ArticleInternational journal of computational biology and drug design2013
An evaluation of allele frequency estimation accuracy using pooled sequencing data.
Article in International journal of computational biology and drug design, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.
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Who cites it
5 citing papers in PubMed.
- High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing.Plant methods · 2022Article
- Multi-perspective quality control of Illumina RNA sequencing data analysis.Briefings in functional genomics · 2017Article
- Comprehensive evaluation of extracellular small RNA isolation methods from serum in high throughput sequencing.BMC genomics · 2017Article
- Expression profile and gene age jointly shaped the genome-wide distribution of premature termination codons in a Drosophila melanogaster population.Molecular biology and evolution · 2015Article
- Statistical strategies for microRNAseq batch effect reduction.Translational cancer research · 2014Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Next generation sequencing technology has matured, and with its current affordability, will replace the SNP chip as the genotyping tool of choice. Even with the current affordability of NGS, large scale studies will require careful study design to reduce cost. In this study, we designed an experiment to assess the accuracy of allele frequency estimated from pooled sequencing data. We compared the allele frequency estimated from sequencing data with the allele frequency estimated from individual SNP chip data and observed high correlations between them. However, by calculating error rate, we found that many SNPs had their allele frequency estimated from sequencing data significantly different from allele frequency estimated from SNP chip data. In conclusion, we found correlation is not an ideal measurement for comparing allele frequencies. And for the purpose of estimating allele frequency, we do not recommend using pooling with NGS as a cheaper alternative to genotype each sample individually.
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Registered trials
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