ArticleBMC genomics2015
Using whole-genome sequences of the LG/J and SM/J inbred mouse strains to prioritize quantitative trait genes and nucleotides.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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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.
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Who cites it
20 citing papers in PubMed, 38 citations in OpenAlex.
- Digit regeneration is expedited in LG/J healer mice compared to SM/J non-healer mice.NPJ Regenerative medicine · 2025Article
- Article
- Integrated transcriptomics contrasts fatty acid metabolism with hypoxia response in β-cell subpopulations associated with glycemic control.BMC genomics · 2023Article
- Genetic, epigenetic, and environmental mechanisms govern allele-specific gene expression.Genome research · 2022Article
- Article
- Brown Adipose Expansion and Remission of Glycemic Dysfunction in Obese SM/J Mice.Cell reports · 2020Article
- Spontaneous restoration of functional β-cell mass in obese SM/J mice.Physiological reports · 2020Article
- Genetic background and diet affect brown adipose gene coexpression networks associated with metabolic phenotypes.Physiological genomics · 2020Article
- Genome-Wide Association Study in Two Cohorts from a Multi-generational Mouse Advanced Intercross Line Highlights the Difficulty of Replication Due to Study-Specific Heterogeneity.G3 (Bethesda, Md.) · 2020Article
- Genome-wide Associations Reveal Human-Mouse Genetic Convergence and Modifiers of Myogenesis, CPNE1 and STC2.American journal of human genetics · 2019Article
- Dietary iron interacts with genetic background to influence glucose homeostasis.Nutrition & metabolism · 2019Article
- Genome wide association analysis in a mouse advanced intercross line.Nature communications · 2018Article
- Replication and discovery of musculoskeletal QTLs in LG/J and SM/J advanced intercross lines.Physiological reports · 2018Article
- Whole exome sequencing of wild-derived inbred strains of mice improves power to link phenotype and genotype.Mammalian genome : official journal of the International Mammalian Genome Society · 2017Article
- Mouse Genome Informatics (MGI) Resource: Genetic, Genomic, and Biological Knowledgebase for the Laboratory Mouse.ILAR journal · 2017Review
- Physiologic and genetic evidence links hemopexin to triglycerides in mice and humans.International journal of obesity (2005) · 2017Article
- Fine-mapping of genes determining extrafusal fiber properties in murine soleus muscle.Physiological genomics · 2017Article
- Construction of an integrative regulatory element and variation map of the murine Tst locus.BMC genetics · 2016Article
- The genetics of bone mass and susceptibility to bone diseases.Nature reviews. Rheumatology · 2016Review
- The Genetic Basis of Baculum Size and Shape Variation in Mice.G3 (Bethesda, Md.) · 2016Article
Corrections and comments
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Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
backgroundThe laboratory mouse is the most commonly used model for studying variation in complex traits relevant to human disease. Here we present the whole-genome sequences of two inbred strains, LG/J and SM/J, which are frequently used to study variation in complex traits as diverse as aging, bone-growth, adiposity, maternal behavior, and methamphetamine sensitivity.
resultsWe identified small nucleotide variants (SNVs) and structural variants (SVs) in the LG/J and SM/J strains relative to the reference genome and discovered novel variants in these two strains by comparing their sequences to other mouse genomes. We find that 39% of the LG/J and SM/J genomes are identical-by-descent (IBD). We characterized amino-acid changing mutations using three algorithms: LRT, PolyPhen-2 and SIFT. We also identified polymorphisms between LG/J and SM/J that fall in regulatory regions and highly informative transcription factor binding sites (TFBS). We intersected these functional predictions with quantitative trait loci (QTL) mapped in advanced intercrosses of these two strains. We find that QTL are both over-represented in non-IBD regions and highly enriched for variants predicted to have a functional impact. Variants in QTL associated with metabolic (231 QTL identified in an F16 generation) and developmental (41 QTL identified in an F34 generation) traits were interrogated and we highlight candidate quantitative trait genes (QTG) and nucleotides (QTN) in a QTL on chr13 associated with variation in basal glucose levels and in a QTL on chr6 associated with variation in tibia length.
conclusionsWe show how integrating genomic sequence with QTL reduces the QTL search space and helps researchers prioritize candidate genes and nucleotides for experimental follow-up. Additionally, given the LG/J and SM/J phylogenetic context among inbred strains, these data contribute important information to the genomic landscape of the laboratory mouse.
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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.