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Lessons learned from Genetic Analysis Workshop 17: transitioning from genome-wide association studies to whole-genome statistical genetic analysis.

ABSTRACT: Genetic Analysis Workshop 17 (GAW17) focused on the transition from genome-wide association study designs and methods to the study designs and statistical genetic methods that will be required for the analysis of next-generation sequence data including both common and rare sequence variants. In the 166 contributions to GAW17, a wide variety of statistical methods were applied to simulated traits in population- and family-based samples, and results from these analyses were compared to the known generating model. In general, many of the statistical genetic methods used in the population-based sample identified causal sequence variants (SVs) when the estimated locus-specific heritability, as measured in the population-based sample, was greater than about 0.08. However, SVs with locus-specific heritabilities less than 0.03 were rarely identified consistently. In the family-based samples, many of the methods detected SVs that were rarer than those detected in the population-based sample, but the estimated locus-specific heritabilities for these rare SVs, as measured in the family-based samples, were substantially higher (>0.2) than their corresponding heritabilities in the population-based samples. Substantial inflation of the type I error rate was observed across a wide variety of statistical methods. Although many of the contributions found little inflation in type I error for Q4, a trait with no causal SVs, type I error rates for Q1 and Q2 were well above their nominal levels with the inflation for Q1 being higher than that for Q2. It seems likely that this inflation in type I error is due to correlations among SVs.

SUBMITTER: Wilson AF

PROVIDER: S-EPMC3277851 | biostudies-literature | 2011

REPOSITORIES: biostudies-literature

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Lessons learned from Genetic Analysis Workshop 17: transitioning from genome-wide association studies to whole-genome statistical genetic analysis.

Wilson Alexander F AF Ziegler Andreas A

Genetic epidemiology 20110101

Genetic Analysis Workshop 17 (GAW17) focused on the transition from genome-wide association study designs and methods to the study designs and statistical genetic methods that will be required for the analysis of next-generation sequence data including both common and rare sequence variants. In the 166 contributions to GAW17, a wide variety of statistical methods were applied to simulated traits in population- and family-based samples, and results from these analyses were compared to the known g ...[more]

PMID: 22128050

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Project description:BackgroundOver the past two decades non-communicable diseases (NCDs) have steadily increased as a cause of worldwide disability and mortality with a concomitant decrease in disease burden from communicable, maternal, neonatal and nutritional conditions. Congenital anomalies, the most common NCD affecting children, have recently become the fifth leading cause of under-five mortality worldwide, ahead of other conditions such as malaria, neonatal sepsis and malnutrition. Genetic counseling has been shown to be an effective method to decrease the impact of congenital anomalies and genetic conditions but is absent in almost all sub-Saharan Africa countries. To address this need for counseling services we designed and implemented the first broad-based genetic counseling curriculum in Ethiopia, launching it at St. Paul's Millennium Medical College (SPHMMC) in Addis Ababa, Ethiopia.MethodsThe curriculum, created by Michigan Medicine and SPHMMC specialists, consisted of medical knowledge and genetic counseling content and was delivered to two cohorts of nurses. Curriculum evaluation consisted of satisfaction surveys and pre- and post-assessments covering medical knowledge and genetic counseling content. Following Cohort 1 training, the curriculum was modified to increase the medical knowledge material and decrease Western genetic counseling principles material.ResultsBoth cohorts reported high levels of satisfaction but felt the workshop was too short. No significant improvements in assessment scores were seen for Cohort 1 in terms of total scores and medical knowledge and genetic counseling-specific questions. Following curriculum modification, improvements were seen in Cohort 2 with an increase in total assessment scores from 63% to 73% (p = 0.043), with medical knowledge-specific questions increasing from 57% to 79% (p = 0.01) with no significant change in genetic counseling-specific scores. Multiple logistic, financial, cultural and systems-specific barriers were identified with recommendations for their consideration presented.ConclusionGenetics medical knowledge of Ethiopian nurses increased significantly following curriculum delivery though difficulty was encountered with Western genetic counseling material.

Dataset Information

Lessons learned from Genetic Analysis Workshop 17: transitioning from genome-wide association studies to whole-genome statistical genetic analysis.

Publications

Lessons learned from Genetic Analysis Workshop 17: transitioning from genome-wide association studies to whole-genome statistical genetic analysis.

Similar Datasets

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