ArticleBMC genomics2013
Estimating DNA polymorphism from next generation sequencing data with high error rate by dual sequencing applications.
Article in BMC genomics, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- Whole-genome sequencing to identify rare variants in East Asian patients with dementia with Lewy bodies.npj aging · 2024Article
- Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping inInternational journal of molecular sciences · 2024Article
- Estimating the Genome-wide Mutation Rate with Three-Way Identity by Descent.American journal of human genetics · 2019Article
- Pronounced genetic differentiation and recent secondary contact in the mangrove tree Lumnitzera racemosa revealed by population genomic analyses.Scientific reports · 2016Article
- Leveraging Distant Relatedness to Quantify Human Mutation and Gene-Conversion Rates.American journal of human genetics · 2015Article
- Article
- Development and Validation of EST-SSR Markers from the Transcriptome of Adzuki Bean (Vigna angularis).PloS one · 2015Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAs the error rate is high and the distribution of errors across sites is non-uniform in next generation sequencing (NGS) data, it has been a challenge to estimate DNA polymorphism (θ) accurately from NGS data.
resultsBy computer simulations, we compare the two methods of data acquisition - sequencing each diploid individual separately and sequencing the pooled sample. Under the current NGS error rate, sequencing each individual separately offers little advantage unless the coverage per individual is high (>20X). We hence propose a new method for estimating θ from pooled samples that have been subjected to two separate rounds of DNA sequencing. Since errors from the two sequencing applications are usually non-overlapping, it is possible to separate low frequency polymorphisms from sequencing errors. Simulation results show that the dual applications method is reliable even when the error rate is high and θ is low.
conclusionsIn studies of natural populations where the sequencing coverage is usually modest (~2X per individual), the dual applications method on pooled samples should be a reasonable choice.
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