The Experts below are selected from a list of 165 Experts worldwide ranked by ideXlab platform
Aurelie Labbe - One of the best experts on this subject based on the ideXlab platform.
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Analysis of case-parent trios for imprinting effect using a Loglinear Model with adjustment for sex-of-parent-specific transmission ratio distortion
Human Genetics, 2017Co-Authors: Lam Opal Huang, Claire Infante-rivard, Aurelie LabbeAbstract:Transmission ratio distortion (TRD) is a phenomenon where parental transmission of disease allele to the child does not follow the Mendelian inheritance ratio. TRD occurs in a sex-of-parent-specific or non-sex-of-parent-specific manner. An offset computed from the transmission probability of the minor allele in control-trios can be added to the Loglinear Model to adjust for TRD. Adjusting the Model removes the inflation in the genotype relative risk (RR) estimate and Type 1 error introduced by non-sex-of-parent-specific TRD. We now propose to further extend this Model to estimate an imprinting parameter. Some evidence suggests that more than 1% of all mammalian genes are imprinted. In the presence of imprinting, for example, the offspring inheriting an over-transmitted disease allele from the parent with a higher expression level in a neighboring gene is over-represented in the sample. TRD mechanisms such as meiotic drive and gametic competition occur in a sex-of-parent-specific manner. Therefore, sex-of-parent-specific TRD (ST) leads to over-representation of maternal or paternal alleles in the affected child. As a result, ST may bias the imprinting effect when present in the sample. We propose a sex-of-parent-specific transmission offset in adjusting the Loglinear Model to account for ST. This extended Model restores the correct RR estimates for child and imprinting effects, adjusts for inflation in Type 1 error, and improves performance on sensitivity and specificity compared to the original Model without ST offset. We conclude that to correctly interpret the association signal of an imprinting effect, adjustment for ST is necessary to ensure valid conclusions.
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analysis of case parent trios using a Loglinear Model with adjustment for transmission ratio distortion
Frontiers in Genetics, 2016Co-Authors: Lam Opal Huang, Claire Infanterivard, Aurelie LabbeAbstract:Transmission of the two parental alleles to offspring deviating from the Mendelian ratio is termed Transmission Ratio Distortion (TRD), occurs throughout gametic and embryonic development. TRD has been well-studied in animals, but remains largely unknown in humans. The Transmission Disequilibrium Test (TDT) was first proposed to test for association and linkage in case-trios (affected offspring and parents); adjusting for TRD using control-trios was recommended. However, the TDT does not provide risk parameter estimates for different genetic Models. A Loglinear Model was later proposed to provide child and maternal relative risk (RR) estimates of disease, assuming Mendelian transmission. Results from our simulation study showed that case-trios RR estimates using this Model are biased in the presence of TRD; power and Type 1 error are compromised. We propose an extended Loglinear Model adjusting for TRD. Under this extended Model, RR estimates, power and Type 1 error are correctly restored. We applied this Model to an intrauterine growth restriction dataset, and showed consistent results with a previous approach that adjusted for TRD using control-trios. Our findings suggested the need to adjust for TRD in avoiding spurious results. Documenting TRD in the population is therefore essential for the correct interpretation of genetic association studies.
Lam Opal Huang - One of the best experts on this subject based on the ideXlab platform.
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Analysis of case-parent trios for imprinting effect using a Loglinear Model with adjustment for sex-of-parent-specific transmission ratio distortion
Human Genetics, 2017Co-Authors: Lam Opal Huang, Claire Infante-rivard, Aurelie LabbeAbstract:Transmission ratio distortion (TRD) is a phenomenon where parental transmission of disease allele to the child does not follow the Mendelian inheritance ratio. TRD occurs in a sex-of-parent-specific or non-sex-of-parent-specific manner. An offset computed from the transmission probability of the minor allele in control-trios can be added to the Loglinear Model to adjust for TRD. Adjusting the Model removes the inflation in the genotype relative risk (RR) estimate and Type 1 error introduced by non-sex-of-parent-specific TRD. We now propose to further extend this Model to estimate an imprinting parameter. Some evidence suggests that more than 1% of all mammalian genes are imprinted. In the presence of imprinting, for example, the offspring inheriting an over-transmitted disease allele from the parent with a higher expression level in a neighboring gene is over-represented in the sample. TRD mechanisms such as meiotic drive and gametic competition occur in a sex-of-parent-specific manner. Therefore, sex-of-parent-specific TRD (ST) leads to over-representation of maternal or paternal alleles in the affected child. As a result, ST may bias the imprinting effect when present in the sample. We propose a sex-of-parent-specific transmission offset in adjusting the Loglinear Model to account for ST. This extended Model restores the correct RR estimates for child and imprinting effects, adjusts for inflation in Type 1 error, and improves performance on sensitivity and specificity compared to the original Model without ST offset. We conclude that to correctly interpret the association signal of an imprinting effect, adjustment for ST is necessary to ensure valid conclusions.
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analysis of case parent trios using a Loglinear Model with adjustment for transmission ratio distortion
Frontiers in Genetics, 2016Co-Authors: Lam Opal Huang, Claire Infanterivard, Aurelie LabbeAbstract:Transmission of the two parental alleles to offspring deviating from the Mendelian ratio is termed Transmission Ratio Distortion (TRD), occurs throughout gametic and embryonic development. TRD has been well-studied in animals, but remains largely unknown in humans. The Transmission Disequilibrium Test (TDT) was first proposed to test for association and linkage in case-trios (affected offspring and parents); adjusting for TRD using control-trios was recommended. However, the TDT does not provide risk parameter estimates for different genetic Models. A Loglinear Model was later proposed to provide child and maternal relative risk (RR) estimates of disease, assuming Mendelian transmission. Results from our simulation study showed that case-trios RR estimates using this Model are biased in the presence of TRD; power and Type 1 error are compromised. We propose an extended Loglinear Model adjusting for TRD. Under this extended Model, RR estimates, power and Type 1 error are correctly restored. We applied this Model to an intrauterine growth restriction dataset, and showed consistent results with a previous approach that adjusted for TRD using control-trios. Our findings suggested the need to adjust for TRD in avoiding spurious results. Documenting TRD in the population is therefore essential for the correct interpretation of genetic association studies.
Leandro Pardo - One of the best experts on this subject based on the ideXlab platform.
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robustness of minimum density power divergence estimators and wald type test statistics in Loglinear Models with multinomial sampling
Journal of Computational and Applied Mathematics, 2020Co-Authors: Aida Calvino, Nirian Martín, Leandro PardoAbstract:Abstract In this paper we propose a new family of estimators, Minimum Density Power Divergence Estimators (MDPDE), as a robust generalization of maximum likelihood estimators (MLE) for the Loglinear Model with multinomial sampling by using the Density Power Divergence (DPD) measure introduced by Basu et al. (1998). Based on these estimators, we further develop two types of confidence intervals (asymptotic and bootstrap ones), as well as a new robust family of Wald-type test statistics for testing a nested sequence of Loglinear Models. Furthermore, we study theoretically the robust properties of both the MDPDE as well as Wald-type tests through the classical influence function analysis. Finally, a simulation study provides further confirmation of the validity of the theoretical results established in the paper.
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new family of estimators for the Loglinear Model of quasi independence based on power divergence measures
Journal of Statistical Computation and Simulation, 2007Co-Authors: A Felipe, Leandro PardoAbstract:In this paper, we study the minimum power-divergence estimator, introduced and studied by Cressie and Read [Cressie, N. and Read, T.R.C., 1984, Multinomial goodness-of-fit tests. Journal of the Royal Statistic Society, Series B, 46, 440–464.], in the Loglinear Model of quasi-independence. A simulation study illustrates that minimum chi-squared estimator and Cressie–Read estimator are good alternatives to the classical maximum-likelihood estimator for this problem. The estimator obtained for λ=2 is the most robust and efficient estimator among the family of the minimum power estimators.
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phi residual based on minimum phi divergence estimator in the Loglinear Model of symmetry
2004Co-Authors: Arjun K Gupta, Truc T Nguyen, Leandro PardoAbstract:In this paper, we introduce and study a new family of standardized residuals for the Loglinear Model of symmetry based on o-Divergence statistic.
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Model checking in Loglinear Models using φ divergences and mles
Journal of Statistical Planning and Inference, 2002Co-Authors: Noel A Cressie, Leandro PardoAbstract:Abstract Consider the Loglinear Model for categorical data under the assumption of either Poisson, multinomial, or product-multinomial sampling. We are interested in testing between various hypotheses on the parameter space. In this paper, the usual likelihood ratio test, with maximum likelihood estimators for the unspecified parameters, is generalized to tests based on φ-divergences, still using maximum likelihood estimators. These tests yield the likelihood ratio test as a special case. Asymptotic distributions for the new test statistics are derived under both the null and the alternative hypotheses. Then it is shown how the φ-divergences can be used to test nested hypotheses, yielding a type of “analysis of divergence”.
Claire Infanterivard - One of the best experts on this subject based on the ideXlab platform.
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analysis of case parent trios using a Loglinear Model with adjustment for transmission ratio distortion
Frontiers in Genetics, 2016Co-Authors: Lam Opal Huang, Claire Infanterivard, Aurelie LabbeAbstract:Transmission of the two parental alleles to offspring deviating from the Mendelian ratio is termed Transmission Ratio Distortion (TRD), occurs throughout gametic and embryonic development. TRD has been well-studied in animals, but remains largely unknown in humans. The Transmission Disequilibrium Test (TDT) was first proposed to test for association and linkage in case-trios (affected offspring and parents); adjusting for TRD using control-trios was recommended. However, the TDT does not provide risk parameter estimates for different genetic Models. A Loglinear Model was later proposed to provide child and maternal relative risk (RR) estimates of disease, assuming Mendelian transmission. Results from our simulation study showed that case-trios RR estimates using this Model are biased in the presence of TRD; power and Type 1 error are compromised. We propose an extended Loglinear Model adjusting for TRD. Under this extended Model, RR estimates, power and Type 1 error are correctly restored. We applied this Model to an intrauterine growth restriction dataset, and showed consistent results with a previous approach that adjusted for TRD using control-trios. Our findings suggested the need to adjust for TRD in avoiding spurious results. Documenting TRD in the population is therefore essential for the correct interpretation of genetic association studies.
H P Riemann - One of the best experts on this subject based on the ideXlab platform.
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associations between campylobacter fetus haemophilus somnus leptospira hardjo and bovine viral diarrhea virus antibody titers in dairy cattle from a california herd
Preventive Veterinary Medicine, 1996Co-Authors: Saeed Akhtar, Thomas B Farver, H P RiemannAbstract:Abstract In a cross-sectional study, the associations of age, serological status against Campylobacter fetus (CF), Haemophilus somnus (HS) and Leptospira hardjo (LH) with the seroprevalence of bovine viral diarrhea virus (BVDV) in dairy cattle were evaluated. Six hundred and thirty cattle from a herd in Tulare county of California were included in the study. Blood samples from the cattle were collected in December 1986. Enzyme-linked immunosorbant assay (ELISA) was used to determine the positive or negative status of cows against CF, HS, LH and BVDV antigens. Loglinear analysis was used to describe the relationships of four categorical variables with the seroprevalence of BVDV. The final Loglinear Model was interpreted as a logit Model and obtained by conditioning on explanatory variables in the Model found to relate significantly with BVDV seropositivity. The hierarchical logit Model included two two-way interactions (BVDV × HS and BVDV × LH) and a three-way interaction ( BVDV × CF × age). HS-seronegative cattle had 4.7 times greater odds of being BVDV-seropositive compared with HS-seropositive cattle. In contrast, LH-seropositive cattle had 2.7 times increased odds of BVDV seropositivity compared with LH-seronegative cattle. The presence of the three-way interaction term in the Model involving age, CF and BVDV seroprevalence implies that among heifers, CF-seronegative and CF-seropositive animals had about the same odds of BVDV seropositivity (e.g. adjusted odds ratios = 20.5 vs. 24.5), whereas, among cows, CF-seronegative animals had at least twice the odds of being BVDV-seropositive than those of CF-seropositive animals (e.g. adjusted odds ratios = 23.0 vs. 11.0).
