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A simulation study of sample size for DNA barcoding.

ABSTRACT: For some groups of organisms, DNA barcoding can provide a useful tool in taxonomy, evolutionary biology, and biodiversity assessment. However, the efficacy of DNA barcoding depends on the degree of sampling per species, because a large enough sample size is needed to provide a reliable estimate of genetic polymorphism and for delimiting species. We used a simulation approach to examine the effects of sample size on four estimators of genetic polymorphism related to DNA barcoding: mismatch distribution, nucleotide diversity, the number of haplotypes, and maximum pairwise distance. Our results showed that mismatch distributions derived from subsamples of ?20 individuals usually bore a close resemblance to that of the full dataset. Estimates of nucleotide diversity from subsamples of ?20 individuals tended to be bell-shaped around that of the full dataset, whereas estimates from smaller subsamples were not. As expected, greater sampling generally led to an increase in the number of haplotypes. We also found that subsamples of ?20 individuals allowed a good estimate of the maximum pairwise distance of the full dataset, while smaller ones were associated with a high probability of underestimation. Overall, our study confirms the expectation that larger samples are beneficial for the efficacy of DNA barcoding and suggests that a minimum sample size of 20 individuals is needed in practice for each population.

SUBMITTER: Luo A

PROVIDER: S-EPMC4717336 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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A simulation study of sample size for DNA barcoding.

Luo Arong A Lan Haiqiang H Ling Cheng C Zhang Aibing A Shi Lei L Ho Simon Y W SY Zhu Chaodong C

Ecology and evolution 20151201 24

For some groups of organisms, DNA barcoding can provide a useful tool in taxonomy, evolutionary biology, and biodiversity assessment. However, the efficacy of DNA barcoding depends on the degree of sampling per species, because a large enough sample size is needed to provide a reliable estimate of genetic polymorphism and for delimiting species. We used a simulation approach to examine the effects of sample size on four estimators of genetic polymorphism related to DNA barcoding: mismatch distri ...[more]

PMID: 26811761

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Project description:Mixture models of item response theory (IRT) can be used to detect inappropriate category use. Data collected by panel surveys where attitudes and traits are typically assessed by short scales with many response categories are prone to response styles indicating inappropriate category use. However, the application of mixed IRT models to this data type can be challenging because of many threshold parameters within items. Up to now, there is very limited knowledge about the sample size required for an appropriate performance of estimation methods as well as goodness-of-fit criteria of mixed IRT models in this case. The present Monte Carlo simulation study examined these issues for two mixed IRT models [the restricted mixed generalized partial credit model (rmGPCM) and the mixed partial credit model (mPCM)]. The population parameters of the simulation study were taken from a real application to survey data which is challenging (a 5-item scale with an 11-point rating scale, and three latent classes). Additional data conditions (e.g., long tests, a reduced number of response categories, and a simple latent mixture) were included in this simulation study to improve the generalizability of the results. Under this challenging data condition, for each model, data were generated based on varying sample sizes (from 500 to 5,000 observations with a 500-step). For the additional conditions, only three sample sizes (consisting of 1,000, 2,500, and 4,500 observations) were examined. The effect of sample size on estimation problems and accuracy of parameter and standard error estimates were evaluated. Results show that the two mixed IRT models require at least 2,500 observations to provide accurate parameter and standard error estimates under the challenging data condition. The rmGPCM produces more estimation problems than the more parsimonious mPCM, mostly because of the sparse tables arising due to many response categories. These models exhibit similar trends of estimation accuracy across sample sizes. Under the additional conditions, no estimation problems are observed. Both models perform well with a smaller sample size when long tests were used or a true latent mixture includes two classes. For model selection, the AIC3 and the SABIC are the most reliable information criteria.

Project description:IntroductionExtrapolation of time-to-event data from clinical trials is commonly used in decision models for health technology assessment (HTA). The objective of this study was to assess performance of standard parametric survival analysis techniques for extrapolation of time-to-event data for a single event from clinical trials with limited data due to small samples or short follow-up.MethodsSimulated populations with 50,000 individuals were generated with an exponential hazard rate for the event of interest. A scenario consisted of 5000 repetitions with six sample size groups (30-500 patients) artificially censored after every 10% of events observed. Goodness-of-fit statistics (AIC, BIC) were used to determine the best-fitting among standard parametric distributions (exponential, Weibull, log-normal, log-logistic, generalized gamma, Gompertz). Median survival, one-year survival probability, time horizon (1% survival time, or 99th percentile of survival distribution) and restricted mean survival time (RMST) were compared to population values to assess coverage and error (e.g., mean absolute percentage error).ResultsThe true exponential distribution was correctly identified using goodness-of-fit according to BIC more frequently compared to AIC (average 92% vs 68%). Under-coverage and large errors were observed for all outcomes when distributions were specified by AIC and for time horizon and RMST with BIC. Error in point estimates were found to be strongly associated with sample size and completeness of follow-up. Small samples produced larger average error, even with complete follow-up, than large samples with short follow-up. Correctly specifying the event distribution reduced magnitude of error in larger samples but not in smaller samples.ConclusionsLimited clinical data from small samples, or short follow-up of large samples, produce large error in estimates relevant to HTA regardless of whether the correct distribution is specified. The associated uncertainty in estimated parameters may not capture the true population values. Decision models that base lifetime time horizon on the model's extrapolated output are not likely to reliably estimate mean survival or its uncertainty. For data with an exponential event distribution, BIC more reliably identified the true distribution than AIC. These findings have important implications for health decision modelling and HTA of novel therapies seeking approval with limited evidence.

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A simulation study of sample size for DNA barcoding.

Publications

A simulation study of sample size for DNA barcoding.

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