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Genes (Basel) ; 10(9)2019 Sep 19.
Artículo en Inglés | MEDLINE | ID: mdl-31546899


Informatics researchers often need to combine data from many different sources to increase statistical power and study subtle or complicated effects. Perfect overlap of measurements across academic studies is rare since virtually every dataset is collected for a unique purpose and without coordination across parties not-at-hand (i.e., informatics researchers in the future). Thus, incomplete concordance of measurements across datasets poses a major challenge for researchers seeking to combine public databases. In any given field, some measurements are fairly standard, but every organization collecting data makes unique decisions on instruments, protocols, and methods of processing the data. This typically denies literal concatenation of the raw data since constituent cohorts do not have the same measurements (i.e., columns of data). When measurements across datasets are similar prima facie, there is a desire to combine the data to increase power, but mixing non-identical measurements could greatly reduce the sensitivity of the downstream analysis. Here, we discuss a statistical method that is applicable when certain patterns of missing data are found; namely, it is possible to combine datasets that measure the same underlying constructs (or latent traits) when there is only partial overlap of measurements across the constituent datasets. Our method, ROSETTA empirically derives a set of common latent trait metrics for each related measurement domain using a novel variation of factor analysis to ensure equivalence across the constituent datasets. The advantage of combining datasets this way is the simplicity, statistical power, and modeling flexibility of a single joint analysis of all the data. Three simulation studies show the performance of ROSETTA on datasets with only partially overlapping measurements (i.e., systematically missing information), benchmarked to a condition of perfectly overlapped data (i.e., full information). The first study examined a range of correlations, while the second study was modeled after the observed correlations in a well-characterized clinical, behavioral cohort. Both studies consistently show significant correlations >0.94, often >0.96, indicating the robustness of the method and validating the general approach. The third study varied within and between domain correlations and compared ROSETTA to multiple imputation and meta-analysis as two commonly used methods that ostensibly solve the same data integration problem. We provide one alternative to meta-analysis and multiple imputation by developing a method that statistically equates similar but distinct manifest metrics into a set of empirically derived metrics that can be used for analysis across all datasets.

J Genet Couns ; 28(3): 664-672, 2019 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-30843639


Pathogenic germline mutations in the BRCA1 or BRCA2 genes are associated with an elevated lifetime risk for breast (50%-85% risk) and ovarian cancer (20%-40% risk). Genome-wide association studies have identified over 100 genetic variants associated with modified breast and/or ovarian cancer risk in BRCA1 and BRCA2 carriers. Risk models generated based on these variants have shown that these genetic modifiers strongly influence absolute risk of developing breast or ovarian cancer in BRCA mutation carriers. There is a lack of understanding, however, about the clinical applicability and utility of these risk models. To investigate this gap, we collected survey data from 274 cancer genetic counselors (GCs) through the National Society of Genetic Counselors Cancer Special Interest Group. Questions assessed perceptions of usefulness and intentions of genetic counselors to use these refined risk models in clinical care based on the Technology Acceptance Model (TAM). We found that GCs' reactions to the estimates were largely positive, though they thought the possibility of changing management based on results was unlikely. Additionally, we found that more experienced GCs were more likely to consider refined risk estimates in clinic. Support also was provided for core predictions within the TAM, whereby the perceived usefulness (indirect effect est. = 0.08, 95% CI: [0.04, 0.13]) and perceived ease of use (indirect effect est. = 0.078, 95% CI: [0.04, 0.13]) of refined risk estimates were indirectly associated with intentions to use via attitudes.

Leuk Lymphoma ; : 1-10, 2019 Mar 01.
Artículo en Inglés | MEDLINE | ID: mdl-30821551


Mantle cell lymphoma (MCL) is an aggressive B-cell malignancy for which novel therapeutics with improved efficacy are greatly needed. To provide support for clinical immune checkpoint blockade, we comprehensively evaluated the expression of therapeutically targetable immune checkpoint molecules on primary MCL cells. MCL cells showed constitutive expression of Programmed Death 1 (PD-1) and Programmed Death Ligand 1 (PD-L1), variable CD200, absent PD-L2, Lymphocyte Activation Gene 3 (LAG-3), and Cytotoxic T-cell Associated Protein 4 (CTLA-4). Effector cells from MCL patients expressed PD-1. Co-culture of MCL cells with T-cells induced PD-L1 surface expression, a phenomenon regulated by IFNγ and CD40:CD40L interaction. Induction of PD-L1 was attenuated by concurrent treatment with ibrutinib or duvelisib, suggesting BTK and PI3K are important mediators of PD-L1 expression. Overall, our data provide further insight into the expression of checkpoint molecules in MCL and support the use of PD-L1 blocking antibodies in MCL patients.

J Vet Intern Med ; 33(2): 680-685, 2019 Mar.
Artículo en Inglés | MEDLINE | ID: mdl-30784117


BACKGROUND: Proteinuria in dogs with kidney disease can contribute to protein-energy wasting and malnutrition. Little is known about amino acid (AA) status in dogs with protein-losing nephropathy (PLN). OBJECTIVES: The purpose of our study was to further elucidate AA status in PLN dogs, with the hypothesis that PLN dogs would have altered AA status as compared to healthy dogs. ANIMALS: Thirty client-owned PLN dogs were compared to 10 healthy control dogs. METHODS: Prospective observational study. Dogs with PLN that were presented to the teaching hospital were enrolled. Plasma AA profiles were measured using an automated high-performance liquid chromatography AA analyzer. RESULTS: Compared to control dogs, PLN dogs had significantly lower concentrations of leucine, threonine, histidine, glycine, proline, asparagine, tyrosine, o-hydroxyproline, and serine, as well as sums of both essential and nonessential AA (P < .05). Dogs with PLN had significantly lower ratios of tyrosine-to-phenylalanine and glycine-to-serine (P < .05), and a significantly greater ratio of valine-to-glycine (P < .05). CONCLUSIONS AND CLINICAL IMPORTANCE: Dogs with PLN have altered AA status compared to healthy dogs. These findings could have therapeutic implications in determining optimal management of PLN dogs, such as providing AA supplementation along with other standard treatment.

Aminoácidos/sangre , Enfermedades de los Perros/sangre , Enfermedades Renales/veterinaria , Proteinuria/veterinaria , Animales , Estudios de Casos y Controles , Cromatografía Líquida de Alta Presión/veterinaria , Perros , Femenino , Enfermedades Renales/sangre , Masculino , Estudios Prospectivos , Proteinuria/sangre
J Cyst Fibros ; 17(4): 454-461, 2018 Jul.
Artículo en Inglés | MEDLINE | ID: mdl-29241629


INTRODUCTION: Cystic fibrosis (CF) is a multi-organ disorder characterized by chronic sino-pulmonary infections and inflammation. Many patients with CF suffer from repeated pulmonary exacerbations that are predictors of worsened long-term morbidity and mortality. There are no reliable markers that associate with the onset or progression of an exacerbation or pulmonary deterioration. Previously, we found that the Mirc1/Mir17-92a cluster which is comprised of 6 microRNAs (Mirs) is highly expressed in CF mice and negatively regulates autophagy which in turn improves CF transmembrane conductance regulator (CFTR) function. Therefore, here we sought to examine the expression of individual Mirs within the Mirc1/Mir17-92 cluster in human cells and biological fluids and determine their role as biomarkers of pulmonary exacerbations and response to treatment. METHODS: Mirc1/Mir17-92 cluster expression was measured in human CF and non-CF plasma, blood-derived neutrophils, and sputum samples. Values were correlated with pulmonary function, exacerbations and use of CFTR modulators. RESULTS: Mirc1/Mir17-92 cluster expression was not significantly elevated in CF neutrophils nor plasma when compared to the non-CF cohort. Cluster expression in CF sputum was significantly higher than its expression in plasma. Elevated CF sputum Mirc1/Mir17-92 cluster expression positively correlated with pulmonary exacerbations and negatively correlated with lung function. Patients with CF undergoing treatment with the CFTR modulator Ivacaftor/Lumacaftor did not demonstrate significant change in the expression Mirc1/Mir17-92 cluster after six months of treatment. CONCLUSIONS: Mirc1/Mir17-92 cluster expression is a promising biomarker of respiratory status in patients with CF including pulmonary exacerbation.