversos , Progresión de la Enfermedad , Hormonas/genética , Hormonas/metabolismo , Humanos , Lutecio/efectos adversos , Masculino , Persona de Mediana Edad , Metástasis de la Neoplasia , Neoplasias Hormono-Dependientes/patología , Neoplasias Hormono-Dependientes/radioterapia , Supervivencia sin Progresión , Neoplasias de la Próstata/patología , Neoplasias de la Próstata/radioterapia , Neoplasias de la Próstata Resistentes a la Castración/patología , Neoplasias de la Próstata Resistentes a la Castración/radioterapia , Calidad de Vida , Radioisótopos/efectos adversos , Radiofármacos/administración & dosificación , Resultado del Tratamiento
8.
Int J Cancer ; 143(4): 758-766, 2018 08 15.
Artículo en Inglés | MEDLINE | ID: mdl-29492965

RESUMEN

Salivary duct carcinoma (SDC) is a subtype of salivary gland cancer with a dismal prognosis and a need for better prognostication and novel treatments. The aim of this national cohort study was to investigate clinical outcome, prognostic factors, androgen receptor (AR) and human epidermal growth factor receptor 2 (HER2) expression. SDC patients diagnosed between 1990 and 2014 were identified by the Nationwide Network and Registry of Histo- and Cytopathology in the Netherlands (PALGA). Subsequently, medical records were evaluated and pathological diagnoses reviewed. Data were analyzed for overall survival (OS), disease-free survival (DFS), distant metastasis-free survival (DMFS) and prognostic factors. AR was evaluated by immunohistochemistry (IHC), HER2 by IHC and fluorescent in-situ hybridization. A total of 177 patients were included. The median age was 65 years, 75% were male. At diagnosis, 68% presented with lymph node metastases and 6% with distant metastases. Median OS, DFS and DMFS were 51, 23 and 26 months, respectively. In patients presenting without distant metastases, the absolute number of positive lymph nodes was associated with poor OS and DMFS in a multivariable analysis. AR and HER2 were positive in 161/168 (96%) and 44/153 (29%) tumors, respectively, and were not prognostic factors. SDC has a dismal prognosis with primary lymph node involvement in the majority of patients. The absolute number of lymph node metastases was found to be the only prognostic factor for DMFS and OS. AR expression and-to a lesser extent-HER2 expression hold promise for systemic treatment in the metastatic and eventually adjuvant setting.


Asunto(s)
Carcinoma/patología , Conductos Salivales/patología , Neoplasias de las Glándulas Salivales/patología , Adulto , Anciano , Anciano de 80 o más Años , Carcinoma/cirugía , Carcinoma/terapia , Quimioradioterapia Adyuvante , Supervivencia sin Enfermedad , Análisis Factorial , Femenino , Humanos , Metástasis Linfática , Masculino , Persona de Mediana Edad , Metástasis de la Neoplasia , Países Bajos , Cuidados Paliativos , Pronóstico , Receptor ErbB-2/metabolismo , Receptores Androgénicos/metabolismo , Recurrencia , Conductos Salivales/cirugía , Neoplasias de las Glándulas Salivales/radioterapia , Neoplasias de las Glándulas Salivales/cirugía , Neoplasias de las Glándulas Salivales/terapia , Tasa de Supervivencia
9.
Biostatistics ; 18(3): 477-494, 2017 Jul 01.
Artículo en Inglés | MEDLINE | ID: mdl-28334077

RESUMEN

For over a decade functional gene-to-gene interaction (epistasis) has been suspected to be a determinant in the "missing heritability" of complex traits. However, searching for epistasis on the genome-wide scale has been challenging due to the prohibitively large number of tests which result in a serious loss of statistical power as well as computational challenges. In this article, we propose a two-stage method applicable to existing case-control data sets, which aims to lessen both of these problems by pre-assessing whether a candidate pair of genetic loci is involved in epistasis before it is actually tested for interaction with respect to a complex phenotype. The pre-assessment is based on a two-locus genotype independence test performed in the sample of cases. Only the pairs of loci that exhibit non-equilibrium frequencies are analyzed via a logistic regression score test, thereby reducing the multiple testing burden. Since only the computationally simple independence tests are performed for all pairs of loci while the more demanding score tests are restricted to the most promising pairs, genome-wide association study (GWAS) for epistasis becomes feasible. By design our method provides strong control of the type I error. Its favourable power properties especially under the practically relevant misspecification of the interaction model are illustrated. Ready-to-use software is available. Using the method we analyzed Parkinson's disease in four cohorts and identified possible interactions within several SNP pairs in multiple cohorts.


Asunto(s)
Epistasis Genética , Estudio de Asociación del Genoma Completo , Programas Informáticos , Genotipo , Humanos , Polimorfismo de Nucleótido Simple
10.
Clin Genet ; 94(6): 521-527, 2018 12.
Artículo en Inglés | MEDLINE | ID: mdl-30211448

RESUMEN

To determine how much of the clinical variability in facioscapulohumeral muscular dystrophy type 1 (FSHD1) can be explained by the D4Z4 repeat array size, D4Z4 methylation and familial factors, we included 152 carriers of an FSHD1 allele (23 single cases, 129 familial cases from 37 families) and performed state-of-the-art genetic testing, extensive clinical evaluation and quantitative muscle MRI. Familial factors accounted for 50% of the variance in disease severity (FSHD clinical score). The explained variance by the D4Z4 repeat array size for disease severity was limited (approximately 10%), and varied per body region (facial muscles, upper and lower extremities approximately 30%, 15% and 3%, respectively). Unaffected gene carriers had longer repeat array sizes compared to symptomatic individuals (7.3 vs 6.0 units, P = 0.000) and slightly higher Delta1 methylation levels (D4Z4 methylation corrected for repeat size, 0.96 vs -2.46, P = 0.048). The D4Z4 repeat array size and D4Z4 methylation contribute to variability in disease severity and penetrance, but other disease modifying factors must be involved as well. The larger effect of the D4Z4 repeat array on facial muscle involvement suggests that these muscles are more sensitive to the influence of the FSHD1 locus itself, whereas leg muscle involvement seems highly dependent on modifying factors.


Asunto(s)
Estudios de Asociación Genética , Predisposición Genética a la Enfermedad , Genotipo , Distrofia Muscular Facioescapulohumeral/diagnóstico , Distrofia Muscular Facioescapulohumeral/genética , Fenotipo , Adolescente , Adulto , Anciano , Anciano de 80 o más Años , Alelos , Biomarcadores , Femenino , Estudios de Asociación Genética/métodos , Haplotipos , Humanos , Imagen por Resonancia Magnética/métodos , Masculino , Persona de Mediana Edad , Penetrancia , Índice de Severidad de la Enfermedad , Adulto Joven
11.
Eur J Nucl Med Mol Imaging ; 44(8): 1319-1327, 2017 Aug.
Artículo en Inglés | MEDLINE | ID: mdl-28421240

RESUMEN

BACKGROUND: Rhenium-188-HEDP is a beta-emitting radiopharmaceutical used for palliation of metastatic bone pain. We investigated whether the addition of rhenium-188-HEDP to docetaxel/prednisone improved efficacy of chemotherapy in patients with CRPC. METHODS: Patients with progressive CRPC and osteoblastic bone metastases were randomised for first-line docetaxel 75 mg/m2 3-weekly plus prednisone with or without 2 injections of rhenium-188-HEDP after the third (40 MBq/kg) and after the sixth (20 MBq/kg) cycle of docetaxel. Primary endpoint was progression-free survival (PFS), defined as either PSA, radiographic or clinical progression. Patients were stratified by extent of bone metastases and hospital. RESULTS: Forty-two patients were randomised for standard treatment and 46 patients for combination therapy. Median number of cycles of docetaxel was 9 in the control group and 8 in the experimental group. Median follow-up was 18.4 months. Two patients from the experimental group did not start treatment after randomisation. In the intention to treat analysis no differences in PFS, survival and PSA became apparent between the two groups. In an exploratory per-protocol analysis median overall survival was significantly longer in the experimental group (33.8 months (95%CI 31.75-35.85)) than in the control group (21.0 months (95%CI 13.61-28.39); p 0.012). Also median PFS in patients with a baseline phosphatase >220U/L was significantly better with combination treatment (9.0 months (95%CI 3.92-14.08) versus 6.2 months (95%CI 3.08-9.32); log rank p 0.005). As expected, thrombocytopenia (grade I/II) was reported more frequently in the experimental group (25% versus 0%). CONCLUSION: Combined treatment with rhenium-188-HEDP and docetaxel did not prolong PFS in patients with CRPC. The observed survival benefit in the per-protocol analysis warrants further studies in the combined treatment of chemotherapy and radiopharmaceuticals.


Asunto(s)
Protocolos de Quimioterapia Combinada Antineoplásica/uso terapéutico , Neoplasias Óseas/secundario , Ácido Etidrónico/uso terapéutico , Compuestos Organometálicos/uso terapéutico , Prednisona/uso terapéutico , Neoplasias de la Próstata Resistentes a la Castración/tratamiento farmacológico , Neoplasias de la Próstata Resistentes a la Castración/patología , Taxoides/uso terapéutico , Anciano , Anciano de 80 o más Años , Supervivencia sin Enfermedad , Docetaxel , Humanos , Estimación de Kaplan-Meier , Masculino , Persona de Mediana Edad
12.
Stat Med ; 36(21): 3412-3421, 2017 Sep 20.
Artículo en Inglés | MEDLINE | ID: mdl-28631295

RESUMEN

In screening and surveillance studies, event times are interval censored. Besides, screening tests are imperfect so that the interval at which an event takes place may be uncertain. We describe an expectation-maximization algorithm to find the nonparametric maximum likelihood estimator of the cumulative incidence function of an event based on screening test data. Our algorithm has a closed-form solution for the combined expectation and maximization step and is computationally undemanding. A simulation study indicated that the bias of the estimator tends to zero for large sample size, and its mean squared error is in general lower than the mean squared error of the estimator that assumes the screening test is perfect. We apply the algorithm to follow-up data from women treated for cervical precancer. Copyright © 2017 John Wiley & Sons, Ltd.


Asunto(s)
Algoritmos , Incidencia , Funciones de Verosimilitud , Vigilancia de la Población , Sesgo , Simulación por Computador , Diagnóstico Precoz , Femenino , Humanos , Sensibilidad y Especificidad , Estadísticas no Paramétricas , Neoplasias del Cuello Uterino/patología , Neoplasias del Cuello Uterino/terapia
13.
BMC Bioinformatics ; 17: 118, 2016 Mar 08.
Artículo en Inglés | MEDLINE | ID: mdl-26951498

RESUMEN

BACKGROUND: Testing for association between RNA-Seq and other genomic data is challenging due to high variability of the former and high dimensionality of the latter. RESULTS: Using the negative binomial distribution and a random-effects model, we develop an omnibus test that overcomes both difficulties. It may be conceptualised as a test of overall significance in regression analysis, where the response variable is overdispersed and the number of explanatory variables exceeds the sample size. CONCLUSIONS: The proposed test can detect genetic and epigenetic alterations that affect gene expression. It can examine complex regulatory mechanisms of gene expression. The R package globalSeq is available from Bioconductor.


Asunto(s)
Algoritmos , Perfilación de la Expresión Génica , Secuenciación de Nucleótidos de Alto Rendimiento/métodos , Neoplasias de la Próstata/genética , ARN/genética , Análisis de Secuencia de ARN/métodos , Humanos , Masculino , Análisis de Regresión
14.
Stat Med ; 35(23): 4183-201, 2016 10 15.
Artículo en Inglés | MEDLINE | ID: mdl-27087571

RESUMEN

In retrospective studies involving recurrent events, it is common to select individuals based on their event history up to the time of selection. In this case, the ascertained subjects might not be representative for the target population, and the analysis should take the selection mechanism into account. The purpose of this paper is two-fold. First, to study what happens when the data analysis is not adjusted for the selection and second, to propose a corrected analysis. Under the Andersen-Gill and shared frailty regression models, we show that the estimators of covariate effects, incidence, and frailty variance can be biased if the ascertainment is ignored, and we show that with a simple adjustment of the likelihood, unbiased and consistent estimators are obtained. The proposed method is assessed by a simulation study and is illustrated on a data set comprising recurrent pneumothoraces. Copyright © 2016 John Wiley & Sons, Ltd.


Asunto(s)
Fragilidad , Análisis de Regresión , Humanos , Probabilidad , Estudios Retrospectivos
15.
Hum Hered ; 80(2): 69-78, 2015.
Artículo en Inglés | MEDLINE | ID: mdl-26540120

RESUMEN

OBJECTIVE: Estimating the total allele frequency of all pathogenic alleles of an autosomal recessive disease is not possible if only mutational data of a sample of affected individuals are available. However, if the affected individuals come from a population where consanguinity is not uncommon, this total allele frequency can be estimated by additionally using the positive individual inbreeding coefficients or an estimate of the population inbreeding coefficient. In this paper, we propose two estimators. METHODS/RESULTS: We propose to estimate the total allele frequency by a conditional maximum likelihood estimator if a part of the affected individuals in the sample comes from consanguineous marriages with known inbreeding coefficients. A simulation study shows that this estimator is unbiased and robust. We propose a second estimator which is based on an estimate of the population inbreeding coefficient. The method is applied to mutational data and individual inbreeding coefficients of Tunisian patients with congenital adrenal hyperplasia. CONCLUSION: Additionally using individual inbreeding coefficients or an estimate of the population inbreeding coefficient makes it possible to estimate the total allele frequency. Since consanguinity is commonly practiced in many parts of the world, the estimators proposed in the paper are of practical importance.


Asunto(s)
Consanguinidad , Frecuencia de los Genes , Genes Recesivos , Predisposición Genética a la Enfermedad/genética , Hiperplasia Suprarrenal Congénita/genética , Alelos , Humanos , Funciones de Verosimilitud , Mutación , Túnez
16.
Oncoimmunology ; 13(1): 2361971, 2024.
Artículo en Inglés | MEDLINE | ID: mdl-38868078

RESUMEN

Colorectal cancer (CRC) raises considerable clinical challenges, including a high mortality rate once the tumor spreads to distant sites. At this advanced stage, more accurate prediction of prognosis and treatment outcome is urgently needed. The role of cancer immunity in metastatic CRC (mCRC) is poorly understood. Here, we explore cellular immune cell status in patients with multi-organ mCRC. We analyzed T cell infiltration in primary tumor sections, surveyed the lymphocytic landscape of liver metastases, and assessed circulating mononuclear immune cells. Besides asking whether immune cells are associated with survival at this stage of the disease, we investigated correlations between the different tissue types; as this could indicate a dominant immune phenotype. Taken together, our analyses corroborate previous observations that higher levels of CD8+ T lymphocytes link to better survival outcomes. Our findings therefore extend evidence from earlier stages of CRC to indicate an important role for cancer immunity in disease control even after metastatic spreading to multiple organs. This finding may help to improve predicting outcome of patients with mCRC and suggests a future role for immunotherapeutic strategies.


Asunto(s)
Neoplasias Colorrectales , Neoplasias Hepáticas , Humanos , Neoplasias Colorrectales/patología , Neoplasias Colorrectales/inmunología , Neoplasias Colorrectales/mortalidad , Masculino , Femenino , Neoplasias Hepáticas/secundario , Neoplasias Hepáticas/inmunología , Neoplasias Hepáticas/mortalidad , Anciano , Persona de Mediana Edad , Pronóstico , Linfocitos T CD8-positivos/inmunología , Linfocitos Infiltrantes de Tumor/inmunología , Metástasis de la Neoplasia , Adulto
17.
J Med Genet ; 48(12): 860-3, 2011 Dec.
Artículo en Inglés | MEDLINE | ID: mdl-22058428

RESUMEN

BACKGROUND: Mutations in the CHEK2 gene confer a moderately increased breast cancer risk. The risk for female carriers of the CHEK2*1100delC mutation is twofold increased. Breast cancer risk for carrier women is higher in a familial breast cancer setting which is due to coinheritance of additional genetic risk factors. This study investigated the occurrence of homozygosity for the CHEK2*1100delC allele among familial breast cancer cases and the associated breast cancer risk. METHODS AND RESULTS: Homozygosity for the CHEK2*1100delC allele was identified in 8/2554 Dutch independent familial non-BRCA1/2 breast cancer cases. The genotype relative risk for breast cancer of homozygous and heterozygous familial breast cancer cases was 101.34 (95% CI 4.47 to 121 000) and 4.04 (95% CI 0.88 to 21.0), respectively. Female homozygotes appeared to have a greater than twofold increased breast cancer risk compared to familial CHEK2*1100delC heterozygotes (p=0.044). These results and the occurrence of multiple primary tumours in 7/10 homozygotes indicate a high cancer risk in homozygous women from non-BRCA1/2 families. CONCLUSIONS: Intensive breast surveillance is therefore justified in these homozygous women. It is concluded that diagnostic testing for biallelic mutations in CHEK2 is indicated in non-BRCA1/2 breast cancer families, especially in populations with a relatively high prevalence of deleterious mutations in CHEK2.


Asunto(s)
Neoplasias de la Mama/genética , Mutación del Sistema de Lectura , Homocigoto , Proteínas Serina-Treonina Quinasas/genética , Adulto , Anciano , Alelos , Proteína BRCA1/genética , Proteína BRCA2/genética , Neoplasias de la Mama/patología , Quinasa de Punto de Control 2 , Femenino , Tamización de Portadores Genéticos , Predisposición Genética a la Enfermedad , Pruebas Genéticas , Heterocigoto , Humanos , Masculino , Persona de Mediana Edad , Linaje , Factores de Riesgo
18.
Eur J Cancer ; 161: 128-137, 2022 01.
Artículo en Inglés | MEDLINE | ID: mdl-34920917

RESUMEN

AIM: Because the tyrosine kinases c-MET and vascular endothelial growth factor receptors (VEGFR) are often overexpressed in salivary gland cancer (SGC), this study evaluated the efficacy and safety of cabozantinib in patients with recurrent/metastatic (R/M) SGC. PATIENTS AND METHODS: A single-centre phase II study was conducted. Patients with immunohistochemical c-MET-positive R/M SGC were included in three cohorts: adenoid cystic carcinoma (ACC); salivary duct carcinoma (SDC) and other miscellaneous SGCs. No prior systemic treatments were required. Patients started cabozantinib 60 mg once daily. The primary outcome was the objective response rate (ORR). Secondary outcomes included survival, safety and quality of life. Per Simon-two-stage design, depending on efficacy, a maximum of 43 patients would be included. RESULTS: In total, 25 patients were included until premature closure owing to severe toxicity. Six patients (24%) had grade 3-5 wound complications, occurring at a median of 7.1 months on cabozantinib treatment (range 2.1-12.6). Remarkably, four of these six patients developed this complication in the area prior exposed to high-dose radiotherapy. Other grade ≥3 adverse events in >1 patient were hypertension (20%), diarrhoea (8%) and dehydration (8%). Twenty-one patients were evaluable for response; 1/15 ACC (ORR: 7%); 1/4 SDC and 0/2 patients with other miscellaneous SGC responded. Median progression-free survival was 9.4 months (95% confidence interval [CI] 7.4-11.4 months), 7.2 months (95%CI 0.0-15.1) and 6.9 months (95%CI 0.0-15.1), respectively. CONCLUSION: This study showed too many severe cabozantinib-associated wound complications in patients with SGC, especially in prior irradiated areas. Therefore, the study closed prematurely. The efficacy in the limited number of evaluable patients was low to moderate. TRIAL REGISTRATION: This trial was registered on ClinicalTrials.gov: NCT03729297.


Asunto(s)
Anilidas/efectos adversos , Piridinas/efectos adversos , Proteínas Tirosina Quinasas Receptoras/uso terapéutico , Neoplasias de las Glándulas Salivales/tratamiento farmacológico , Anciano , Anilidas/farmacología , Femenino , Humanos , Masculino , Persona de Mediana Edad , Metástasis de la Neoplasia , Recurrencia Local de Neoplasia , Piridinas/farmacología , Proteínas Tirosina Quinasas Receptoras/farmacología
19.
Methods Mol Biol ; 2212: 69-92, 2021.
Artículo en Inglés | MEDLINE | ID: mdl-33733351

RESUMEN

Undiscovered gene-to-gene interaction (epistasis) is a possible explanation for the "missing heritability" of complex traits and diseases. On a genome-wide scale, screening for epistatic effects among all possible pairs of genetic markers faces two main complications. Firstly, the classical statistical methods for modeling epistasis are computationally very expensive, which makes them impractical on such large scale. Secondly, straightforward corrections for multiple testing using the classical methods tend to be too coarse and inefficient at discovering the epistatic effects in such a large scale application. In this chapter, we describe both the underlying framework and practical examples of two-stage statistical testing methods that alleviate both of the aforementioned complications.


Asunto(s)
Epistasis Genética , Pruebas Genéticas/métodos , Modelos Genéticos , Polimorfismo de Nucleótido Simple , Carácter Cuantitativo Heredable , Programas Informáticos , Estudios de Asociación Genética , Genoma Humano , Genotipo , Humanos , Patrón de Herencia , Fenotipo , Sitios de Carácter Cuantitativo
20.
Cancers (Basel) ; 13(14)2021 Jul 14.
Artículo en Inglés | MEDLINE | ID: mdl-34298742

RESUMEN

Patients suffering from recurrent or metastatic (R/M) salivary duct carcinoma (SDC) are often treated with combined androgen blockade (CAB). However, CAB frequently fails, resulting in a worse prognosis. Therefore, biomarkers that can predict treatment failure are urgently needed. mRNA from 76 R/M androgen receptor (AR)-positive SDC patients treated with leuprorelin acetate combined with bicalutamide was extracted from pre-treatment tumor specimens. AR, Notch, MAPK, TGFß, estrogen receptor (ER), Hedgehog (HH), and PI3K signaling pathway activity scores (PAS) were determined based on the expression levels of target genes. Additionally, 5-alpha reductase type 1 (SRD5A1) expression was determined. These markers were related to clinical benefit (complete/partial response or stable disease ≥6 months) and progression-free and overall survival (PFS/OS). SRD5A1 expression had the highest general predictive value for clinical benefit and positive predictive value (PPV: 85.7%). AR PAS had the highest negative predictive value (NPV: 93.3%). The fitting of a multivariable model led to the identification of SRD5A1, TGFß, and Notch PAS as the most predictive combination. High AR, high Notch, high ER, low HH PAS, and high SRD5A1 expression were also of prognostic importance regarding PFS and SRD5A1 expression levels for OS. AR, Notch PAS, and SRD5A1 expression have the potential to predict the clinical benefit of CAB treatment in SDC patients. SRD5A1 expression can identify patients that will and AR PAS patients that will not experience clinical benefit (85.7% and 93.3% for PPV and NPV, respectively). The predictive potential of SRD5A1 expression forms a rational basis for including SRD5A1-inhibitors in SDC patients' treatment.

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