Keita Ishiwari

Genomic SEM reveals shared genetic architecture and expands locus discovery for locomotor activity in heterogeneous stock rats

The paper uses Genomic SEM to identify loci underlying locomotor activity in rats, finding 31 loci compared to fewer from other methods.

Novel insights into the genetic architecture and mechanisms of host/microbiome interactions from a multi-cohort analysis of outbred laboratory rats

The paper identifies host genetic effects on microbiome composition in rats and finds evidence of indirect genetic effects contributing to missing heritability.

RatXcan: A framework for cross-species integration of genome-wide association and gene expression data

RatXcan extends transcriptome-wide association studies to rats, enabling cross-species integration of GWAS and gene expression data to identify shared genetic mechanisms of complex traits.

Genomic Loci Influencing Cue-Reactivity in Heterogeneous Stock Rats

This study identifies genomic loci associated with cue-reactivity in rats, linking them to incentive salience and drug abuse-related traits.

Y and Mitochondrial Chromosomes in the Heterogeneous Stock Rat Population

The paper genotypes Y and mitochondrial chromosomes in heterogeneous stock rats and finds no significant associations with complex traits, except for gene expression on these chromosomes.

Genome-wide association study and sequence similarity analysis for unilateral renal agenesis using heterogeneous stock rats undercovers the KIT gene and AHR, ATF3, GATA3, HNF1B, POU2F2, and TFCP2 transcription factors as potential candidates to explain incomplete penetrance

This paper identifies genetic variants and transcription factors associated with unilateral renal agenesis in rats, suggesting a threshold mechanism involving KIT and interacting transcription factors.

Automated quantitative trait locus analysis (AutoQTL)

AutoQTL automates QTL analysis and GWAS by applying machine learning to detect both additive and non-additive genetic effects in genetic data.

Exponential increase in QTL detection with increased sample size.

The paper simulates GWAS in rats to show that larger sample sizes lead to an exponential increase in the number of significant loci detected.

Genome wide association study in 3,173 outbred rats identifies multiple loci for body weight, adiposity, and fasting glucose