ArticleGenome research2013
Estimating inbreeding coefficients from NGS data: Impact on genotype calling and allele frequency estimation.
Article in Genome research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
50 citing papers in PubMed.
- Tuberculosis Susceptibility and Inbreeding Depression HinderEvolutionary applications · 2026Article
- Unraveling genome- and immunome-wide genetic diversity in modern and historical Jaguars.Genome biology · 2025Article
- Must Epidemiologically Impactful Vector Control Interventions Disrupt Mosquito Population Structure? A Case Study of a Cluster-Randomised Controlled Trial.Evolutionary applications · 2025Article
- Contrasting Genomic Responses of Hydrothermal Vent Animals and Their Symbionts to Population Decline After the Hunga Volcanic Eruption.Molecular ecology · 2025Article
- Urban Life Shapes Genetic Diversity in the Green Anole, Anolis carolinensis.Molecular ecology · 2025Article
- Evolutionary history and seascape genomics of Harbour porpoises (Phocoena phocoena) across environmental gradients in the North Atlantic and adjacent waters.Molecular ecology resources · 2025Article
- Translocations spur population growth but fail to prevent genetic erosion in imperiled Florida Scrub-Jays.Current biology : CB · 2025Article
- Time-lagged genomic erosion and future environmental risks in a bird on the brink of extinction.Proceedings. Biological sciences · 2025Article
- Modeling Biases from Low-Pass Genome Sequencing to Enable Accurate Population Genetic Inferences.Molecular biology and evolution · 2025Article
- Evidence for gene flow from the Gulf of Mexico to the Atlantic Ocean in bonnethead sharks (Ecology and evolution · 2024Article
- Modeling biases from low-pass genome sequencing to enable accurate population genetic inferences.bioRxiv : the preprint server for biology · 2024Article
- Large variance in inbreeding within the Iberian wolf population.The Journal of heredity · 2024Article
- Cleave and Rescue gamete killers create conditions for gene drive in plants.Nature plants · 2024Article
- Signatures of adaptation at key insecticide resistance loci in Anopheles gambiae in Southern Ghana revealed by reduced-coverage WGS.Scientific reports · 2024Article
- Genomic signatures of climate adaptation in bank voles.Ecology and evolution · 2024Article
- Cleave and Rescue gamete killers create conditions for gene drive in plants.bioRxiv : the preprint server for biology · 2024Article
- Genetic and environmental drivers of migratory behavior in western burrowing owls and implications for conservation and management.Evolutionary applications · 2023Article
- Purging due to self-fertilization does not prevent accumulation of expansion load.PLoS genetics · 2023Article
- Genetic evidence of population subdivision among Masai giraffes separated by the Gregory Rift Valley in Tanzania.Ecology and evolution · 2023Article
- Moment estimators of relatedness from low-depth whole-genome sequencing data.BMC bioinformatics · 2022Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Most methods for next-generation sequencing (NGS) data analyses incorporate information regarding allele frequencies using the assumption of Hardy-Weinberg equilibrium (HWE) as a prior. However, many organisms including those that are domesticated, partially selfing, or with asexual life cycles show strong deviations from HWE. For such species, and specially for low-coverage data, it is necessary to obtain estimates of inbreeding coefficients (F) for each individual before calling genotypes. Here, we present two methods for estimating inbreeding coefficients from NGS data based on an expectation-maximization (EM) algorithm. We assess the impact of taking inbreeding into account when calling genotypes or estimating the site frequency spectrum (SFS), and demonstrate a marked increase in accuracy on low-coverage highly inbred samples. We demonstrate the applicability and efficacy of these methods in both simulated and real data sets.
Indexed as
Identifiers
What OpenQuestion holds
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.