Title |
Population- and individual-specific regulatory variation in Sardinia
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Published in |
Nature Genetics, April 2017
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DOI | 10.1038/ng.3840 |
Pubmed ID | |
Authors |
Mauro Pala, Zachary Zappala, Mara Marongiu, Xin Li, Joe R Davis, Roberto Cusano, Francesca Crobu, Kimberly R Kukurba, Michael J Gloudemans, Frederic Reinier, Riccardo Berutti, Maria G Piras, Antonella Mulas, Magdalena Zoledziewska, Michele Marongiu, Elena P Sorokin, Gaelen T Hess, Kevin S Smith, Fabio Busonero, Andrea Maschio, Maristella Steri, Carlo Sidore, Serena Sanna, Edoardo Fiorillo, Michael C Bassik, Stephen J Sawcer, Alexis Battle, John Novembre, Chris Jones, Andrea Angius, Gonçalo R Abecasis, David Schlessinger, Francesco Cucca, Stephen B Montgomery |
Abstract |
Genetic studies of complex traits have mainly identified associations with noncoding variants. To further determine the contribution of regulatory variation, we combined whole-genome and transcriptome data for 624 individuals from Sardinia to identify common and rare variants that influence gene expression and splicing. We identified 21,183 expression quantitative trait loci (eQTLs) and 6,768 splicing quantitative trait loci (sQTLs), including 619 new QTLs. We identified high-frequency QTLs and found evidence of selection near genes involved in malarial resistance and increased multiple sclerosis risk, reflecting the epidemiological history of Sardinia. Using family relationships, we identified 809 segregating expression outliers (median z score of 2.97), averaging 13.3 genes per individual. Outlier genes were enriched for proximal rare variants, providing a new approach to study large-effect regulatory variants and their relevance to traits. Our results provide insight into the effects of regulatory variants and their relationship to population history and individual genetic risk. |
X Demographics
Geographical breakdown
Country | Count | As % |
---|---|---|
United States | 18 | 35% |
United Kingdom | 8 | 16% |
Italy | 5 | 10% |
Germany | 1 | 2% |
Canada | 1 | 2% |
Korea, Republic of | 1 | 2% |
Spain | 1 | 2% |
France | 1 | 2% |
Russia | 1 | 2% |
Other | 1 | 2% |
Unknown | 13 | 25% |
Demographic breakdown
Type | Count | As % |
---|---|---|
Members of the public | 25 | 49% |
Scientists | 25 | 49% |
Science communicators (journalists, bloggers, editors) | 1 | 2% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
---|---|---|
Mexico | 1 | <1% |
United States | 1 | <1% |
Unknown | 124 | 98% |
Demographic breakdown
Readers by professional status | Count | As % |
---|---|---|
Researcher | 31 | 25% |
Student > Ph. D. Student | 27 | 21% |
Student > Bachelor | 10 | 8% |
Professor > Associate Professor | 9 | 7% |
Student > Master | 9 | 7% |
Other | 20 | 16% |
Unknown | 20 | 16% |
Readers by discipline | Count | As % |
---|---|---|
Biochemistry, Genetics and Molecular Biology | 47 | 37% |
Agricultural and Biological Sciences | 33 | 26% |
Medicine and Dentistry | 8 | 6% |
Computer Science | 5 | 4% |
Neuroscience | 3 | 2% |
Other | 8 | 6% |
Unknown | 22 | 17% |