Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate

Anna J Jasinska; Ivette Zelaya; Susan K Service; Christine B Peterson; Rita M Cantor; Oi-Wa Choi; Joseph DeYoung; Eleazar Eskin; Lynn A Fairbanks; Scott Fears; Allison E Furterer; Yu S Huang; Vasily Ramensky; Christopher A Schmitt; Hannes Svardal; Matthew J Jorgensen; Jay R Kaplan; Diego Villar; Bronwen L Aken; Paul Flicek; Rishi Nag; Emily S Wong; John Blangero; Thomas D Dyer; Marina Bogomolov; Yoav Benjamini; George M Weinstock; Ken Dewar; Chiara Sabatti; Richard K Wilson; J David Jentsch; Wesley Warren; Giovanni Coppola; Roger P Woods; Nelson B Freimer

doi:10.1038/ng.3959

Genetic variation and gene expression across multiple tissues and developmental stages in a nonhuman primate

Nat Genet. 2017 Dec;49(12):1714-1721. doi: 10.1038/ng.3959. Epub 2017 Oct 30.

Authors

Anna J Jasinska^{1

2}, Ivette Zelaya³, Susan K Service¹, Christine B Peterson⁴, Rita M Cantor^{1

5}, Oi-Wa Choi¹, Joseph DeYoung¹, Eleazar Eskin^{5

6}, Lynn A Fairbanks¹, Scott Fears¹, Allison E Furterer⁷, Yu S Huang¹, Vasily Ramensky¹, Christopher A Schmitt¹, Hannes Svardal⁸, Matthew J Jorgensen⁹, Jay R Kaplan⁹, Diego Villar¹⁰, Bronwen L Aken¹¹, Paul Flicek¹¹, Rishi Nag¹¹, Emily S Wong¹¹, John Blangero¹², Thomas D Dyer¹², Marina Bogomolov¹³, Yoav Benjamini¹⁴, George M Weinstock¹⁵, Ken Dewar¹⁶, Chiara Sabatti^{17

18}, Richard K Wilson¹⁹, J David Jentsch^{20

21}, Wesley Warren¹⁹, Giovanni Coppola^{1

22}, Roger P Woods^{21

22}, Nelson B Freimer^{1

5}

Affiliations

¹ Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA.
² Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
³ Interdepartmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, California, USA.
⁴ Department of Biostatistics, University of Texas MD Anderson Cancer Center, Houston, Texas, USA.
⁵ Department of Human Genetics, University of California, Los Angeles, Los Angeles, California, USA.
⁶ Department of Computer Science, University of California, Los Angeles, Los Angeles, California, USA.
⁷ Interdepartmental Graduate Program in Neuroscience, University of California, Los Angeles, Los Angeles, California, USA.
⁸ Wellcome Trust Sanger Institute, Hinxton, UK.
⁹ Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.
¹⁰ University of Cambridge, Cancer Research UK Cambridge Institute, Cambridge, UK.
¹¹ European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, UK.
¹² South Texas Diabetes and Obesity Institute, UTHSCSA/UTRGV, Brownsville, Texas, USA.
¹³ Faculty of Industrial Engineering and Management, Technion, Haifa, Israel.
¹⁴ Department of Statistics and Operation Research, Tel Aviv University, Tel Aviv, Israel.
¹⁵ Jackson Laboratory for Genomic Medicine, Farmington, Connecticut, USA.
¹⁶ Department of Human Genetics, McGill University, Montreal, Quebec, Canada.
¹⁷ Department of Biomedical Data Science, Stanford University, Stanford, California, USA.
¹⁸ Department of Statistics, Stanford University, Stanford, California, USA.
¹⁹ McDonnell Genome Institute, Washington University School of Medicine, St. Louis, Missouri, USA.
²⁰ Department of Psychology, University of California, Los Angeles, Los Angeles, California, USA.
²¹ Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA.
²² Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, California, USA.

PMID: 29083405
PMCID: PMC5714271
DOI: 10.1038/ng.3959

Abstract

By analyzing multitissue gene expression and genome-wide genetic variation data in samples from a vervet monkey pedigree, we generated a transcriptome resource and produced the first catalog of expression quantitative trait loci (eQTLs) in a nonhuman primate model. This catalog contains more genome-wide significant eQTLs per sample than comparable human resources and identifies sex- and age-related expression patterns. Findings include a master regulatory locus that likely has a role in immune function and a locus regulating hippocampal long noncoding RNAs (lncRNAs), whose expression correlates with hippocampal volume. This resource will facilitate genetic investigation of quantitative traits, including brain and behavioral phenotypes relevant to neuropsychiatric disorders.

MeSH terms

Animals
Brain / growth & development
Brain / metabolism
Chlorocebus aethiops / genetics*
Chlorocebus aethiops / growth & development
Gene Expression Profiling*
Genetic Variation*
Genome-Wide Association Study
Genotype
Humans
Phenotype
Polymorphism, Single Nucleotide
Quantitative Trait Loci / genetics*

Abstract

MeSH terms

Grants and funding