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Journal articles on the topic 'Genome wide association studies'

Author: Grafiati

Published: 4 June 2021

Last updated: 11 January 2025

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1

Shaffer, J. R., E. Feingold, and M. L. Marazita. "Genome-wide Association Studies." Journal of Dental Research 91, no. 7 (May 4, 2012): 637–41. http://dx.doi.org/10.1177/0022034512446968.

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The genomic era of biomedical research has given rise to the genome-wide association study (GWAS) approach, which attempts to discover novel genes affecting an outcome by testing a large number ( i.e., hundreds of thousands to millions) of genetic variants for association. This article discusses the issues surrounding the GWAS approach with emphasis on the prospects and challenges relevant to the oral health research community.

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2

Al-Chalabi, A. "Genome-Wide Association Studies." Cold Spring Harbor Protocols 2009, no. 12 (December 1, 2009): pdb.top66. http://dx.doi.org/10.1101/pdb.top66.

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3

Guo, Xiuqing, and Jerome I. Rotter. "Genome-Wide Association Studies." JAMA 322, no. 17 (November 5, 2019): 1705. http://dx.doi.org/10.1001/jama.2019.16479.

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4

Kuniholm;, M. H., and D. B. Goldstein. "Replicating Genome-Wide Association Studies." Science 318, no. 5849 (October 19, 2007): 390c—391c. http://dx.doi.org/10.1126/science.318.5849.390c.

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5

Meschia, James F. "Stroke Genome-Wide Association Studies." Stroke 41, no. 4 (April 2010): 579–80. http://dx.doi.org/10.1161/strokeaha.109.576769.

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6

Welch, Carrie L. "Beyond Genome-Wide Association Studies." Arteriosclerosis, Thrombosis, and Vascular Biology 32, no. 2 (February 2012): 207–15. http://dx.doi.org/10.1161/atvbaha.111.232694.

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7

Christiani, David C. "Pulmonary Function: From Genome-Wide Association Studies to Genome-Wide Interaction Studies." American Journal of Respiratory and Critical Care Medicine 199, no. 5 (March 2019): 557–59. http://dx.doi.org/10.1164/rccm.201810-1986ed.

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8

Huang, Wenhui, Pengyuan Wang, Zhen Liu, and Liqing Zhang. "Identifying disease associations via genome-wide association studies." BMC Bioinformatics 10, Suppl 1 (2009): S68. http://dx.doi.org/10.1186/1471-2105-10-s1-s68.

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9

Li, Gengxin, and Hongjiang Zhu. "Genetic Studies: The Linear Mixed Models in Genome-wide Association Studies." Open Bioinformatics Journal 7, no. 1 (December 13, 2013): 27–33. http://dx.doi.org/10.2174/1875036201307010027.

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With the availability of high-density genomic data containing millions of single nucleotide polymorphisms and tens or hundreds of thousands of individuals, genetic association study is likely to identify the variants contributing to complex traits in a genome-wide scale. However, genome-wide association studies are confounded by some spurious associations due to not properly interpreting sample structure (containing population structure, family structure and cryptic relatedness). The absence of complete genealogy of population in the genome-wide association studies model greatly motivates the development of new methods to correct the inflation of false positive. In this process, linear mixed model based approaches with the advantage of capturing multilevel relatedness have gained large ground. We summarize current literatures dealing with sample structure, and our review focuses on the following four areas: (i) The approaches handling population structure in genome-wide association studies; (ii) The linear mixed model based approaches in genome-wide association studies; (iii) The performance of linear mixed model based approaches in genome-wide association studies and (iv) The unsolved issues and future work of linear mixed model based approaches.

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10

Nathan, David G., and Stuart H. Orkin. "Musings on genome medicine: genome wide association studies." Genome Medicine 1, no. 1 (2009): 3. http://dx.doi.org/10.1186/gm3.

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11

Benyamin, Beben, Peter M. Visscher, and Allan F. McRae. "Family-based genome-wide association studies." Pharmacogenomics 10, no. 2 (February 2009): 181–90. http://dx.doi.org/10.2217/14622416.10.2.181.

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12

Jorgenson, Eric, and John S. Witte. "Genome-wide association studies of cancer." Future Oncology 3, no. 4 (August 2007): 419–27. http://dx.doi.org/10.2217/14796694.3.4.419.

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13

Tamari, Mayumi, Kaori Tomita, and Tomomitsu Hirota. "Genome-Wide Association Studies of Asthma." Allergology International 60, no. 3 (2011): 247–52. http://dx.doi.org/10.2332/allergolint.11-rai-0320.

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14

Wjst, Matthias, Muralidharan Sargurupremraj, and Matthias Arnold. "Genome-wide association studies in asthma." Current Opinion in Allergy and Clinical Immunology 13, no. 1 (February 2013): 112–18. http://dx.doi.org/10.1097/aci.0b013e32835c1674.

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15

Bush, William S., and Jason H. Moore. "Chapter 11: Genome-Wide Association Studies." PLoS Computational Biology 8, no. 12 (December 27, 2012): e1002822. http://dx.doi.org/10.1371/journal.pcbi.1002822.

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16

Easton, D. F., and R. A. Eeles. "Genome-wide association studies in cancer." Human Molecular Genetics 17, R2 (October 15, 2008): R109—R115. http://dx.doi.org/10.1093/hmg/ddn287.

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17

Shriner, D., L. K. Vaughan, M. A. Padilla, H. K. Tiwari;, S. M. Williams, J. A. Canter, D. C. Crawford, J. H. Moore, M. D. Ritchie, and J. L. Haines. "Problems with Genome-Wide Association Studies." Science 316, no. 5833 (June 7, 2007): 1840c—1842c. http://dx.doi.org/10.1126/science.316.5833.1840c.

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18

Kinnersley, Ben, Richard S. Houlston, and Melissa L. Bondy. "Genome-Wide Association Studies in Glioma." Cancer Epidemiology Biomarkers & Prevention 27, no. 4 (January 30, 2018): 418–28. http://dx.doi.org/10.1158/1055-9965.epi-17-1080.

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19

Witte, John S. "Genome-Wide Association Studies and Beyond." Annual Review of Public Health 31, no. 1 (March 2010): 9–20. http://dx.doi.org/10.1146/annurev.publhealth.012809.103723.

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20

Bergen, Sarah E., and Tracey L. Petryshen. "Genome-wide association studies of schizophrenia." Current Opinion in Psychiatry 25, no. 2 (March 2012): 76–82. http://dx.doi.org/10.1097/yco.0b013e32835035dd.

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21

Rhodin, K., K. Divaris, K. E. North, S. P. Barros, K. Moss, J. D. Beck, and S. Offenbacher. "Chronic Periodontitis Genome-wide Association Studies." Journal of Dental Research 93, no. 9 (July 23, 2014): 882–90. http://dx.doi.org/10.1177/0022034514544506.

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22

Barsh, Gregory S., Gregory P. Copenhaver, Greg Gibson, and Scott M. Williams. "Guidelines for Genome-Wide Association Studies." PLoS Genetics 8, no. 7 (July 5, 2012): e1002812. http://dx.doi.org/10.1371/journal.pgen.1002812.

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23

Adamski, Jerzy. "Genome-wide association studies with metabolomics." Genome Medicine 4, no. 4 (2012): 34. http://dx.doi.org/10.1186/gm333.

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24

Motsinger-Reif, Alison A., Eric Jorgenson, Mary V. Relling, Deanna L. Kroetz, Richard Weinshilboum, Nancy J. Cox, and Dan M. Roden. "Genome-wide association studies in pharmacogenomics." Pharmacogenetics and Genomics 23, no. 8 (August 2013): 383–94. http://dx.doi.org/10.1097/fpc.0b013e32833d7b45.

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25

Hopper, J., E. Makalic, D. Schmidt, M. Bui, J. Stone, M. Kapuscinski, D. Park, M. Jenkins, and M. Southey. "‘Next-generation’ genome wide association studies." Hereditary Cancer in Clinical Practice 10, Suppl 2 (2012): A48. http://dx.doi.org/10.1186/1897-4287-10-s2-a48.

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26

Thompson, P. A. "Genome-wide Association Studies Meet Chemoprevention." JNCI Journal of the National Cancer Institute 105, no. 24 (December 7, 2013): 1847–48. http://dx.doi.org/10.1093/jnci/djt353.

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27

Stadler, Zsofia K., Peter Thom, Mark E. Robson, Jeffrey N. Weitzel, Noah D. Kauff, Karen E. Hurley, Vincent Devlin, Bert Gold, Robert J. Klein, and Kenneth Offit. "Genome-Wide Association Studies of Cancer." Journal of Clinical Oncology 28, no. 27 (September 20, 2010): 4255–67. http://dx.doi.org/10.1200/jco.2009.25.7816.

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Knowledge of the inherited risk for cancer is an important component of preventive oncology. In addition to well-established syndromes of cancer predisposition, much remains to be discovered about the genetic variation underlying susceptibility to common malignancies. Increased knowledge about the human genome and advances in genotyping technology have made possible genome-wide association studies (GWAS) of human diseases. These studies have identified many important regions of genetic variation associated with an increased risk for human traits and diseases including cancer. Understanding the principles, major findings, and limitations of GWAS is becoming increasingly important for oncologists as dissemination of genomic risk tests directly to consumers is already occurring through commercial companies. GWAS have contributed to our understanding of the genetic basis of cancer and will shed light on biologic pathways and possible new strategies for targeted prevention. To date, however, the clinical utility of GWAS-derived risk markers remains limited.

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28

Corvin, A., N. Craddock, and P. F. Sullivan. "Genome-wide association studies: a primer." Psychological Medicine 40, no. 7 (November 9, 2009): 1063–77. http://dx.doi.org/10.1017/s0033291709991723.

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There have been nearly 400 genome-wide association studies (GWAS) published since 2005. The GWAS approach has been exceptionally successful in identifying common genetic variants that predispose to a variety of complex human diseases and biochemical and anthropometric traits. Although this approach is relatively new, there are many excellent reviews of different aspects of the GWAS method. Here, we provide a primer, an annotated overview of the GWAS method with particular reference to psychiatric genetics. We dissect the GWAS methodology into its components and provide a brief description with citations and links to reviews that cover the topic in detail.

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29

Nyholt, Dale R., and Arn M. J. M. van den Maagdenberg. "Genome-wide association studies in migraine." Current Opinion in Neurology 29, no. 3 (June 2016): 302–8. http://dx.doi.org/10.1097/wco.0000000000000316.

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30

Ferguson, Lynnette R. "Genome-Wide Association Studies and Diet." Journal of Nutrigenetics and Nutrigenomics 3, no. 4-6 (2010): 144–50. http://dx.doi.org/10.1159/000324348.

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31

Glessner, Joseph T., John J. Connolly, and Hakon Hakonarson. "Genome-Wide Association Studies of Autism." Current Behavioral Neuroscience Reports 1, no. 4 (October 23, 2014): 234–41. http://dx.doi.org/10.1007/s40473-014-0023-0.

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32

Daly, Ann K. "Genome-wide association studies in pharmacogenomics." Nature Reviews Genetics 11, no. 4 (April 2010): 241–46. http://dx.doi.org/10.1038/nrg2751.

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33

Flint, Jonathan, and Eleazar Eskin. "Genome-wide association studies in mice." Nature Reviews Genetics 13, no. 11 (October 9, 2012): 807–17. http://dx.doi.org/10.1038/nrg3335.

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34

Wang, Xiaoling, and Harold Snieder. "Genome-Wide Association Studies and Beyond." Hypertension 56, no. 6 (December 2010): 1035–37. http://dx.doi.org/10.1161/hypertensionaha.110.157214.

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35

Glazer, Nicole L. "Moving Beyond Genome-Wide Association Studies." Circulation: Cardiovascular Genetics 4, no. 1 (February 2011): 91–93. http://dx.doi.org/10.1161/circgenetics.110.958785.

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36

MacRae, Calum A., and Ramachandran S. Vasan. "Next-Generation Genome-Wide Association Studies." Circulation: Cardiovascular Genetics 4, no. 4 (August 2011): 334–36. http://dx.doi.org/10.1161/circgenetics.111.960765.

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37

Legro, Richard. "Lessons from Genome Wide Association Studies." Seminars in Reproductive Medicine 34, no. 04 (August 11, 2016): 191–92. http://dx.doi.org/10.1055/s-0036-1586216.

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38

Kraft, Peter, Eleftheria Zeggini, and John P. A. Ioannidis. "Replication in Genome-Wide Association Studies." Statistical Science 24, no. 4 (November 2009): 561–73. http://dx.doi.org/10.1214/09-sts290.

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39

Karlsen, Tom H. "Genome-wide association studies reach hepatology." Journal of Hepatology 50, no. 6 (June 2009): 1278–80. http://dx.doi.org/10.1016/j.jhep.2009.03.002.

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40

Sivapalaratnam, S., M. M. Motazacker, S. Maiwald, G. K. Hovingh, J. J. P. Kastelein, M. Levi, M. D. Trip, and G. M. Dallinga-Thie. "Genome-Wide Association Studies in Atherosclerosis." Current Atherosclerosis Reports 13, no. 3 (March 3, 2011): 225–32. http://dx.doi.org/10.1007/s11883-011-0173-4.

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41

Klein, Robert J., Xing Xu, Semanti Mukherjee, Jason Willis, and James Hayes. "Successes of Genome-wide Association Studies." Cell 142, no. 3 (August 2010): 350–51. http://dx.doi.org/10.1016/j.cell.2010.07.026.

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42

Lotta, Luca Andrea. "Genome-wide association studies in atherothrombosis." European Journal of Internal Medicine 21, no. 2 (April 2010): 74–78. http://dx.doi.org/10.1016/j.ejim.2009.11.003.

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43

Franke, Barbara, Benjamin M. Neale, and Stephen V. Faraone. "Genome-wide association studies in ADHD." Human Genetics 126, no. 1 (April 22, 2009): 13–50. http://dx.doi.org/10.1007/s00439-009-0663-4.

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44

Sazonovs, A., and J. C. Barrett. "Rare-Variant Studies to Complement Genome-Wide Association Studies." Annual Review of Genomics and Human Genetics 19, no. 1 (August 31, 2018): 97–112. http://dx.doi.org/10.1146/annurev-genom-083117-021641.

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Genome-wide association studies (GWASs) have revolutionized human disease genetics by discovering tens of thousands of associations between common variants and complex diseases. In parallel, huge technological advances in DNA sequencing have made it possible to measure and analyze rare variation in populations. This review considers these two stories and how they have come together. We first review the history of GWASs and sequencing. We then consider how to understand the biological mechanisms that drive signals of strong association in the absence of rare-variant studies. We describe how rare-variant studies complement these approaches and highlight both data generation and statistical challenges in their interpretation. Finally, we consider how certain special study designs, such as those for families and isolated populations, fit in this paradigm.

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45

Kostem, Emrah, and Eleazar Eskin. "Efficiently Identifying Significant Associations in Genome-wide Association Studies." Journal of Computational Biology 20, no. 10 (October 2013): 817–30. http://dx.doi.org/10.1089/cmb.2013.0087.

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46

Zeggini, Eleftheria, and John PA Ioannidis. "Meta-analysis in genome-wide association studies." Pharmacogenomics 10, no. 2 (February 2009): 191–201. http://dx.doi.org/10.2217/14622416.10.2.191.

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47

Bowcock, Anne M. "Genome-Wide Association Studies and Infectious Disease." Critical Reviews™ in Immunology 30, no. 3 (2010): 305–9. http://dx.doi.org/10.1615/critrevimmunol.v30.i3.80.

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48

Lukic, Ana, and Simon Mead. "Genome wide association studies and prion disease." Prion 5, no. 3 (July 2011): 154–60. http://dx.doi.org/10.4161/pri.5.3.16892.

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49

Tamari, Mayumi, ShotaTanaka, and Tomomitsu Hirota. "Genome-Wide Association Studies of Allergic Diseases." Allergology International 62, no. 1 (2013): 21–28. http://dx.doi.org/10.2332/allergolint.13-rai-0539.

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50

Speliotes, Elizabeth. "Genome-Wide Association Studies and Liver Disease." Seminars in Liver Disease 35, no. 04 (December 16, 2015): 355–60. http://dx.doi.org/10.1055/s-0035-1567833.

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