ArticleGenome research2010
Estimating population genetic parameters and comparing model goodness-of-fit using DNA sequences with error.
Article in Genome research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
12 citing papers in PubMed, 16 citations in OpenAlex.
- Article
- Bridgehead effect and multiple introductions shape the global invasion history of a termite.Communications biology · 2021Article
- Properties of Samples With Segregating Polymerase Chain Reaction (PCR) Dropout Mutations Within a Species.Evolutionary bioinformatics online · 2019Article
- Efficiency of ddRAD target enriched sequencing across spiny rock lobster species (Palinuridae: Jasus).Scientific reports · 2017Article
- Population genetic studies in the genomic sequencing era.Dong wu xue yan jiu = Zoological research · 2015Review
- Exploring population size changes using SNP frequency spectra.Nature genetics · 2015Article
- Characterizing bias in population genetic inferences from low-coverage sequencing data.Molecular biology and evolution · 2014Article
- Article
- Calculation of Tajima's D and other neutrality test statistics from low depth next-generation sequencing data.BMC bioinformatics · 2013Article
- jPopGen Suite: population genetic analysis of DNA polymorphism from nucleotide sequences with errors.Methods in ecology and evolution · 2012Article
- Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster.PloS one · 2012Article
- Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 1 country.
Funding
Abstract
It is known that sequencing error can bias estimation of evolutionary or population genetic parameters. This problem is more prominent in deep resequencing studies because of their large sample size n, and a higher probability of error at each nucleotide site. We propose a new method based on the composite likelihood of the observed SNP configurations to infer population mutation rate theta = 4N(e)micro, population exponential growth rate R, and error rate epsilon, simultaneously. Using simulation, we show the combined effects of the parameters, theta, n, epsilon, and R on the accuracy of parameter estimation. We compared our maximum composite likelihood estimator (MCLE) of theta with other theta estimators that take into account the error. The results show the MCLE performs well when the sample size is large or the error rate is high. Using parametric bootstrap, composite likelihood can also be used as a statistic for testing the model goodness-of-fit of the observed DNA sequences. The MCLE method is applied to sequence data on the ANGPTL4 gene in 1832 African American and 1045 European American individuals.
Indexed as
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What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.