ArticleGenetic epidemiology2011
On optimal pooling designs to identify rare variants through massive resequencing.
Article in Genetic epidemiology, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
13 citing papers in PubMed.
- A permutation test for oligoset DNA pooling studies.PloS one · 2015Article
- Design of DNA pooling to allow incorporation of covariates in rare variants analysis.PloS one · 2014Article
- Two-phase and family-based designs for next-generation sequencing studies.Frontiers in genetics · 2013Review
- eALPS: estimating abundance levels in pooled sequencing using available genotyping data.Journal of computational biology : a journal of computational molecular cell biology · 2013Article
- On Estimation of Allele Frequencies via Next-Generation DNA Resequencing with Barcoding.Statistics in biosciences · 2013Article
- Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data.Statistics in biosciences · 2013Article
- A unified approach for allele frequency estimation, SNP detection and association studies based on pooled sequencing data using EM algorithms.BMC genomics · 2013Article
- Article
- Rare variant discovery and calling by sequencing pooled samples with overlaps.Bioinformatics (Oxford, England) · 2013Article
- Analysis and optimal design for association studies using next-generation sequencing with case-control pools.Genetic epidemiology · 2012Article
- Detecting selective sweeps from pooled next-generation sequencing samples.Molecular biology and evolution · 2012Article
- Biases and errors on allele frequency estimation and disease association tests of next-generation sequencing of pooled samples.Genetic epidemiology · 2012Article
- SNVer: a statistical tool for variant calling in analysis of pooled or individual next-generation sequencing data.Nucleic acids research · 2011Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The advent of next-generation sequencing technologies has facilitated the detection of rare variants. Despite the significant cost reduction, sequencing cost is still high for large-scale studies. In this article, we examine DNA pooling as a cost-effective strategy for rare variant detection. We consider the optimal number of individuals in a DNA pool to detect an allele with a specific minor allele frequency (MAF) under a given coverage depth and detection threshold. We found that the optimal number of individuals in a pool is indifferent to the MAF at the same coverage depth and detection threshold. In addition, when the individual contributions to each pool are equal, the total number of individuals across different pools required in an optimal design to detect a variant with a desired power is similar at different coverage depths. When the contributions are more variable, more individuals tend to be needed for higher coverage depths. Our study provides general guidelines on using DNA pooling for more cost-effective identifications of rare variants.
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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.