ArticleBMC bioinformatics2011
Statistical mutation calling from sequenced overlapping DNA pools in TILLING experiments.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Unraveling the role of Cullin3 of E3 ubiquitin ligase in salt stress tolerance via proteomics.BMC plant biology · 2025Article
- Combining Genome and Gene Co-expression Network Analyses for the Identification of Genes Potentially Regulating Salt Tolerance in Rice.Frontiers in plant science · 2021Article
- Accurate, Efficient and User-Friendly Mutation Calling and Sample Identification for TILLING Experiments.Frontiers in genetics · 2021Article
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- Article
- Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress.Genes · 2019Article
- Genome-wide association study for salinity tolerance at the flowering stage in a panel of rice accessions from Thailand.BMC genomics · 2019Article
- A highly mutagenised barley (Plant methods · 2019Article
- Two-State Co-Expression Network Analysis to Identify Genes Related to Salt Tolerance in Thai rice.Genes · 2018Article
- Rapid identification and recovery of ENU-induced mutations with next-generation sequencing and Paired-End Low-Error analysis.BMC genomics · 2015Article
- Discovery of rare mutations in extensively pooled DNA samples using multiple target enrichment.Plant biotechnology journal · 2014Article
- A labor- and cost-effective non-optical semiconductor (Ion Torrent) next-generation sequencing of the SLC12A3 and CLCNKA/B genes in Gitelman's syndrome patients.Journal of human genetics · 2014Article
- A two-dimensional pooling strategy for rare variant detection on next-generation sequencing platforms.PloS one · 2014Article
- Production of a high-efficiency TILLING population through polyploidization.Plant physiology · 2013Article
- Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA.PloS one · 2013Article
- Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing.BMC genomics · 2012Article
- The quest for rare variants: pooled multiplexed next generation sequencing in plants.Frontiers in plant science · 2012Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTILLING (Targeting induced local lesions IN genomes) is an efficient reverse genetics approach for detecting induced mutations in pools of individuals. Combined with the high-throughput of next-generation sequencing technologies, and the resolving power of overlapping pool design, TILLING provides an efficient and economical platform for functional genomics across thousands of organisms.
resultsWe propose a probabilistic method for calling TILLING-induced mutations, and their carriers, from high throughput sequencing data of overlapping population pools, where each individual occurs in two pools. We assign a probability score to each sequence position by applying Bayes' Theorem to a simplified binomial model of sequencing error and expected mutations, taking into account the coverage level. We test the performance of our method on variable quality, high-throughput sequences from wheat and rice mutagenized populations.
conclusionsWe show that our method effectively discovers mutations in large populations with sensitivity of 92.5% and specificity of 99.8%. It also outperforms existing SNP detection methods in detecting real mutations, especially at higher levels of coverage variability across sequenced pools, and in lower quality short reads sequence data. The implementation of our method is available from: http://www.cs.ucdavis.edu/filkov/CAMBa/.
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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.