Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation
Joint Authors
Shyr, Yu
Samuels, David C.
Li, Jiang
Clark, Travis
Li, Chung-I
Guo, Yan
Source
Issue
Vol. 2013, Issue 2013 (31 Dec. 2013), pp.1-9, 9 p.
Publisher
Hindawi Publishing Corporation
Publication Date
2013-02-07
Country of Publication
Egypt
No. of Pages
9
Main Subjects
Medicine
Information Technology and Computer Science
Abstract EN
Next-generation sequencing (NGS) technology has provided researchers with opportunities to study the genome in unprecedented detail.
In particular, NGS is applied to disease association studies.
Unlike genotyping chips, NGS is not limited to a fixed set of SNPs.
Prices for NGS are now comparable to the SNP chip, although for large studies the cost can be substantial.
Pooling techniques are often used to reduce the overall cost of large-scale studies.
In this study, we designed a rigorous simulation model to test the practicability of estimating allele frequency from pooled sequencing data.
We took crucial factors into consideration, including pool size, overall depth, average depth per sample, pooling variation, and sampling variation.
We used real data to demonstrate and measure reference allele preference in DNAseq data and implemented this bias in our simulation model.
We found that pooled sequencing data can introduce high levels of relative error rate (defined as error rate divided by targeted allele frequency) and that the error rate is more severe for low minor allele frequency SNPs than for high minor allele frequency SNPs.
In order to overcome the error introduced by pooling, we recommend a large pool size and high average depth per sample.
American Psychological Association (APA)
Guo, Yan& Samuels, David C.& Li, Jiang& Clark, Travis& Li, Chung-I& Shyr, Yu. 2013. Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation. The Scientific World Journal،Vol. 2013, no. 2013, pp.1-9.
https://search.emarefa.net/detail/BIM-1033411
Modern Language Association (MLA)
Guo, Yan…[et al.]. Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation. The Scientific World Journal No. 2013 (2013), pp.1-9.
https://search.emarefa.net/detail/BIM-1033411
American Medical Association (AMA)
Guo, Yan& Samuels, David C.& Li, Jiang& Clark, Travis& Li, Chung-I& Shyr, Yu. Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation. The Scientific World Journal. 2013. Vol. 2013, no. 2013, pp.1-9.
https://search.emarefa.net/detail/BIM-1033411
Data Type
Journal Articles
Language
English
Notes
Includes bibliographical references
Record ID
BIM-1033411