ArticleTheScientificWorldJournal2013
Evaluation of allele frequency estimation using pooled sequencing data simulation.
Article in TheScientificWorldJournal, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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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
14 citing papers in PubMed.
- Biostatistical Aspects of Whole Genome Sequencing Studies: Preprocessing and Quality Control.Biometrical journal. Biometrische Zeitschrift · 2024Article
- Comparing Pool-seq, Rapture, and GBS genotyping for inferring weak population structure: The American lobster (Ecology and evolution · 2019Article
- Allele balance bias identifies systematic genotyping errors and false disease associations.Human mutation · 2019Article
- Power and sample size calculations for high-throughput sequencing-based experiments.Briefings in bioinformatics · 2018Article
- Targeted sequencing of established and candidate colorectal cancer genes in the Colon Cancer Family Registry Cohort.Oncotarget · 2017Article
- The discrepancy among single nucleotide variants detected by DNA and RNA high throughput sequencing data.BMC genomics · 2017Article
- Multi-perspective quality control of Illumina RNA sequencing data analysis.Briefings in functional genomics · 2017Article
- Sequence analysis of pooled bacterial samples enables identification of strain variation in group A streptococcus.Scientific reports · 2017Article
- Evaluation of Quality Assessment Protocols for High Throughput Genome Resequencing Data.Frontiers in genetics · 2017Review
- Mitochondrial DNA heteroplasmy in the emerging field of massively parallel sequencing.Forensic science international. Genetics · 2015Review
- Alternative applications for distinct RNA sequencing strategies.Briefings in bioinformatics · 2015Article
- Three-stage quality control strategies for DNA re-sequencing data.Briefings in bioinformatics · 2014Review
- High-throughput sequencing in mitochondrial DNA research.Mitochondrion · 2014Review
- Statistical strategies for microRNAseq batch effect reduction.Translational cancer research · 2014Article
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
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.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.