ArticleBMC genomics2014
Estimating the information value of polymorphic sites using pooled sequences.
Article in BMC genomics, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.
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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
2 citing papers in PubMed.
Corrections and comments
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Authors and funding
1 author.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundHigh-throughput sequencing is a cost effective method for identifying genetic variation, and it is currently in use on a large scale across the field of biology, including ecology and population genetics. Correctly identifying variable sites and allele frequencies from sequencing data remains challenging, in large part due to artifacts and biases inherent in the sequencing process. Selecting variants that are diagnostic is commonly done using diversity statistics like FST, but these measures are not ideal for the task.
resultsHere, we develop a method that directly calculates the expected amount of information gained from observing each variant site. We then develop and implement a conservative estimator that takes into account uncertainity introduced by sampling bias and sequencing error. This estimator is applied to simulated and real sequencing data, and we discuss how it performs compared to the commonly used existing methods for identifying diagnostic polymorphisms.
conclusionThe expected information content gives an easy to interpret measure for the usefulness of variant sites. The results show that we achieve a clear separation between true variants and noise, allowing us to select candidate sites with a high degree of confidence.
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