Literature DB >> 29727686

The Post-GWAS Era: From Association to Function.

Michael D Gallagher1, Alice S Chen-Plotkin2.   

Abstract

During the past 12 years, genome-wide association studies (GWASs) have uncovered thousands of genetic variants that influence risk for complex human traits and diseases. Yet functional studies aimed at delineating the causal genetic variants and biological mechanisms underlying the observed statistical associations with disease risk have lagged. In this review, we highlight key advances in the field of functional genomics that may facilitate the derivation of biological meaning post-GWAS. We highlight the evidence suggesting that causal variants underlying disease risk often function through regulatory effects on the expression of target genes and that these expression effects might be modest and cell-type specific. We moreover discuss specific studies as proof-of-principle examples for current statistical, bioinformatic, and empirical bench-based approaches to downstream elucidation of GWAS-identified disease risk loci.
Copyright © 2018 American Society of Human Genetics. Published by Elsevier Inc. All rights reserved.

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Year:  2018        PMID: 29727686      PMCID: PMC5986732          DOI: 10.1016/j.ajhg.2018.04.002

Source DB:  PubMed          Journal:  Am J Hum Genet        ISSN: 0002-9297            Impact factor:   11.025


  107 in total

Review 1.  The role of regulatory variation in complex traits and disease.

Authors:  Frank W Albert; Leonid Kruglyak
Journal:  Nat Rev Genet       Date:  2015-02-24       Impact factor: 53.242

2.  Complement factor H polymorphism and age-related macular degeneration.

Authors:  Albert O Edwards; Robert Ritter; Kenneth J Abel; Alisa Manning; Carolien Panhuysen; Lindsay A Farrer
Journal:  Science       Date:  2005-03-10       Impact factor: 47.728

3.  Complement factor H variant increases the risk of age-related macular degeneration.

Authors:  Jonathan L Haines; Michael A Hauser; Silke Schmidt; William K Scott; Lana M Olson; Paul Gallins; Kylee L Spencer; Shu Ying Kwan; Maher Noureddine; John R Gilbert; Nathalie Schnetz-Boutaud; Anita Agarwal; Eric A Postel; Margaret A Pericak-Vance
Journal:  Science       Date:  2005-03-10       Impact factor: 47.728

4.  HERC2 rs12913832 modulates human pigmentation by attenuating chromatin-loop formation between a long-range enhancer and the OCA2 promoter.

Authors:  Mijke Visser; Manfred Kayser; Robert-Jan Palstra
Journal:  Genome Res       Date:  2012-01-10       Impact factor: 9.043

5.  FTO Obesity Variant Circuitry and Adipocyte Browning in Humans.

Authors:  Melina Claussnitzer; Simon N Dankel; Kyoung-Han Kim; Gerald Quon; Wouter Meuleman; Christine Haugen; Viktoria Glunk; Isabel S Sousa; Jacqueline L Beaudry; Vijitha Puviindran; Nezar A Abdennur; Jannel Liu; Per-Arne Svensson; Yi-Hsiang Hsu; Daniel J Drucker; Gunnar Mellgren; Chi-Chung Hui; Hans Hauner; Manolis Kellis
Journal:  N Engl J Med       Date:  2015-08-19       Impact factor: 91.245

6.  Long-Range Modulation of PAG1 Expression by 8q21 Allergy Risk Variants.

Authors:  Cristina T Vicente; Stacey L Edwards; Kristine M Hillman; Susanne Kaufmann; Hayley Mitchell; Lisa Bain; Dylan M Glubb; Jason S Lee; Juliet D French; Manuel A R Ferreira
Journal:  Am J Hum Genet       Date:  2015-07-23       Impact factor: 11.025

7.  HBS1L-MYB intergenic variants modulate fetal hemoglobin via long-range MYB enhancers.

Authors:  Ralph Stadhouders; Suleyman Aktuna; Supat Thongjuea; Ali Aghajanirefah; Farzin Pourfarzad; Wilfred van Ijcken; Boris Lenhard; Helen Rooks; Steve Best; Stephan Menzel; Frank Grosveld; Swee Lay Thein; Eric Soler
Journal:  J Clin Invest       Date:  2014-03-10       Impact factor: 14.808

8.  A global reference for human genetic variation.

Authors:  Adam Auton; Lisa D Brooks; Richard M Durbin; Erik P Garrison; Hyun Min Kang; Jan O Korbel; Jonathan L Marchini; Shane McCarthy; Gil A McVean; Gonçalo R Abecasis
Journal:  Nature       Date:  2015-10-01       Impact factor: 49.962

9.  Identification of genes associated with dissociation of cognitive performance and neuropathological burden: Multistep analysis of genetic, epigenetic, and transcriptional data.

Authors:  Charles C White; Hyun-Sik Yang; Lei Yu; Lori B Chibnik; Robert J Dawe; Jingyun Yang; Hans-Ulrich Klein; Daniel Felsky; Alfredo Ramos-Miguel; Konstantinos Arfanakis; William G Honer; Reisa A Sperling; Julie A Schneider; David A Bennett; Philip L De Jager
Journal:  PLoS Med       Date:  2017-04-25       Impact factor: 11.069

10.  Integrative analysis of 111 reference human epigenomes.

Authors:  Anshul Kundaje; Wouter Meuleman; Jason Ernst; Misha Bilenky; Angela Yen; Alireza Heravi-Moussavi; Pouya Kheradpour; Zhizhuo Zhang; Jianrong Wang; Michael J Ziller; Viren Amin; John W Whitaker; Matthew D Schultz; Lucas D Ward; Abhishek Sarkar; Gerald Quon; Richard S Sandstrom; Matthew L Eaton; Yi-Chieh Wu; Andreas R Pfenning; Xinchen Wang; Melina Claussnitzer; Yaping Liu; Cristian Coarfa; R Alan Harris; Noam Shoresh; Charles B Epstein; Elizabeta Gjoneska; Danny Leung; Wei Xie; R David Hawkins; Ryan Lister; Chibo Hong; Philippe Gascard; Andrew J Mungall; Richard Moore; Eric Chuah; Angela Tam; Theresa K Canfield; R Scott Hansen; Rajinder Kaul; Peter J Sabo; Mukul S Bansal; Annaick Carles; Jesse R Dixon; Kai-How Farh; Soheil Feizi; Rosa Karlic; Ah-Ram Kim; Ashwinikumar Kulkarni; Daofeng Li; Rebecca Lowdon; GiNell Elliott; Tim R Mercer; Shane J Neph; Vitor Onuchic; Paz Polak; Nisha Rajagopal; Pradipta Ray; Richard C Sallari; Kyle T Siebenthall; Nicholas A Sinnott-Armstrong; Michael Stevens; Robert E Thurman; Jie Wu; Bo Zhang; Xin Zhou; Arthur E Beaudet; Laurie A Boyer; Philip L De Jager; Peggy J Farnham; Susan J Fisher; David Haussler; Steven J M Jones; Wei Li; Marco A Marra; Michael T McManus; Shamil Sunyaev; James A Thomson; Thea D Tlsty; Li-Huei Tsai; Wei Wang; Robert A Waterland; Michael Q Zhang; Lisa H Chadwick; Bradley E Bernstein; Joseph F Costello; Joseph R Ecker; Martin Hirst; Alexander Meissner; Aleksandar Milosavljevic; Bing Ren; John A Stamatoyannopoulos; Ting Wang; Manolis Kellis
Journal:  Nature       Date:  2015-02-19       Impact factor: 69.504

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  219 in total

Review 1.  Genetics of Atrial Fibrillation in 2020: GWAS, Genome Sequencing, Polygenic Risk, and Beyond.

Authors:  Carolina Roselli; Michiel Rienstra; Patrick T Ellinor
Journal:  Circ Res       Date:  2020-06-18       Impact factor: 17.367

Review 2.  Interpretation of risk loci from genome-wide association studies of Alzheimer's disease.

Authors:  Shea J Andrews; Brian Fulton-Howard; Alison Goate
Journal:  Lancet Neurol       Date:  2020-01-24       Impact factor: 44.182

Review 3.  Clinical-pathological correlations of BAV and the attendant thoracic aortopathies. Part 2: Pluridisciplinary perspective on their genetic and molecular origins.

Authors:  Ares Pasipoularides
Journal:  J Mol Cell Cardiol       Date:  2019-06-06       Impact factor: 5.000

4.  Using Transcriptomic Hidden Variables to Infer Context-Specific Genotype Effects in the Brain.

Authors:  Bernard Ng; William Casazza; Ellis Patrick; Shinya Tasaki; Gherman Novakovsky; Daniel Felsky; Yiyi Ma; David A Bennett; Chris Gaiteri; Philip L De Jager; Sara Mostafavi
Journal:  Am J Hum Genet       Date:  2019-08-22       Impact factor: 11.025

Review 5.  Deciphering the Emerging Complexities of Molecular Mechanisms at GWAS Loci.

Authors:  Maren E Cannon; Karen L Mohlke
Journal:  Am J Hum Genet       Date:  2018-11-01       Impact factor: 11.025

6.  Functional Interrogation of a Depression-Related Serotonergic Single Nucleotide Polymorphism, rs6295, Using a Humanized Mouse Model.

Authors:  Ashley M Cunningham; Tabia L Santos; Vanessa A Gutzeit; Heather Hamilton; René Hen; Zoe R Donaldson
Journal:  ACS Chem Neurosci       Date:  2019-02-12       Impact factor: 4.418

7.  Novel Variants of ELP2 and PIAS1 in the Interferon Gamma Signaling Pathway Are Associated with Non-Small Cell Lung Cancer Survival.

Authors:  Yu Chen Zhao; Dongfang Tang; Sen Yang; Hongliang Liu; Sheng Luo; Thomas E Stinchcombe; Carolyn Glass; Li Su; Sipeng Shen; David C Christiani; Qingyi Wei
Journal:  Cancer Epidemiol Biomarkers Prev       Date:  2020-06-03       Impact factor: 4.254

8.  Evaluating marginal genetic correlation of associated loci for complex diseases and traits between European and East Asian populations.

Authors:  Haojie Lu; Ting Wang; Jinhui Zhang; Shuo Zhang; Shuiping Huang; Ping Zeng
Journal:  Hum Genet       Date:  2021-06-06       Impact factor: 4.132

9.  Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits.

Authors:  Chelsea K Raulerson; Arthur Ko; John C Kidd; Kevin W Currin; Sarah M Brotman; Maren E Cannon; Ying Wu; Cassandra N Spracklen; Anne U Jackson; Heather M Stringham; Ryan P Welch; Christian Fuchsberger; Adam E Locke; Narisu Narisu; Aldons J Lusis; Mete Civelek; Terrence S Furey; Johanna Kuusisto; Francis S Collins; Michael Boehnke; Laura J Scott; Dan-Yu Lin; Michael I Love; Markku Laakso; Päivi Pajukanta; Karen L Mohlke
Journal:  Am J Hum Genet       Date:  2019-09-26       Impact factor: 11.025

10.  Genetic variants of DOCK2, EPHB1 and VAV2 in the natural killer cell-related pathway are associated with non-small cell lung cancer survival.

Authors:  Hailei Du; Lihua Liu; Hongliang Liu; Sheng Luo; Edward F Patz; Carolyn Glass; Li Su; Mulong Du; David C Christiani; Qingyi Wei
Journal:  Am J Cancer Res       Date:  2021-05-15       Impact factor: 6.166

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