The DOI matches its Crossref record; 12 of the 12 references it cites were found in a registry or an index.
The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples
Open accessAbstract
Next generation sequencing (NGS) is about to revolutionize genetic analysis. Currently NGS techniques are mainly used to sequence individual genomes. Due to the high sequence coverage required, the costs for population-scale analyses are still too high to allow an extension to nonmodel organisms. Here, we show that NGS of pools of individuals is often more effective in SNP discovery and provides more accurate allele frequency estimates, even when taking sequencing errors into account. We modify the population genetic estimators Tajima's π and Watterson's θ to obtain unbiased estimates from NGS pooling data. Given the same sequencing effort, the resulting estimators often show a better performance than those obtained from individual sequencing. Although our analysis also shows that NGS of pools of individuals will not be preferable under all circumstances, it provides a cost-effective approach to estimate allele frequencies on a genome-wide scale.
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Cites
Generating samples under a Wright–Fisher neutral model of genetic variation
Hudson, R. R. (2002) · Bioinformatics · doi:10.1093/bioinformatics/18.2.337 · Cited by 2,364
SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries
Van Tassell, C. P., Smith, T. P. L., Matukumalli, L. K., Taylor, J. F., Schnabel, R. D., Lawley, C. T., Haudenschild, C. D., Moore, S. S., Warren, W. C., & Sonstegard, T. S. (2008) · Nature Methods · doi:10.1038/nmeth.1185 · Cited by 631
DNA Pooling: a tool for large-scale association studies
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DNA Sudoku—harnessing high-throughput sequencing for multiplexed specimen analysis
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Lynch, M. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn185 · Cited by 122
Estimation of Allele Frequencies From High-Coverage Genome-Sequencing Projects
Lynch, M. (2009) · Genetics · doi:10.1534/genetics.109.100479 · Cited by 104
Testing for Neutrality in Samples With Sequencing Errors
Achaz, G. (2008) · Genetics · doi:10.1534/genetics.107.082198 · Cited by 89
An analysis of strategies for discovery of single-nucleotide polymorphisms
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Recurrent Positive Selection of the Drosophila Hybrid Incompatibility Gene Hmr
Maheshwari, S., Wang, J., & Barbash, D. A. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn190 · Cited by 45
Population Genetic Inference From Resequencing Data
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Self-citationTørresen, O. K., Star, B., Mier, P., Andrade-Navarro, M. A., Bateman, A., Jarnot, P., Gruca, A., Grynberg, M., Kajava, A. V., Promponas, V. J., et al. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz841 · Cited by 347
Gautier, M., Gharbi, K., Cezard, T., Foucaud, J., Kerdelhué, C., Pudlo, P., Cornuet, J., & Estoup, A. (2013) · Molecular Ecology · doi:10.1111/mec.12089 · Cited by 288
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Metadata
- Authors
- Futschik, A., & Schlötterer, C.
- Venue
- Genetics
- Publisher
- Oxford University Press (OUP)
- Published
- 2010-09-01
- Volume
- 186
- Issue
- 1
- Pages
- 207-218
- ISSN
- 0016-6731 (ISSN-L)
- 1943-2631
- OpenAlex
- W2133372013
- Cited by
- 373
- References
- 12
- FWCI
- 10.40
- Type
- journal article
- Language
- en
- Open access
- bronze
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Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
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