Dataset Information

Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost.

ABSTRACT:

Background

Commercial breeding programs seek to maximise the rate of genetic gain while minimizing the costs of attaining that gain. Genomic information offers great potential to increase rates of genetic gain but it is expensive to generate. Low-cost genotyping strategies combined with genotype imputation offer dramatically reduced costs. However, both the costs and accuracy of imputation of these strategies are highly sensitive to several factors. The objective of this paper was to explore the cost and imputation accuracy of several alternative genotyping strategies in pedigreed populations.

Methods

Pedigree and genotype data from a commercial pig population were used. Several alternative genotyping strategies were explored. The strategies differed in the density of genotypes used for the ancestors and the individuals to be imputed. Parents, grandparents, and other relatives that were not descendants, were genotyped at high-density, low-density, or extremely low-density, and associated costs and imputation accuracies were evaluated.

Results

Imputation accuracy and cost were influenced by the alternative genotyping strategies. Given the mating ratios and the numbers of offspring produced by males and females, an optimized low-cost genotyping strategy for a commercial pig population could involve genotyping male parents at high-density, female parents at low-density (e.g. 3000 SNP), and selection candidates at very low-density (384 SNP).

Conclusions

Among the selection candidates, 95.5% and 93.5% of the genotype variation contained in the high-density SNP panels were recovered using a genotyping strategy that costs respectively, $24.74 and $20.58 per candidate.

SUBMITTER: Huang Y

PROVIDER: S-EPMC3436735 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature

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Publications

Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost.

Huang Yijian Y Hickey John M JM Cleveland Matthew A MA Maltecca Christian C

Genetics, selection, evolution : GSE 20120731

<h4>Background</h4>Commercial breeding programs seek to maximise the rate of genetic gain while minimizing the costs of attaining that gain. Genomic information offers great potential to increase rates of genetic gain but it is expensive to generate. Low-cost genotyping strategies combined with genotype imputation offer dramatically reduced costs. However, both the costs and accuracy of imputation of these strategies are highly sensitive to several factors. The objective of this paper was to exp ...[more]

PMID: 22849718

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Project description:IntroductionIn the United States, tens of thousands of inspections of tobacco retailers are conducted each year. Various sampling choices can reduce travel costs, emphasize enforcement in areas with greater noncompliance, and allow for comparability between states and over time. We sought to develop a model sampling strategy for state tobacco retailer inspections.MethodsUsing a 2014 list of 10,161 North Carolina tobacco retailers, we compared results from simple random sampling; stratified, clustered at the ZIP code sampling; and, stratified, clustered at the census tract sampling. We conducted a simulation of repeated sampling and compared approaches for their comparative level of precision, coverage, and retailer dispersion.ResultsWhile maintaining an adequate design effect and statistical precision appropriate for a public health enforcement program, both stratified, clustered ZIP- and tract-based approaches were feasible. Both ZIP and tract strategies yielded improvements over simple random sampling, with relative improvements, respectively, of average distance between retailers (reduced 5.0% and 1.9%), percent Black residents in sampled neighborhoods (increased 17.2% and 32.6%), percent Hispanic residents in sampled neighborhoods (reduced 2.2% and increased 18.3%), percentage of sampled retailers located near schools (increased 61.3% and 37.5%), and poverty rate in sampled neighborhoods (increased 14.0% and 38.2%).ConclusionsStates can make retailer inspections more efficient and targeted with stratified, clustered sampling. Use of statistically appropriate sampling strategies like these should be considered by states, researchers, and the Food and Drug Administration to improve program impact and allow for comparisons over time and across states.ImplicationsThe authors present a model tobacco retailer sampling strategy for promoting compliance and reducing costs that could be used by US states and the Food and Drug Administration (FDA). The design is feasible to implement in North Carolina. Use of the sampling design would help document the impact of FDA's compliance and enforcement program, save money, and emphasize inspections in areas where they are needed most. FDA should consider requiring probability-based sampling in their inspections contracts with states and private contractors.

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Dataset Information

Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost.

Background

Methods

Results

Conclusions

Publications

Assessment of alternative genotyping strategies to maximize imputation accuracy at minimal cost.

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