Literature DB >> 33691767

Editing GWAS: experimental approaches to dissect and exploit disease-associated genetic variation.

Shuquan Rao1, Yao Yao2,3, Daniel E Bauer4.   

Abstract

Genome-wide association studies (GWAS) have uncovered thousands of genetic variants that influence risk for human diseases and traits. Yet understanding the mechanisms by which these genetic variants, mainly noncoding, have an impact on associated diseases and traits remains a significant hurdle. In this review, we discuss emerging experimental approaches that are being applied for functional studies of causal variants and translational advances from GWAS findings to disease prevention and treatment. We highlight the use of genome editing technologies in GWAS functional studies to modify genomic sequences, with proof-of-principle examples. We discuss the challenges in interrogating causal variants, points for consideration in experimental design and interpretation of GWAS locus mechanisms, and the potential for novel therapeutic opportunities. With the accumulation of knowledge of functional genetics, therapeutic genome editing based on GWAS discoveries will become increasingly feasible.

Entities:  

Keywords:  CRISPR/Cas; GWAS; Genome editing; High throughput

Mesh:

Year:  2021        PMID: 33691767      PMCID: PMC7948363          DOI: 10.1186/s13073-021-00857-3

Source DB:  PubMed          Journal:  Genome Med        ISSN: 1756-994X            Impact factor:   11.117


  144 in total

Review 1.  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

2.  Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets.

Authors:  Zhihong Zhu; Futao Zhang; Han Hu; Andrew Bakshi; Matthew R Robinson; Joseph E Powell; Grant W Montgomery; Michael E Goddard; Naomi R Wray; Peter M Visscher; Jian Yang
Journal:  Nat Genet       Date:  2016-03-28       Impact factor: 38.330

3.  Deciphering Gene Regulation Using Massively Parallel Reporter Assays.

Authors:  Max Trauernicht; Miguel Martinez-Ara; Bas van Steensel
Journal:  Trends Biochem Sci       Date:  2019-11-11       Impact factor: 13.807

4.  Integrative approaches for large-scale transcriptome-wide association studies.

Authors:  Alexander Gusev; Arthur Ko; Huwenbo Shi; Gaurav Bhatia; Wonil Chung; Brenda W J H Penninx; Rick Jansen; Eco J C de Geus; Dorret I Boomsma; Fred A Wright; Patrick F Sullivan; Elina Nikkola; Marcus Alvarez; Mete Civelek; Aldons J Lusis; Terho Lehtimäki; Emma Raitoharju; Mika Kähönen; Ilkka Seppälä; Olli T Raitakari; Johanna Kuusisto; Markku Laakso; Alkes L Price; Päivi Pajukanta; Bogdan Pasaniuc
Journal:  Nat Genet       Date:  2016-02-08       Impact factor: 38.330

5.  Therapeutic base editing of human hematopoietic stem cells.

Authors:  Jing Zeng; Yuxuan Wu; Chunyan Ren; Jasmine Bonanno; Anne H Shen; Devlin Shea; Jason M Gehrke; Kendell Clement; Kevin Luk; Qiuming Yao; Rachel Kim; Scot A Wolfe; John P Manis; Luca Pinello; J Keith Joung; Daniel E Bauer
Journal:  Nat Med       Date:  2020-03-16       Impact factor: 53.440

6.  Systematic Functional Dissection of Common Genetic Variation Affecting Red Blood Cell Traits.

Authors:  Jacob C Ulirsch; Satish K Nandakumar; Li Wang; Felix C Giani; Xiaolan Zhang; Peter Rogov; Alexandre Melnikov; Patrick McDonel; Ron Do; Tarjei S Mikkelsen; Vijay G Sankaran
Journal:  Cell       Date:  2016-06-02       Impact factor: 41.582

Review 7.  10 Years of GWAS Discovery: Biology, Function, and Translation.

Authors:  Peter M Visscher; Naomi R Wray; Qian Zhang; Pamela Sklar; Mark I McCarthy; Matthew A Brown; Jian Yang
Journal:  Am J Hum Genet       Date:  2017-07-06       Impact factor: 11.025

8.  Dissecting ELANE neutropenia pathogenicity by human HSC gene editing.

Authors:  Shuquan Rao; Yao Yao; Josias Soares de Brito; Qiuming Yao; Anne H Shen; Ruth E Watkinson; Alyssa L Kennedy; Steven Coyne; Chunyan Ren; Jing Zeng; Anna Victoria Serbin; Sabine Studer; Kaitlyn Ballotti; Chad E Harris; Kevin Luk; Christian S Stevens; Myriam Armant; Luca Pinello; Scot A Wolfe; Roberto Chiarle; Akiko Shimamura; Benhur Lee; Peter E Newburger; Daniel E Bauer
Journal:  Cell Stem Cell       Date:  2021-01-28       Impact factor: 24.633

9.  An enhanced CRISPR repressor for targeted mammalian gene regulation.

Authors:  Nan Cher Yeo; Alejandro Chavez; Alissa Lance-Byrne; Yingleong Chan; David Menn; Denitsa Milanova; Chih-Chung Kuo; Xiaoge Guo; Sumana Sharma; Angela Tung; Ryan J Cecchi; Marcelle Tuttle; Swechchha Pradhan; Elaine T Lim; Noah Davidsohn; Mo R Ebrahimkhani; James J Collins; Nathan E Lewis; Samira Kiani; George M Church
Journal:  Nat Methods       Date:  2018-07-16       Impact factor: 28.547

10.  Continuous evolution of SpCas9 variants compatible with non-G PAMs.

Authors:  Shannon M Miller; Tina Wang; Peyton B Randolph; Mandana Arbab; Max W Shen; Tony P Huang; Zaneta Matuszek; Gregory A Newby; Holly A Rees; David R Liu
Journal:  Nat Biotechnol       Date:  2020-02-10       Impact factor: 54.908

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  4 in total

Review 1.  Understanding Regulatory Mechanisms of Brain Function and Disease through 3D Genome Organization.

Authors:  Weifang Liu; Wujuan Zhong; Jiawen Chen; Bo Huang; Ming Hu; Yun Li
Journal:  Genes (Basel)       Date:  2022-03-25       Impact factor: 4.141

2.  The landscape of GWAS validation; systematic review identifying 309 validated non-coding variants across 130 human diseases.

Authors:  Ammar J Alsheikh; Sabrina Wollenhaupt; Emily A King; Jonas Reeb; Sujana Ghosh; Lindsay R Stolzenburg; Saleh Tamim; Jozef Lazar; J Wade Davis; Howard J Jacob
Journal:  BMC Med Genomics       Date:  2022-04-01       Impact factor: 3.063

Review 3.  ULK4 in Neurodevelopmental and Neuropsychiatric Disorders.

Authors:  Shilin Luo; Nanxi Zheng; Bing Lang
Journal:  Front Cell Dev Biol       Date:  2022-04-12

4.  Genetic analyses of the electrocardiographic QT interval and its components identify additional loci and pathways.

Authors:  William J Young; Najim Lahrouchi; Aaron Isaacs; ThuyVy Duong; Luisa Foco; Farah Ahmed; Jennifer A Brody; Reem Salman; Raymond Noordam; Jan-Walter Benjamins; Jeffrey Haessler; Leo-Pekka Lyytikäinen; Linda Repetto; Maria Pina Concas; Marten E van den Berg; Stefan Weiss; Antoine R Baldassari; Traci M Bartz; James P Cook; Daniel S Evans; Rebecca Freudling; Oliver Hines; Jonas L Isaksen; Honghuang Lin; Hao Mei; Arden Moscati; Martina Müller-Nurasyid; Casia Nursyifa; Yong Qian; Anne Richmond; Carolina Roselli; Kathleen A Ryan; Eduardo Tarazona-Santos; Sébastien Thériault; Stefan van Duijvenboden; Helen R Warren; Jie Yao; Dania Raza; Stefanie Aeschbacher; Gustav Ahlberg; Alvaro Alonso; Laura Andreasen; Joshua C Bis; Eric Boerwinkle; Archie Campbell; Eulalia Catamo; Massimiliano Cocca; Michael J Cutler; Dawood Darbar; Alessandro De Grandi; Antonio De Luca; Jun Ding; Christina Ellervik; Patrick T Ellinor; Stephan B Felix; Philippe Froguel; Christian Fuchsberger; Martin Gögele; Claus Graff; Mariaelisa Graff; Xiuqing Guo; Torben Hansen; Susan R Heckbert; Paul L Huang; Heikki V Huikuri; Nina Hutri-Kähönen; M Arfan Ikram; Rebecca D Jackson; Juhani Junttila; Maryam Kavousi; Jan A Kors; Thiago P Leal; Rozenn N Lemaitre; Henry J Lin; Lars Lind; Allan Linneberg; Simin Liu; Peter W MacFarlane; Massimo Mangino; Thomas Meitinger; Massimo Mezzavilla; Pashupati P Mishra; Rebecca N Mitchell; Nina Mononen; May E Montasser; Alanna C Morrison; Matthias Nauck; Victor Nauffal; Pau Navarro; Kjell Nikus; Guillaume Pare; Kristen K Patton; Giulia Pelliccione; Alan Pittman; David J Porteous; Peter P Pramstaller; Michael H Preuss; Olli T Raitakari; Alexander P Reiner; Antonio Luiz P Ribeiro; Kenneth M Rice; Lorenz Risch; David Schlessinger; Ulrich Schotten; Claudia Schurmann; Xia Shen; M Benjamin Shoemaker; Gianfranco Sinagra; Moritz F Sinner; Elsayed Z Soliman; Monika Stoll; Konstantin Strauch; Kirill Tarasov; Kent D Taylor; Andrew Tinker; Stella Trompet; André Uitterlinden; Uwe Völker; Henry Völzke; Melanie Waldenberger; Lu-Chen Weng; Eric A Whitsel; James G Wilson; Christy L Avery; David Conen; Adolfo Correa; Francesco Cucca; Marcus Dörr; Sina A Gharib; Giorgia Girotto; Niels Grarup; Caroline Hayward; Yalda Jamshidi; Marjo-Riitta Järvelin; J Wouter Jukema; Stefan Kääb; Mika Kähönen; Jørgen K Kanters; Charles Kooperberg; Terho Lehtimäki; Maria Fernanda Lima-Costa; Yongmei Liu; Ruth J F Loos; Steven A Lubitz; Dennis O Mook-Kanamori; Andrew P Morris; Jeffrey R O'Connell; Morten Salling Olesen; Michele Orini; Sandosh Padmanabhan; Cristian Pattaro; Annette Peters; Bruce M Psaty; Jerome I Rotter; Bruno Stricker; Pim van der Harst; Cornelia M van Duijn; Niek Verweij; James F Wilson; Dan E Arking; Julia Ramirez; Pier D Lambiase; Nona Sotoodehnia; Borbala Mifsud; Christopher Newton-Cheh; Patricia B Munroe
Journal:  Nat Commun       Date:  2022-09-01       Impact factor: 17.694

  4 in total

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