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The expanded BXD family of mice: A cohort for experimental systems genetics and precision medicine

By David G Ashbrook, Danny Arends, Pjotr Prins, Megan Mulligan, Suheeta Roy, Evan G Williams, Cathleen M Lutz, Alicia Valenzuela, Casey J Bohl, Jesse F Ingels, Melinda S McCarty, Arthur G. Centeno, Reinmar Hager, Johan Auwerx, Saunak Sen, Lu Lu, Robert W. Williams

Posted 23 Jun 2019
bioRxiv DOI: 10.1101/672097

The challenge of precision medicine is to model complex interactions among DNA variants, sets of phenotypes, and complex environmental factors and confounders. We have expanded the BXD family, creating a powerful and extensible test bed for experimental precision medicine and an ideal cohort to study gene-by-environmental interactions. These BXD segregate for over 6 million variants, with a mean minor allele frequency close to 0.5. We have increased the family two-fold to 150 inbred strains, all derived from C57BL/6J and DBA/2J. We have also generated updated and comprehensive genotypes and an unrivaled deep phenome. Approximately 10,000 recombinations have been located, allowing precision of quantitative trait loci mapping of ±2.0 Mb over much of the genome and ±0.5 Mb for Mendelian loci. The BXD phenome includes more than 100 ‘omics data sets and >7000 quantitative and clinical phenotypes, all of which is publicly available. The BXD family is an enduring, collaborative, and replicable resource to test causal and mechanistic links between genomes and phenomes at many stages and under a wide variety of treatments and interventions. * List of abbreviations : AD : Alzheimer’s Disease AI : advanced intercross B6 : C57BL/6J mouse strain BLAST : Basic Local Alignment Search Tool BXD : BXD family of recombinant inbred strains of mice, produced by crossing the B6 and D2 parental strains CC : Collaborative Cross Chr : Chromosome cM : centimorgan D2 : DBA/2J mouse strain DO : Diversity Outbred DX : diallel cross EMRs : electronic medical records eQTL : Expression quantitative trait locus F2 : Filial generation 2 GEMMA : Genome-wide Efficient Mixed Model Association GigaMUGA : Giga Mouse Universal Genotyping Array GN : GeneNetwork (<http://genenetwork.org>) GN2 : GeneNetwork2 (<http://gn2.genenetwork.org>) GWAS : genome-wide association study H2ix̅ : heritability of isogenic strain means H2RIx̅ : heritability of recombinant inbred strain means HMDP : Hybrid Mouse Diversity Panel IMPC : International Mouse Phenotyping Consortium JAX : The Jackson Laboratory Kb : kilobase KOMP : Knockout Mouse project LOD : logarithm of odds LRS : likelihood ratio statistic Mb : Megabase MMRRC : Mutant Mouse Resource & Research Centers MUGA : Mouse Universal Genotyping Array nRecP : number of observed recombinations from one position to the next nRecS : number of observed recombinations per strain PheWAS : phenome-wide association studies QT : quantitative trait QTL : quantitative trait locus r2 : Coefficient of determination RI : Recombinant inbred RIXs : Recombinant inbred intercrosses SE : Standard error of the mean SNP : single nucleotide polymorphism UTHSC : University of Tennessee Health Science Center

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