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

Research output: Contribution to journalArticlepeer-review

4 Citations (Scopus)

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.

Original languageEnglish
Pages (from-to)279-293
Number of pages15
JournalInternational Journal of Computational Biology and Drug Design
Volume6
Issue number4
DOIs
Publication statusPublished - 2013

All Science Journal Classification (ASJC) codes

  • Drug Discovery
  • Computer Science Applications

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