Dataset Information

Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster.

ABSTRACT: The genomic best linear unbiased prediction (GBLUP) model has proven to be useful for prediction of complex traits as well as estimation of population genetic parameters. Improved inference and prediction accuracy of GBLUP may be achieved by identifying genomic regions enriched for causal genetic variants. We aimed at searching for patterns in GBLUP-derived single-marker statistics, by including them in genetic marker set tests, that could reveal associations between a set of genetic markers (genomic feature) and a complex trait. GBLUP-derived set tests proved to be powerful for detecting genomic features, here defined by gene ontology (GO) terms, enriched for causal variants affecting a quantitative trait in a population with low degree of relatedness. Different set test approaches were compared using simulated data illustrating the impact of trait- and genomic feature-specific factors on detection power. We extended the most powerful single trait set test, covariance association test (CVAT), to a multiple trait setting. The multiple trait CVAT (MT-CVAT) identified functionally relevant GO categories associated with the quantitative trait, chill coma recovery time, in the unrelated, sequenced inbred lines of the Drosophila melanogaster Genetic Reference Panel.

SUBMITTER: Sorensen IF

PROVIDER: S-EPMC5445101 | biostudies-literature | 2017 May

REPOSITORIES: biostudies-literature

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Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster.

Sørensen Izel Fourie IF Edwards Stefan M SM Rohde Palle Duun PD Sørensen Peter P

Scientific reports 20170525 1

The genomic best linear unbiased prediction (GBLUP) model has proven to be useful for prediction of complex traits as well as estimation of population genetic parameters. Improved inference and prediction accuracy of GBLUP may be achieved by identifying genomic regions enriched for causal genetic variants. We aimed at searching for patterns in GBLUP-derived single-marker statistics, by including them in genetic marker set tests, that could reveal associations between a set of genetic markers (ge ...[more]

PMID: 28546557

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Project description:This study aimed to empirically evaluate the hierarchical structure of the Coma Recovery Scale-Revised (CRS-R) rating scale categories and their alignment with the Aspen consensus criteria for determining disorders of consciousness (DoC) following a severe brain injury. CRS-R data from 262 patients with DoC following a severe brain injury were analyzed applying the partial credit Rasch Measurement Model. Rasch Analysis produced logit calibrations for each rating scale category. Twenty-eight of the 29 CRS-R rating scale categories were operationalized to the Aspen consensus criteria. We expected the hierarchical order of the calibrations to reflect Aspen consensus criteria. We also examined the association between the CRS-R Rasch person measures (indicative of performance ability) and states of consciousness as determined by the Aspen consensus criteria. Overall, the order of the 29 rating scale category calibrations reflected current literature regarding the continuum of neurobehavioral function: category 6 "Functional Object Use" of the Motor item was hardest for patients to achieve; category 0 "None" of the Oromotor/Verbal item was easiest to achieve. Of the 29 rating scale categories, six were not ordered as expected. Four rating scale categories reflecting the Vegetative State (VS)/Unresponsive Wakefulness Syndrome (UWS) had higher calibrations (reflecting greater neurobehavioral function) than the easiest Minimally Conscious State (MCS) item (category 2 "Fixation" of the Visual item). Two rating scale categories, one reflecting MCS and one not operationalized to the Aspen consensus criteria, had higher calibrations than the easiest eMCS item (category 2 "Functional: Accurate" of the Communication item). CRS-R person measures (indicating amount of neurobehavioral function) and states of consciousness, based on Aspen consensus criteria, showed a strong correlation (rs = 0.86; p < 0.01). Our study provides empirical evidence for revising the diagnostic criteria for MCS to also include category 2 "Localization to Sound" of the Auditory item and for Emerged from Minimally Conscious State (eMCS) to include category 4 "Consistent Movement to Command" of the Auditory item.

Dataset Information

Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster.

Publications

Multiple Trait Covariance Association Test Identifies Gene Ontology Categories Associated with Chill Coma Recovery Time in Drosophila melanogaster.

Similar Datasets

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