Conditional entropy in variation-adjusted windows detects selection signatures associated with expression quantitative trait loci (eQTLs)

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• 作者：Samuel K Handelman ; Michal Seweryn ; Ryan M Smith ; Katherine Hartmann…
• 关键词：Haplotype ; Positive Selection ; Selective Sweep ; Conditional Entropy ; eQTL ; Conditional Logistic Regression
• 刊名：BMC Genomics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：8-supp
• 全文大小：872 KB
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• 作者单位：Samuel K Handelman (1)
  Michal Seweryn (2) (3) (4)
  Ryan M Smith (1)
  Katherine Hartmann (1)
  Danxin Wang (1)
  Maciej Pietrzak (1) (4)
  Andrew D Johnson (5)
  Andrzej Kloczkowski (6) (7) (8)
  Wolfgang Sadee (1)
  
  1. Center for Pharmacogenomics, The Ohio State University College of Medicine, Graves Hall, 330 W. 10th Ave., Columbus, OH, 43210, USA
  2. Mathematical Biosciences Institute, Jennings Hall 3rd Floor, 1735 Neil Ave., Columbus, OH, 43210, USA
  3. Faculty of Mathematics and Computer Science, Łódź University, Narutowicza 65, 90-131, Łódź, Poland
  4. Division of Biostatistics, The Ohio State University College of Public Health, Cunz Hall, 1841 Neil Avenue, Columbus, OH, 43210-1240, USA
  5. Division of Intramural Research, National Heart, Lung and Blood Institute, Cardiovascular Epidemiology and Human Genomics Branch, The Framingham Heart Study, 73 Mt. Wayte Ave., Suite #2, Framingham, MA, USA
  6. Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, 700 Children's Drive, Columbus, OH, 43205, USA
  7. Department of Pediatrics, The Ohio State University College of Medicine, 700 Children's Drive, Columbus, OH, 43205, USA
  8. Kavli Institute for Theoretical Physics China, Chinese Academy of Sciences, Beijing, 100190, China
  
• 刊物主题：Life Sciences, general; Microarrays; Proteomics; Animal Genetics and Genomics; Microbial Genetics and Genomics; Plant Genetics & Genomics;
• 出版者：BioMed Central
• ISSN：1471-2164

文摘

Background Over the past 50,000 years, shifts in human-environmental or human-human interactions shaped genetic differences within and among human populations, including variants under positive selection. Shaped by environmental factors, such variants influence the genetics of modern health, disease, and treatment outcome. Because evolutionary processes tend to act on gene regulation, we test whether regulatory variants are under positive selection. We introduce a new approach to enhance detection of genetic markers undergoing positive selection, using conditional entropy to capture recent local selection signals. Results We use conditional logistic regression to compare our Adjusted Haplotype Conditional Entropy (H|H) measure of positive selection to existing positive selection measures. H|H and existing measures were applied to published regulatory variants acting in cis (cis-eQTLs), with conditional logistic regression testing whether regulatory variants undergo stronger positive selection than the surrounding gene.