ArticleGenetics2012
Imputation of single-nucleotide polymorphisms in inbred mice using local phylogeny.
Article in Genetics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 36 papers, 1 of them a synthesis that pooled it.
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
36 citing papers in PubMed, 1 synthesis or guideline pooled it, 44 citations in OpenAlex.
- GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis.Genome research · 2024Pooled it
- Celebrating discovery across the tree of life.G3 (Bethesda, Md.) · 2023Article
- Differences in Diurnal Rhythm of Rod Outer Segment Renewal between 129T2/SvEmsJ and C57BL/6J Mice.International journal of molecular sciences · 2022Article
- Genetic determinants of ammonia-induced acute lung injury in mice.American journal of physiology. Lung cellular and molecular physiology · 2021Article
- IMPUTOR: Phylogenetically Aware Software for Imputation of Errors in Next-Generation Sequencing.Genome biology and evolution · 2018Article
- Whole Genome Sequence of Two Wild-Derived Mus musculus domesticus Inbred Strains, LEWES/EiJ and ZALENDE/EiJ, with Different Diploid Numbers.G3 (Bethesda, Md.) · 2016Article
- Mouse genotypes drive the liver and adrenal gland clocks.Scientific reports · 2016Article
- Integration of genome-wide association and extant brain expression QTL identifies candidate genes influencing prepulse inhibition in inbred F1 mice.Genes, brain, and behavior · 2016Article
- Informatics resources for the Collaborative Cross and related mouse populations.Mammalian genome : official journal of the International Mammalian Genome Society · 2015Review
- MAGIC populations in crops: current status and future prospects.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2015Review
- Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides.BMC genomics · 2015Article
- Splicing landscape of the eight collaborative cross founder strains.BMC genomics · 2015Article
- Article
- Fine-mapping QTLs in advanced intercross lines and other outbred populations.Mammalian genome : official journal of the International Mammalian Genome Society · 2014Review
- A systems biology approach utilizing a mouse diversity panel identifies genetic differences influencing isoniazid-induced microvesicular steatosis.Toxicological sciences : an official journal of the Society of Toxicology · 2014Article
- The Collaborative Cross as a resource for modeling human disease: CC011/Unc, a new mouse model for spontaneous colitis.Mammalian genome : official journal of the International Mammalian Genome Society · 2014Article
- Searching for genomic region of high-fat diet-induced type 2 diabetes in mouse chromosome 2 by analysis of congenic strains.PloS one · 2014Article
- Article
- Impact of the environment on the skeleton: is it modulated by genetic factors?Current osteoporosis reports · 2013Review
- Functional genomic assessment of phosgene-induced acute lung injury in mice.American journal of respiratory cell and molecular biology · 2013Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
We present full-genome genotype imputations for 100 classical laboratory mouse strains, using a novel method. Using genotypes at 549,683 SNP loci obtained with the Mouse Diversity Array, we partitioned the genome of 100 mouse strains into 40,647 intervals that exhibit no evidence of historical recombination. For each of these intervals we inferred a local phylogenetic tree. We combined these data with 12 million loci with sequence variations recently discovered by whole-genome sequencing in a common subset of 12 classical laboratory strains. For each phylogenetic tree we identified strains sharing a leaf node with one or more of the sequenced strains. We then imputed high- and medium-confidence genotypes for each of 88 nonsequenced genomes. Among inbred strains, we imputed 92% of SNPs genome-wide, with 71% in high-confidence regions. Our method produced 977 million new genotypes with an estimated per-SNP error rate of 0.083% in high-confidence regions and 0.37% genome-wide. Our analysis identified which of the 88 nonsequenced strains would be the most informative for improving full-genome imputation, as well as which additional strain sequences will reveal more new genetic variants. Imputed sequences and quality scores can be downloaded and visualized online.
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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.