Literature DB >> 30978304

The Future of Genomic Studies Must Be Globally Representative: Perspectives from PAGE.

Stephanie A Bien1, Genevieve L Wojcik2, Chani J Hodonsky3, Christopher R Gignoux4, Iona Cheng5, Tara C Matise6, Ulrike Peters1, Eimear E Kenny7, Kari E North3.   

Abstract

The past decade has seen a technological revolution in human genetics that has empowered population-level investigations into genetic associations with phenotypes. Although these discoveries rely on genetic variation across individuals, association studies have overwhelmingly been performed in populations of European descent. In this review, we describe limitations faced by single-population studies and provide an overview of strategies to improve global representation in existing data sets and future human genomics research via diversity-focused, multiethnic studies. We highlight the successes of individual studies and meta-analysis consortia that have provided unique knowledge. Additionally, we outline the approach taken by the Population Architecture Using Genomics and Epidemiology (PAGE) study to develop best practices for performing genetic epidemiology in multiethnic contexts. Finally, we discuss how limiting investigations to single populations impairs findings in the clinical domain for both rare-variant identification and genetic risk prediction.

Entities:  

Keywords:  PAGE; diversity; fine mapping; genomics; multiethnic; transethnic

Mesh:

Year:  2019        PMID: 30978304      PMCID: PMC7012212          DOI: 10.1146/annurev-genom-091416-035517

Source DB:  PubMed          Journal:  Annu Rev Genomics Hum Genet        ISSN: 1527-8204            Impact factor:   8.929


  122 in total

Review 1.  Five years of GWAS discovery.

Authors:  Peter M Visscher; Matthew A Brown; Mark I McCarthy; Jian Yang
Journal:  Am J Hum Genet       Date:  2012-01-13       Impact factor: 11.025

2.  Model-free Estimation of Recent Genetic Relatedness.

Authors:  Matthew P Conomos; Alexander P Reiner; Bruce S Weir; Timothy A Thornton
Journal:  Am J Hum Genet       Date:  2016-01-07       Impact factor: 11.025

3.  Principal components analysis corrects for stratification in genome-wide association studies.

Authors:  Alkes L Price; Nick J Patterson; Robert M Plenge; Michael E Weinblatt; Nancy A Shadick; David Reich
Journal:  Nat Genet       Date:  2006-07-23       Impact factor: 38.330

4.  RFMix: a discriminative modeling approach for rapid and robust local-ancestry inference.

Authors:  Brian K Maples; Simon Gravel; Eimear E Kenny; Carlos D Bustamante
Journal:  Am J Hum Genet       Date:  2013-08-01       Impact factor: 11.025

5.  Fine Mapping and Identification of BMI Loci in African Americans.

Authors:  Jian Gong; Fredrick Schumacher; Unhee Lim; Lucia A Hindorff; Jeff Haessler; Steven Buyske; Christopher S Carlson; Stephanie Rosse; Petra Bůžková; Myriam Fornage; Myron Gross; Nathan Pankratz; James S Pankow; Pamela J Schreiner; Richard Cooper; Georg Ehret; C Charles Gu; Denise Houston; Marguerite R Irvin; Rebecca Jackson; Lew Kuller; Brian Henderson; Iona Cheng; Lynne Wilkens; Mark Leppert; Cora E Lewis; Rongling Li; Khanh-Dung H Nguyen; Robert Goodloe; Eric Farber-Eger; Jonathan Boston; Holli H Dilks; Marylyn D Ritchie; Jay Fowke; Loreall Pooler; Misa Graff; Lindsay Fernandez-Rhodes; Barbara Cochrane; Eric Boerwinkle; Charles Kooperberg; Tara C Matise; Loic Le Marchand; Dana C Crawford; Christopher A Haiman; Kari E North; Ulrike Peters
Journal:  Am J Hum Genet       Date:  2013-10-03       Impact factor: 11.025

6.  Worldwide Frequencies of APOL1 Renal Risk Variants.

Authors:  Girish N Nadkarni; Christopher R Gignoux; Elena P Sorokin; Michelle Daya; Rayees Rahman; Kathleen C Barnes; Christina L Wassel; Eimear E Kenny
Journal:  N Engl J Med       Date:  2018-12-27       Impact factor: 91.245

7.  Robust inference of population structure for ancestry prediction and correction of stratification in the presence of relatedness.

Authors:  Matthew P Conomos; Michael B Miller; Timothy A Thornton
Journal:  Genet Epidemiol       Date:  2015-03-23       Impact factor: 2.135

8.  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

9.  Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals.

Authors:  Alexis Battle; Sara Mostafavi; Xiaowei Zhu; James B Potash; Myrna M Weissman; Courtney McCormick; Christian D Haudenschild; Kenneth B Beckman; Jianxin Shi; Rui Mei; Alexander E Urban; Stephen B Montgomery; Douglas F Levinson; Daphne Koller
Journal:  Genome Res       Date:  2013-10-03       Impact factor: 9.043

10.  Strategies for Enriching Variant Coverage in Candidate Disease Loci on a Multiethnic Genotyping Array.

Authors:  Stephanie A Bien; Genevieve L Wojcik; Niha Zubair; Christopher R Gignoux; Alicia R Martin; Jonathan M Kocarnik; Lisa W Martin; Steven Buyske; Jeffrey Haessler; Ryan W Walker; Iona Cheng; Mariaelisa Graff; Lucy Xia; Nora Franceschini; Tara Matise; Regina James; Lucia Hindorff; Loic Le Marchand; Kari E North; Christopher A Haiman; Ulrike Peters; Ruth J F Loos; Charles L Kooperberg; Carlos D Bustamante; Eimear E Kenny; Christopher S Carlson
Journal:  PLoS One       Date:  2016-12-14       Impact factor: 3.240

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  10 in total

1.  Variable prediction accuracy of polygenic scores within an ancestry group.

Authors:  Hakhamanesh Mostafavi; Arbel Harpak; Ipsita Agarwal; Dalton Conley; Jonathan K Pritchard; Molly Przeworski
Journal:  Elife       Date:  2020-01-30       Impact factor: 8.140

2.  Genome sequencing as a first-line diagnostic test for hospitalized infants.

Authors:  Kevin M Bowling; Michelle L Thompson; Candice R Finnila; Susan M Hiatt; Donald R Latner; Michelle D Amaral; James M J Lawlor; Kelly M East; Meagan E Cochran; Veronica Greve; Whitley V Kelley; David E Gray; Stephanie A Felker; Hannah Meddaugh; Ashley Cannon; Amanda Luedecke; Kelly E Jackson; Laura G Hendon; Hillary M Janani; Marla Johnston; Lee Ann Merin; Sarah L Deans; Carly Tuura; Heather Williams; Kelly Laborde; Matthew B Neu; Jessica Patrick-Esteve; Anna C E Hurst; Jegen Kandasamy; Wally Carlo; Kyle B Brothers; Brian M Kirmse; Renate Savich; Duane Superneau; Steven B Spedale; Sara J Knight; Gregory S Barsh; Bruce R Korf; Gregory M Cooper
Journal:  Genet Med       Date:  2021-11-27       Impact factor: 8.864

3.  Multi-Omic Approaches to Identify Genetic Factors in Metabolic Syndrome.

Authors:  Karen C Clark; Anne E Kwitek
Journal:  Compr Physiol       Date:  2021-12-29       Impact factor: 8.915

4.  Editorial: Polygenic Risk Scores in Child Psychiatry, Research Promise, and Potential Clinical Pitfalls.

Authors:  Philip Shaw
Journal:  J Am Acad Child Adolesc Psychiatry       Date:  2021-10-23       Impact factor: 13.113

Review 5.  Strategic vision for improving human health at The Forefront of Genomics.

Authors:  Eric D Green; Chris Gunter; Leslie G Biesecker; Valentina Di Francesco; Carla L Easter; Elise A Feingold; Adam L Felsenfeld; David J Kaufman; Elaine A Ostrander; William J Pavan; Adam M Phillippy; Anastasia L Wise; Jyoti Gupta Dayal; Britny J Kish; Allison Mandich; Christopher R Wellington; Kris A Wetterstrand; Sarah A Bates; Darryl Leja; Susan Vasquez; William A Gahl; Bettie J Graham; Daniel L Kastner; Paul Liu; Laura Lyman Rodriguez; Benjamin D Solomon; Vence L Bonham; Lawrence C Brody; Carolyn M Hutter; Teri A Manolio
Journal:  Nature       Date:  2020-10-28       Impact factor: 49.962

6.  A variant-centric perspective on geographic patterns of human allele frequency variation.

Authors:  Arjun Biddanda; Daniel P Rice; John Novembre
Journal:  Elife       Date:  2020-12-22       Impact factor: 8.140

7.  Distinguishable DNA methylation defines disease susceptibility influenced by race and ethnicity.

Authors:  Jairo A Pinzon Cortes; Assam El-Osta
Journal:  Clin Epigenetics       Date:  2021-10-11       Impact factor: 6.551

Review 8.  Genomics and Functional Genomics of Alzheimer's Disease.

Authors:  M Ilyas Kamboh
Journal:  Neurotherapeutics       Date:  2021-12-21       Impact factor: 6.088

9.  Genetic analysis of hsCRP in American Indians: The Strong Heart Family Study.

Authors:  Lyle G Best; Poojitha Balakrishnan; Shelley A Cole; Karin Haack; Jonathan M Kocarnik; Nathan Pankratz; Matthew Z Anderson; Nora Franceschini; Barbara V Howard; Elisa T Lee; Kari E North; Jason G Umans; Joseph M Yracheta; Ana Navas-Acien; V Saroja Voruganti
Journal:  PLoS One       Date:  2019-10-17       Impact factor: 3.240

Review 10.  Evaluating the promise of inclusion of African ancestry populations in genomics.

Authors:  Amy R Bentley; Shawneequa L Callier; Charles N Rotimi
Journal:  NPJ Genom Med       Date:  2020-02-25       Impact factor: 8.617

  10 in total

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