Mouse genomic variation and its effect on phenotypes and gene regulation

By Thomas M. Keane, L. Goodstadt, Petr Danecek, Michael A. White, K. Wong, Binnaz Yalcin, Andreas Heger, A. Agam, G. Slater, Martin Goodson and 31 more. Nature, 2011

1,549 citations recorded by the source corpus.

We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/7c95e2613295cd565632db3a66f475e42d12a2d9

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Citations in the corpus

Integrative deep models for alternative splicing (2017, methodology): “The second dataset, denoted MGP 80 Data, was prepared by [8] and it contains RNA-Seq data from six tissues (heart, hippocampus, liver, lung, spleen, thymus) 81 with average read coverage of 60 million reads.”
Single-cell mRNA quantification and differential analysis with Census (2017, background): “This index consisted of cDNA sequences from GENCODE vM9, corresponding to the paternal (C57BL/6J) alleles, plus the same sequences with maternal (CAST/EiJ) SNP alleles overlaid (CAST genotypes from Keane et al. 52 ; only homozygous variants relative to the C57BL/6J reference were used).”
All SNPs Are Not Created Equal: Genome-Wide Association Studies Reveal a Consistent Pattern of Enrichment among Functionally Annotated SNPs (2013, methodology): “previous suggestions from both model organisms [27] and humans”
Ensembl 2017 (2016, background): “Whole genome sequencing of key laboratory mouse strains has been ongoing over the last several years (5,41).”
Characterization of ancient and modern genomes by SNP detection and phylogenomic and metagenomic analysis using PALEOMIX (2014, background): “The recent development of next-generation sequencing (NGS) technologies has revolutionized genomics, delivering complete genome sequences of model and non-model organisms in a cost-and time-efficient manner 1,2 .”