Joint impact of clinical and behavioral variables on the risk of unplanned readmission and death after a heart failure hospitalization

Most current methods for modeling rehospitalization events in heart failure patients make use of only clinical and medications data that is available in the electronic health records. However, information about patient-reported functional limitations, behavioral variables and socio-economic background of patients may also play an important role in predicting the risk of readmission in heart failure patients. We developed methods for predicting the risk of rehospitalization in heart failure patients using models that integrate clinical characteristics with patient-reported functional limitations, behavioral and socio-economic characteristics. Our goal was to estimate the predictive accuracy of the joint model and compare it with models that make use of clinical data alone or behavioral and socio-economic characteristics alone, using real patient data. We collected data about the occurrence of hospital readmissions from a cohort of 789 heart failure patients for whom a range of clinical and behavioral characteristics data is also available. We applied the Cox model, four different variants of the Cox proportional hazards framework as well as an alternative non-parametric approach and determined the predictive accuracy for different categories of variables. The concordance index obtained from the joint prediction model including all types of variables was significantly higher than the accuracy obtained from using only clinical factors or using only behavioral, socioeconomic background and functional limitations in patients as predictors. Collecting information on behavior, patient-reported estimates of physical limitations and frailty and socio-economic data has significant value in the predicting the risk of readmissions with regards to heart failure events and can lead to substantially more accurate events prediction models

Probability that a chromosome is lost without trace under the neutral Wright-Fisher model with recombination

I describe an analytical approximation for calculating the short-term probability of loss of a chromosome under the neutral Wright-Fisher model with recombination. I also present an upper and lower bound for this probability. Exact analytical calculation of this quantity is difficult and computationally expensive because the number of different ways in which a chromosome can be lost, grows very large in the presence of recombination. Simulations indicate that the probabilities obtained using my approximate formula are always comparable to the true expectations provided that the number of generations remains small. These results are useful in the context of an algorithm that we recently developed for simulating Wright-Fisher populations forward in time. C++ programs that can efficiently calculate these formulas are available on request.Comment: Additional Information, Padhukasahasram et al. 2008, Genetics, FORWSIM algorith

Discovery and Fine-Mapping of Adiposity Loci Using High Density Imputation of Genome-Wide Association Studies in Individuals of African Ancestry: African Ancestry Anthropometry Genetics Consortium

Genome-wide association studies (GWAS) have identified \u3e 300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes. In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHRadjBMI and eight previously established loci at P \u3c 5×10−8: seven for BMI, and one for WHRadjBMI in African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHRadjBMI when combined with European GWAS. In the sex-stratified analyses, we identified three novel loci for BMI (INTS10/LPL and MLC1 in men, IRX4/IRX2 in women) and four for WHRadjBMI (SSX2IP, CASC8, PDE3B and ZDHHC1/HSD11B2 in women) in individuals of African ancestry or both African and European ancestry. For four of the novel variants, the minor allele frequency was low (\u3c5%). In the trans-ethnic fine mapping of 47 BMI loci and 27 WHRadjBMI loci that were locus-wide significant (P \u3c 0.05 adjusted for effective number of variants per locus) from the African ancestry sex-combined and sex-stratified analyses, 26 BMI loci and 17 WHRadjBMI loci contained ≤ 20 variants in the credible sets that jointly account for 99% posterior probability of driving the associations. The lead variants in 13 of these loci had a high probability of being causal. As compared to our previous HapMap imputed GWAS for BMI and WHRadjBMI including up to 71,412 and 27,350 African ancestry individuals, respectively, our results suggest that 1000 Genomes imputation showed modest improvement in identifying GWAS loci including low frequency variants. Trans-ethnic meta-analyses further improved fine mapping of putative causal variants in loci shared between the African and European ancestry populations

Discovery and fine-mapping of adiposity loci using high density imputation of genome-wide association studies in individuals of African ancestry: African Ancestry Anthropometry Genetics Consortium

Genome-wide association studies (GWAS) have identified >300 loci associated with measures of adiposity including body mass index (BMI) and waist-to-hip ratio (adjusted for BMI, WHRadjBMI), but few have been identified through screening of the African ancestry genomes. We performed large scale meta-analyses and replications in up to 52,895 individuals for BMI and up to 23,095 individuals for WHRadjBMI from the African Ancestry Anthropometry Genetics Consortium (AAAGC) using 1000 Genomes phase 1 imputed GWAS to improve coverage of both common and low frequency variants in the low linkage disequilibrium African ancestry genomes. In the sex-combined analyses, we identified one novel locus (TCF7L2/HABP2) for WHRadjBMI and eight previously established loci at P < 5×10−8: seven for BMI, and one for WHRadjBMI in African ancestry individuals. An additional novel locus (SPRYD7/DLEU2) was identified for WHRadjBMI when combined with European GWAS. In the sex-stratified analyses, we identified three novel loci for BMI (INTS10/LPL and MLC1 in men, IRX4/IRX2 in women) and four for WHRadjBMI (SSX2IP, CASC8, PDE3B and ZDHHC1/HSD11B2 in women) in individuals of African ancestry or both African and European ancestry. For four of the novel variants, the minor allele frequency was low (<5%). In the trans-ethnic fine mapping of 47 BMI loci and 27 WHRadjBMI loci that were locus-wide significant (P < 0.05 adjusted for effective number of variants per locus) from the African ancestry sex-combined and sex-stratified analyses, 26 BMI loci and 17 WHRadjBMI loci contained ≤ 20 variants in the credible sets that jointly account for 99% posterior probability of driving the associations. The lead variants in 13 of these loci had a high probability of being causal. As compared to our previous HapMap imputed GWAS for BMI and WHRadjBMI including up to 71,412 and 27,350 African ancestry individuals, respectively, our results suggest that 1000 Genomes imputation showed modest improvement in identifying GWAS loci including low frequency variants. Trans-ethnic meta-analyses further improved fine mapping of putative causal variants in loci shared between the African and European ancestry populations

Joint impact of clinical and behavioral variables on the risk of unplanned readmission and death after a heart failure hospitalization.

Most current methods for modeling rehospitalization events in heart failure patients make use of only clinical and medications data that is available in the electronic health records. However, information about patient-reported functional limitations, behavioral variables and socio-economic background of patients may also play an important role in predicting the risk of readmission in heart failure patients. We developed methods for predicting the risk of rehospitalization in heart failure patients using models that integrate clinical characteristics with patient-reported functional limitations, behavioral and socio-economic characteristics. Our goal was to estimate the predictive accuracy of the joint model and compare it with models that make use of clinical data alone or behavioral and socio-economic characteristics alone, using real patient data. We collected data about the occurrence of hospital readmissions from a cohort of 789 heart failure patients for whom a range of clinical and behavioral characteristics data is also available. We applied the Cox model, four different variants of the Cox proportional hazards framework as well as an alternative non-parametric approach and determined the predictive accuracy for different categories of variables. The concordance index obtained from the joint prediction model including all types of variables was significantly higher than the accuracy obtained from using only clinical factors or using only behavioral, socioeconomic background and functional limitations in patients as predictors. Collecting information on behavior, patient-reported estimates of physical limitations and frailty and socio-economic data has significant value in the predicting the risk of readmissions with regards to heart failure events and can lead to substantially more accurate events prediction models

Model performance based on concordance index.

<p>Model performance based on concordance index.</p

Effect size estimates, fraction of patients with events (F) and number of Samples (N) for most important clinical variables (n = 789).

<p>Effect size estimates, fraction of patients with events (F) and number of Samples (N) for most important clinical variables (n = 789).</p

Sample characteristics of the HFHS heart failure study cohort.

<p>Sample characteristics of the HFHS heart failure study cohort.</p

Powerful Tests for Multi-Marker Association Analysis Using Ensemble Learning

<div><p>Multi-marker approaches have received a lot of attention recently in genome wide association studies and can enhance power to detect new associations under certain conditions. Gene-, gene-set- and pathway-based association tests are increasingly being viewed as useful supplements to the more widely used single marker association analysis which have successfully uncovered numerous disease variants. A major drawback of single-marker based methods is that they do not look at the joint effects of multiple genetic variants which individually may have weak or moderate signals. Here, we describe novel tests for multi-marker association analyses that are based on phenotype predictions obtained from machine learning algorithms. Instead of assuming a linear or logistic regression model, we propose the use of ensembles of diverse machine learning algorithms for prediction. We show that phenotype predictions obtained from ensemble learning algorithms provide a new framework for multi-marker association analysis. They can be used for constructing tests for the joint association of multiple variants, adjusting for covariates and testing for the presence of interactions. To demonstrate the power and utility of this new approach, we first apply our method to simulated SNP datasets. We show that the proposed method has the correct Type-1 error rates and can be considerably more powerful than alternative approaches in some situations. Then, we apply our method to previously studied asthma-related genes in 2 independent asthma cohorts to conduct association tests.</p></div