ArticleGenetics, selection, evolution : GSE2012
Estimating the effect of SNP genotype on quantitative traits from pooled DNA samples.
Article in Genetics, selection, evolution : GSE, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed, 23 citations in OpenAlex.
- Pooled DNA sequencing in hairy vetch (Frontiers in plant science · 2024Article
- Using pooled data for genomic prediction in a bivariate framework with missing data.Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie · 2022Article
- Use of DNA pools of a reference population for genomic selection of a binary trait in Atlantic salmon.Frontiers in genetics · 2022Article
- In silico validation of pooled genotyping strategies for genomic evaluation in Angus cattle.Journal of animal science · 2020Article
- Genomic prediction using pooled data in a single-step genomic best linear unbiased prediction framework.Journal of animal science · 2020Article
- Pooled genotyping strategies for the rapid construction of genomic reference populations1.Journal of animal science · 2019Article
- Considerations for Maintaining Family Diversity in Commercially Mass-Spawned Penaeid Shrimp: A Case Study onFrontiers in genetics · 2019Article
- The State of "Frontiers in genetics · 2018Review
- Estimating the genetic merit of sires by using pooled DNA from progeny of undetermined pedigree.Genetics, selection, evolution : GSE · 2017Article
- Single Nucleotide Polymorphism Discovery in Bovine Pituitary Gland Using RNA-Seq Technology.PloS one · 2016Article
- Machine learning approach for pooled DNA sample calibration.BMC bioinformatics · 2015Article
- Quantitative analysis of low-density SNP data for parentage assignment and estimation of family contributions to pooled samples.Genetics, selection, evolution : GSE · 2014Article
- Evidence for positive selection of taurine genes within a QTL region on chromosome X associated with testicular size in Australian Brahman cattle.BMC genetics · 2014Article
- RNA-seq analysis of single bovine blastocysts.BMC genomics · 2013Article
Corrections and comments
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundStudies to detect associations between DNA markers and traits of interest in humans and livestock benefit from increasing the number of individuals genotyped. Performing association studies on pooled DNA samples can provide greater power for a given cost. For quantitative traits, the effect of an SNP is measured in the units of the trait and here we propose and demonstrate a method to estimate SNP effects on quantitative traits from pooled DNA data.
methodsTo obtain estimates of SNP effects from pooled DNA samples, we used logistic regression of estimated allele frequencies in pools on phenotype. The method was tested on a simulated dataset, and a beef cattle dataset using a model that included principal components from a genomic correlation matrix derived from the allele frequencies estimated from the pooled samples. The performance of the obtained estimates was evaluated by comparison with estimates obtained using regression of phenotype on genotype from individual samples of DNA.
resultsFor the simulated data, the estimates of SNP effects from pooled DNA are similar but asymptotically different to those from individual DNA data. Error in estimating allele frequencies had a large effect on the accuracy of estimated SNP effects. For the beef cattle dataset, the principal components of the genomic correlation matrix from pooled DNA were consistent with known breed groups, and could be used to account for population stratification. Correctly modeling the contemporary group structure was essential to achieve estimates similar to those from individual DNA data, and pooling DNA from individuals within groups was superior to pooling DNA across groups. For a fixed number of assays, pooled DNA samples produced results that were more correlated with results from individual genotyping data than were results from one random individual assayed from each pool.
conclusionsUse of logistic regression of allele frequency on phenotype makes it possible to estimate SNP effects on quantitative traits from pooled DNA samples. With pooled DNA samples, genotyping costs are reduced, and in cases where trait records are abundant this approach is promising to obtain SNP associations for marker-assisted selection.
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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.