ArticleGenetic epidemiology2011
Efficient study design for next generation sequencing.
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 23 papers.
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Who cites it
23 citing papers in PubMed.
- Towards density-optimal DNA storage with practical bijective coding.Nature communications · 2026Article
- Effects of gintonin-enriched fraction on hippocampal gene expressions.Integrative medicine research · 2021Article
- Sub-multiplicative interaction between polygenic risk score and household coal use in relation to lung adenocarcinoma among never-smoking women in Asia.Environment international · 2021Article
- The effects of taxonomy, diet, and ecology on the microbiota of riverine macroinvertebrates.Ecology and evolution · 2020Article
- Targeted insertional mutagenesis libraries for deep domain insertion profiling.Nucleic acids research · 2020Article
- Bioinformatics Strategies, Challenges, and Opportunities for Next Generation Sequencing-Based HLA Genotyping.Transfusion medicine and hemotherapy : offizielles Organ der Deutschen Gesellschaft fur Transfusionsmedizin und Immunhamatologie · 2019Review
- Selection Has Countered High Mutability to Preserve the Ancestral Copy Number of Y Chromosome Amplicons in Diverse Human Lineages.American journal of human genetics · 2018Article
- A method for allocating low-coverage sequencing resources by targeting haplotypes rather than individuals.Genetics, selection, evolution : GSE · 2017Article
- Initiating maize pre-breeding programs using genomic selection to harness polygenic variation from landrace populations.BMC genomics · 2016Article
- On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative reads.Methods (San Diego, Calif.) · 2015Article
- Potential of genotyping-by-sequencing for genomic selection in livestock populations.Genetics, selection, evolution : GSE · 2015Article
- Sequencing depth and coverage: key considerations in genomic analyses.Nature reviews. Genetics · 2014Review
- Next Generation Statistical Genetics: Modeling, Penalization, and Optimization in High-Dimensional Data.Annual review of statistics and its application · 2014Article
- Haplotype kernel association test as a powerful method to identify chromosomal regions harboring uncommon causal variants.Genetic epidemiology · 2013Article
- Single Nucleotide Polymorphism (SNP) Detection and Genotype Calling from Massively Parallel Sequencing (MPS) Data.Statistics in biosciences · 2013Article
- One thousand genomes imputation in the National Cancer Institute Breast and Prostate Cancer Cohort Consortium aggressive prostate cancer genome-wide association study.The Prostate · 2013Article
- AbCD: arbitrary coverage design for sequencing-based genetic studies.Bioinformatics (Oxford, England) · 2013Article
- Genotype imputation via matrix completion.Genome research · 2013Article
- Re-ranking sequencing variants in the post-GWAS era for accurate causal variant identification.PLoS genetics · 2013Article
- Rapid whole-genome sequencing for genetic disease diagnosis in neonatal intensive care units.Science translational medicine · 2012Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
Next Generation Sequencing represents a powerful tool for detecting genetic variation associated with human disease. Because of the high cost of this technology, it is critical that we develop efficient study designs that consider the trade-off between the number of subjects (n) and the coverage depth (µ). How we divide our resources between the two can greatly impact study success, particularly in pilot studies. We propose a strategy for selecting the optimal combination of n and µ for studies aimed at detecting rare variants and for studies aimed at detecting associations between rare or uncommon variants and disease. For detecting rare variants, we find the optimal coverage depth to be between 2 and 8 reads when using the likelihood ratio test. For association studies, we find the strategy of sequencing all available subjects to be preferable. In deriving these combinations, we provide a detailed analysis describing the distribution of depth across a genome and the depth needed to identify a minor allele in an individual. The optimal coverage depth depends on the aims of the study, and the chosen depth can have a large impact on study success.
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