ArticleG3 (Bethesda, Md.)2017
Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders.
Article in G3 (Bethesda, Md.), 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
What it found
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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.
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
20 citing papers in PubMed.
- A Locus on Chromosome 15 Contributes to Acute Ozone-induced Lung Injury in Collaborative Cross Mice.American journal of respiratory cell and molecular biology · 2022Article
- Intermittent fasting and caloric restriction interact with genetics to shape physiological health in mice.Genetics · 2022Article
- Human-relevant mechanisms and risk factors for TAK-875-Induced liver injury identified via a gene pathway-based approach in Collaborative Cross mice.Toxicology · 2021Article
- Know Your Model: Why mouse inbred strain contribution matters.Lab animal · 2020Article
- Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation.PLoS genetics · 2020Article
- Identification of Candidate Risk Factor Genes for Human Idelalisib Toxicity Using a Collaborative Cross Approach.Toxicological sciences : an official journal of the Society of Toxicology · 2019Article
- A Diallel of the Mouse Collaborative Cross Founders Reveals Strong Strain-Specific Maternal Effects on Litter Size.G3 (Bethesda, Md.) · 2019Article
- Whole Genome Sequencing and Progress Toward Full Inbreeding of the Mouse Collaborative Cross Population.G3 (Bethesda, Md.) · 2019Article
- R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations.Genetics · 2019Article
- Reciprocal F1 Hybrids of Two Inbred Mouse Strains Reveal Parent-of-Origin and Perinatal Diet Effects on Behavior and Expression.G3 (Bethesda, Md.) · 2018Article
- Giving the Genes a Shuffle: Using Natural Variation to Understand Host Genetic Contributions to Viral Infections.Trends in genetics : TIG · 2018Review
- Bayesian Diallel Analysis RevealsG3 (Bethesda, Md.) · 2018Article
- Advancing chemical risk assessment decision-making with population variability data: challenges and opportunities.Mammalian genome : official journal of the International Mammalian Genome Society · 2018Article
- Back to the Future: Multiparent Populations Provide the Key to Unlocking the Genetic Basis of Complex Traits.G3 (Bethesda, Md.) · 2017Article
- Oas1b-dependent Immune Transcriptional Profiles of West Nile Virus Infection in the Collaborative Cross.G3 (Bethesda, Md.) · 2017Article
- Allelic Variation in the Toll-Like Receptor Adaptor ProteinG3 (Bethesda, Md.) · 2017Article
- Inbred Strain Variant Database (ISVdb): A Repository for Probabilistically Informed Sequence Differences Among the Collaborative Cross Strains and Their Founders.G3 (Bethesda, Md.) · 2017Article
- Genomes of the Mouse Collaborative Cross.Genetics · 2017Article
- Male Infertility Is Responsible for Nearly Half of the Extinction Observed in the Mouse Collaborative Cross.Genetics · 2017Article
- Back to the Future: Multiparent Populations Provide the Key to Unlocking the Genetic Basis of Complex Traits.Genetics · 2017Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
The Collaborative Cross (CC) is a panel of recently established multiparental recombinant inbred mouse strains. For the CC, as for any multiparental population (MPP), effective experimental design and analysis benefit from detailed knowledge of the genetic differences between strains. Such differences can be directly determined by sequencing, but until now whole-genome sequencing was not publicly available for individual CC strains. An alternative and complementary approach is to infer genetic differences by combining two pieces of information: probabilistic estimates of the CC haplotype mosaic from a custom genotyping array, and probabilistic variant calls from sequencing of the CC founders. The computation for this inference, especially when performed genome-wide, can be intricate and time-consuming, requiring the researcher to generate nontrivial and potentially error-prone scripts. To provide standardized, easy-to-access CC sequence information, we have developed the Inbred Strain Variant Database (ISVdb). The ISVdb provides, for all the exonic variants from the Sanger Institute mouse sequencing dataset, direct sequence information for CC founders and, critically, the imputed sequence information for CC strains. Notably, the ISVdb also: (1) provides predicted variant consequence metadata; (2) allows rapid simulation of F1 populations; and (3) preserves imputation uncertainty, which will allow imputed data to be refined in the future as additional sequencing and genotyping data are collected. The ISVdb information is housed in an SQL database and is easily accessible through a custom online interface (http://isvdb.unc.edu), reducing the analytic burden on any researcher using the CC.
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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.