ArticleGenetic epidemiology2010
Design of association studies with pooled or un-pooled next-generation sequencing data.
Article in Genetic epidemiology, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 49 papers.
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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.
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Who cites it
49 citing papers in PubMed.
- Evaluation of nine statistics to identify QTLs in bulk segregant analysis using next generation sequencing approaches.BMC genomics · 2022Article
- Establishment and Characterization of a Cell Line (S-RMS1) Derived from an Infantile Spindle Cell Rhabdomyosarcoma withInternational journal of molecular sciences · 2021Article
- Developmental plasticity shapes social traits and selection in a facultatively eusocial bee.Proceedings of the National Academy of Sciences of the United States of America · 2020Article
- The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments.Journal of animal science and biotechnology · 2019Article
- Advances in the genome-wide association study of chronic hepatitis B susceptibility in Asian population.European journal of medical research · 2017Review
- Genome-wide analysis of ivermectin response by Onchocerca volvulus reveals that genetic drift and soft selective sweeps contribute to loss of drug sensitivity.PLoS neglected tropical diseases · 2017Article
- Identification of Sex-determining Loci in Pacific White Shrimp Litopeneaus vannamei Using Linkage and Association Analysis.Marine biotechnology (New York, N.Y.) · 2017Article
- Bulked sample analysis in genetics, genomics and crop improvement.Plant biotechnology journal · 2016Review
- Wham: Identifying Structural Variants of Biological Consequence.PLoS computational biology · 2015Article
- Likelihood-based complex trait association testing for arbitrary depth sequencing data.Bioinformatics (Oxford, England) · 2015Article
- Fast imputation using medium or low-coverage sequence data.BMC genetics · 2015Article
- On the design and analysis of next-generation sequencing genotyping for a cohort with haplotype-informative reads.Methods (San Diego, Calif.) · 2015Article
- Fast and accurate site frequency spectrum estimation from low coverage sequence data.Bioinformatics (Oxford, England) · 2015Article
- Fast individual ancestry inference from DNA sequence data leveraging allele frequencies for multiple populations.BMC bioinformatics · 2015Article
- Article
- A Scale-Corrected Comparison of Linkage Disequilibrium Levels between Genic and Non-Genic Regions.PloS one · 2015Article
- Use of a targeted, combinatorial next-generation sequencing approach for the study of bicuspid aortic valve.BMC medical genomics · 2014Article
- Genome-wide estimation of linkage disequilibrium from population-level high-throughput sequencing data.Genetics · 2014Article
- A stepwise likelihood ratio test procedure for rare variant selection in case-control studies.Journal of human genetics · 2014Article
- A survey of tools for variant analysis of next-generation genome sequencing data.Briefings in bioinformatics · 2014Article
Corrections and comments
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Authors and funding
9 authors.
Funding
Abstract
Most common hereditary diseases in humans are complex and multifactorial. Large-scale genome-wide association studies based on SNP genotyping have only identified a small fraction of the heritable variation of these diseases. One explanation may be that many rare variants (a minor allele frequency, MAF <5%), which are not included in the common genotyping platforms, may contribute substantially to the genetic variation of these diseases. Next-generation sequencing, which would allow the analysis of rare variants, is now becoming so cheap that it provides a viable alternative to SNP genotyping. In this paper, we present cost-effective protocols for using next-generation sequencing in association mapping studies based on pooled and un-pooled samples, and identify optimal designs with respect to total number of individuals, number of individuals per pool, and the sequencing coverage. We perform a small empirical study to evaluate the pooling variance in a realistic setting where pooling is combined with exon-capturing. To test for associations, we develop a likelihood ratio statistic that accounts for the high error rate of next-generation sequencing data. We also perform extensive simulations to determine the power and accuracy of this method. Overall, our findings suggest that with a fixed cost, sequencing many individuals at a more shallow depth with larger pool size achieves higher power than sequencing a small number of individuals in higher depth with smaller pool size, even in the presence of high error rates. Our results provide guidelines for researchers who are developing association mapping studies based on next-generation sequencing.
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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.