An evaluation of allele frequency estimation accuracy using pooled sequencing data

Yan Guo, Qiuyin Cai, Chun Li, Jiang Li, Chung I. Li, Regina Courtney, Wei Zheng, Jirong Long

研究成果: Article同行評審

4 引文 斯高帕斯(Scopus)

摘要

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.

原文English
頁(從 - 到)279-293
頁數15
期刊International Journal of Computational Biology and Drug Design
6
發行號4
DOIs
出版狀態Published - 2013

All Science Journal Classification (ASJC) codes

  • 藥物發現
  • 電腦科學應用

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