ArticleBMC bioinformatics2012
High-resolution genetic mapping with pooled sequencing.
Article in BMC bioinformatics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers.
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Who cites it
36 citing papers in PubMed, 76 citations in OpenAlex.
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- Variation in ubiquitin system genes creates substrate-specific effects on proteasomal protein degradation.eLife · 2022Article
- Polygenic Analysis of Tolerance to Carbon Dioxide Inhibition of Isoamyl Acetate "Banana" Flavor Production in Yeast RevealsApplied and environmental microbiology · 2022Article
- A combinatorial strategy to identify various types of QTLs for quantitative traits using extreme phenotype individuals in an FPlant communications · 2022Article
- High-throughput estimation of allele frequencies using combined pooled-population sequencing and haplotype-based data processing.Plant methods · 2022Article
- Harnessing the potential of bulk segregant analysis sequencing and its related approaches in crop breeding.Frontiers in genetics · 2022Review
- Restoring fertility in yeast hybrids: Breeding and quantitative genetics of beneficial traits.Proceedings of the National Academy of Sciences of the United States of America · 2021Article
- A combined BSA-Seq and linkage mapping approach identifies genomic regions associated with Phytophthora root and crown rot resistance in squash.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Article
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- A natural variant of the essential host geneeLife · 2020Article
- Genetic background mutations drive neural circuit hyperconnectivity in a fragile X syndrome model.BMC biology · 2020Article
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- QTL analysis reveals genomic variants linked to high-temperature fermentation performance in the industrial yeast.Biotechnology for biofuels · 2019Article
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- Genome-Wide Screen forG3 (Bethesda, Md.) · 2018Article
- Deciphering the Genic Basis of Yeast Fitness Variation by Simultaneous Forward and Reverse Genetics.Molecular biology and evolution · 2017Article
- Rapid identification of genes controlling virulence and immunity in malaria parasites.PLoS pathogens · 2017Article
Corrections and comments
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundModern genetics has been transformed by high-throughput sequencing. New experimental designs in model organisms involve analyzing many individuals, pooled and sequenced in groups for increased efficiency. However, the uncertainty from pooling and the challenge of noisy sequencing data demand advanced computational methods.
resultsWe present MULTIPOOL, a computational method for genetic mapping in model organism crosses that are analyzed by pooled genotyping. Unlike other methods for the analysis of pooled sequence data, we simultaneously consider information from all linked chromosomal markers when estimating the location of a causal variant. Our use of informative sequencing reads is formulated as a discrete dynamic Bayesian network, which we extend with a continuous approximation that allows for rapid inference without a dependence on the pool size. MULTIPOOL generalizes to include biological replicates and case-only or case-control designs for binary and quantitative traits.
conclusionsOur increased information sharing and principled inclusion of relevant error sources improve resolution and accuracy when compared to existing methods, localizing associations to single genes in several cases. MULTIPOOL is freely available at http://cgs.csail.mit.edu/multipool/.
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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.