Literature DB >> 23650636

Expression quantitative trait loci: present and future.

Alexandra C Nica1, Emmanouil T Dermitzakis.   

Abstract

The last few years have seen the development of large efforts for the analysis of genome function, especially in the context of genome variation. One of the most prominent directions has been the extensive set of studies on expression quantitative trait loci (eQTLs), namely, the discovery of genetic variants that explain variation in gene expression levels. Such studies have offered promise not just for the characterization of functional sequence variation but also for the understanding of basic processes of gene regulation and interpretation of genome-wide association studies. In this review, we discuss some of the key directions of eQTL research and its implications.

Keywords:  expression quantitative trait loci; genetics; regulation

Mesh:

Year:  2013        PMID: 23650636      PMCID: PMC3682727          DOI: 10.1098/rstb.2012.0362

Source DB:  PubMed          Journal:  Philos Trans R Soc Lond B Biol Sci        ISSN: 0962-8436            Impact factor:   6.237


  41 in total

1.  Common genetic variants account for differences in gene expression among ethnic groups.

Authors:  Richard S Spielman; Laurel A Bastone; Joshua T Burdick; Michael Morley; Warren J Ewens; Vivian G Cheung
Journal:  Nat Genet       Date:  2007-01-07       Impact factor: 38.330

2.  Gene-expression variation within and among human populations.

Authors:  John D Storey; Jennifer Madeoy; Jeanna L Strout; Mark Wurfel; James Ronald; Joshua M Akey
Journal:  Am J Hum Genet       Date:  2007-01-11       Impact factor: 11.025

Review 3.  The evolutionary significance of cis-regulatory mutations.

Authors:  Gregory A Wray
Journal:  Nat Rev Genet       Date:  2007-03       Impact factor: 53.242

4.  Reconstruction of a functional human gene network, with an application for prioritizing positional candidate genes.

Authors:  Lude Franke; Harm van Bakel; Like Fokkens; Edwin D de Jong; Michael Egmont-Petersen; Cisca Wijmenga
Journal:  Am J Hum Genet       Date:  2006-04-25       Impact factor: 11.025

5.  Genetic dissection of transcriptional regulation in budding yeast.

Authors:  Rachel B Brem; Gaël Yvert; Rebecca Clinton; Leonid Kruglyak
Journal:  Science       Date:  2002-03-28       Impact factor: 47.728

6.  Genetic interactions between polymorphisms that affect gene expression in yeast.

Authors:  Rachel B Brem; John D Storey; Jacqueline Whittle; Leonid Kruglyak
Journal:  Nature       Date:  2005-08-04       Impact factor: 49.962

7.  Genome-wide expression profiling of lymphoblastoid cell lines distinguishes different forms of autism and reveals shared pathways.

Authors:  Yuhei Nishimura; Christa L Martin; Araceli Vazquez-Lopez; Sarah J Spence; Ana Isabel Alvarez-Retuerto; Marian Sigman; Corinna Steindler; Sandra Pellegrini; N Carolyn Schanen; Stephen T Warren; Daniel H Geschwind
Journal:  Hum Mol Genet       Date:  2007-05-21       Impact factor: 6.150

8.  Discovery and fine mapping of serum protein loci through transethnic meta-analysis.

Authors:  Nora Franceschini; Frank J A van Rooij; Bram P Prins; Mary F Feitosa; Mahir Karakas; John H Eckfeldt; Aaron R Folsom; Jeffrey Kopp; Ahmad Vaez; Jeanette S Andrews; Jens Baumert; Vesna Boraska; Linda Broer; Caroline Hayward; Julius S Ngwa; Yukinori Okada; Ozren Polasek; Harm-Jan Westra; Ying A Wang; Fabiola Del Greco M; Nicole L Glazer; Karen Kapur; Ido P Kema; Lorna M Lopez; Arne Schillert; Albert V Smith; Cheryl A Winkler; Lina Zgaga; Stefania Bandinelli; Sven Bergmann; Mladen Boban; Murielle Bochud; Y D Chen; Gail Davies; Abbas Dehghan; Jingzhong Ding; Angela Doering; J Peter Durda; Luigi Ferrucci; Oscar H Franco; Lude Franke; Grog Gunjaca; Albert Hofman; Fang-Chi Hsu; Ivana Kolcic; Aldi Kraja; Michiaki Kubo; Karl J Lackner; Lenore Launer; Laura R Loehr; Guo Li; Christa Meisinger; Yusuke Nakamura; Christine Schwienbacher; John M Starr; Atsushi Takahashi; Vesela Torlak; André G Uitterlinden; Veronique Vitart; Melanie Waldenberger; Philipp S Wild; Mirna Kirin; Tanja Zeller; Tatijana Zemunik; Qunyuan Zhang; Andreas Ziegler; Stefan Blankenberg; Eric Boerwinkle; Ingrid B Borecki; Harry Campbell; Ian J Deary; Timothy M Frayling; Christian Gieger; Tamara B Harris; Andrew A Hicks; Wolfgang Koenig; Christopher J O' Donnell; Caroline S Fox; Peter P Pramstaller; Bruce M Psaty; Alex P Reiner; Jerome I Rotter; Igor Rudan; Harold Snieder; Toshihiro Tanaka; Cornelia M van Duijn; Peter Vollenweider; Gerard Waeber; James F Wilson; Jacqueline C M Witteman; Bruce H R Wolffenbuttel; Alan F Wright; Qingyu Wu; Yongmei Liu; Nancy S Jenny; Kari E North; Janine F Felix; Behrooz Z Alizadeh; L Adrienne Cupples; John R B Perry; Andrew P Morris
Journal:  Am J Hum Genet       Date:  2012-09-27       Impact factor: 11.025

9.  Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls.

Authors: 
Journal:  Nature       Date:  2007-06-07       Impact factor: 49.962

10.  Novel Crohn disease locus identified by genome-wide association maps to a gene desert on 5p13.1 and modulates expression of PTGER4.

Authors:  Cécile Libioulle; Edouard Louis; Sarah Hansoul; Cynthia Sandor; Frédéric Farnir; Denis Franchimont; Séverine Vermeire; Olivier Dewit; Martine de Vos; Anna Dixon; Bruno Demarche; Ivo Gut; Simon Heath; Mario Foglio; Liming Liang; Debby Laukens; Myriam Mni; Diana Zelenika; André Van Gossum; Paul Rutgeerts; Jacques Belaiche; Mark Lathrop; Michel Georges
Journal:  PLoS Genet       Date:  2007-03-05       Impact factor: 5.917

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  143 in total

1.  Characterising cis-regulatory variation in the transcriptome of histologically normal and tumour-derived pancreatic tissues.

Authors:  Mingfeng Zhang; Soren Lykke-Andersen; Bin Zhu; Wenming Xiao; Jason W Hoskins; Xijun Zhang; Lauren M Rost; Irene Collins; Martijn van de Bunt; Jinping Jia; Hemang Parikh; Tongwu Zhang; Lei Song; Ashley Jermusyk; Charles C Chung; Bin Zhu; Weiyin Zhou; Gail L Matters; Robert C Kurtz; Meredith Yeager; Torben Heick Jensen; Kevin M Brown; Halit Ongen; William R Bamlet; Bradley A Murray; Mark I McCarthy; Stephen J Chanock; Nilanjan Chatterjee; Brian M Wolpin; Jill P Smith; Sara H Olson; Gloria M Petersen; Jianxin Shi; Laufey Amundadottir
Journal:  Gut       Date:  2017-06-20       Impact factor: 23.059

Review 2.  Methods, Tools and Current Perspectives in Proteogenomics.

Authors:  Kelly V Ruggles; Karsten Krug; Xiaojing Wang; Karl R Clauser; Jing Wang; Samuel H Payne; David Fenyö; Bing Zhang; D R Mani
Journal:  Mol Cell Proteomics       Date:  2017-04-29       Impact factor: 5.911

3.  Potentially functional variants of HBEGF and ITPR3 in GnRH signaling pathway genes predict survival of non-small cell lung cancer patients.

Authors:  Yufeng Wu; Zhensheng Liu; Dongfang Tang; Hongliang Liu; Sheng Luo; Thomas E Stinchcombe; Carolyn Glass; Li Su; Lijuan Lin; David C Christiani; Qiming Wang; Qingyi Wei
Journal:  Transl Res       Date:  2021-01-02       Impact factor: 7.012

4.  The challenge of determining the impact of FUT3 tumor-associated polymorphism rs2306969 (-6951 C> T) in invasive breast cancer cells.

Authors:  Jessica Catarine Frutuoso do Nascimento; Anderson de Oliveira Vasconcelos; Maria Aparecida Barreto Lopes Seabra; Eduardo Isidoro Carneiro Beltrão; Cíntia Renata Costa Rocha
Journal:  Mol Biol Rep       Date:  2019-03-30       Impact factor: 2.316

Review 5.  Evolutionary dynamics of coding and non-coding transcriptomes.

Authors:  Anamaria Necsulea; Henrik Kaessmann
Journal:  Nat Rev Genet       Date:  2014-10-09       Impact factor: 53.242

6.  An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease.

Authors:  Liuyang Wang; Kelly J Pittman; Jeffrey R Barker; Raul E Salinas; Ian B Stanaway; Graham D Williams; Robert J Carroll; Tom Balmat; Andy Ingham; Anusha M Gopalakrishnan; Kyle D Gibbs; Alejandro L Antonia; Joseph Heitman; Soo Chan Lee; Gail P Jarvik; Joshua C Denny; Stacy M Horner; Mark R DeLong; Raphael H Valdivia; David R Crosslin; Dennis C Ko
Journal:  Cell Host Microbe       Date:  2018-08-08       Impact factor: 21.023

7.  A METHYLATION-TO-EXPRESSION FEATURE MODEL FOR GENERATING ACCURATE PROGNOSTIC RISK SCORES AND IDENTIFYING DISEASE TARGETS IN CLEAR CELL KIDNEY CANCER.

Authors:  Jeffrey A Thompson; Carmen J Marsit
Journal:  Pac Symp Biocomput       Date:  2017

8.  DNA methylation near the INS gene is associated with INS genetic variation (rs689) and type 1 diabetes in the Diabetes Autoimmunity Study in the Young.

Authors:  Patrick M Carry; Lauren A Vanderlinden; Randi K Johnson; Fran Dong; Andrea K Steck; Brigitte I Frohnert; Marian Rewers; Ivana V Yang; Katerina Kechris; Jill M Norris
Journal:  Pediatr Diabetes       Date:  2020-02-28       Impact factor: 4.866

Review 9.  Insights into pancreatic islet cell dysfunction from type 2 diabetes mellitus genetics.

Authors:  Nicole A J Krentz; Anna L Gloyn
Journal:  Nat Rev Endocrinol       Date:  2020-02-25       Impact factor: 43.330

10.  Integrative Multi-omic Analysis of Human Platelet eQTLs Reveals Alternative Start Site in Mitofusin 2.

Authors:  Lukas M Simon; Edward S Chen; Leonard C Edelstein; Xianguo Kong; Seema Bhatlekar; Isidore Rigoutsos; Paul F Bray; Chad A Shaw
Journal:  Am J Hum Genet       Date:  2016-04-28       Impact factor: 11.025

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