Literature DB >> 27140283

Developing and evaluating polygenic risk prediction models for stratified disease prevention.

Nilanjan Chatterjee1,2,3, Jianxin Shi3, Montserrat García-Closas3.   

Abstract

Knowledge of genetics and its implications for human health is rapidly evolving in accordance with recent events, such as discoveries of large numbers of disease susceptibility loci from genome-wide association studies, the US Supreme Court ruling of the non-patentability of human genes, and the development of a regulatory framework for commercial genetic tests. In anticipation of the increasing relevance of genetic testing for the assessment of disease risks, this Review provides a summary of the methodologies used for building, evaluating and applying risk prediction models that include information from genetic testing and environmental risk factors. Potential applications of models for primary and secondary disease prevention are illustrated through several case studies, and future challenges and opportunities are discussed.

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Year:  2016        PMID: 27140283      PMCID: PMC6021129          DOI: 10.1038/nrg.2016.27

Source DB:  PubMed          Journal:  Nat Rev Genet        ISSN: 1471-0056            Impact factor:   53.242


  104 in total

1.  Estimation of SNP heritability from dense genotype data.

Authors:  S Hong Lee; Jian Yang; Guo-Bo Chen; Stephan Ripke; Eli A Stahl; Christina M Hultman; Pamela Sklar; Peter M Visscher; Patrick F Sullivan; Michael E Goddard; Naomi R Wray
Journal:  Am J Hum Genet       Date:  2013-12-05       Impact factor: 11.025

2.  Testing calibration of risk models at extremes of disease risk.

Authors:  Minsun Song; Peter Kraft; Amit D Joshi; Myrto Barrdahl; Nilanjan Chatterjee
Journal:  Biostatistics       Date:  2014-07-14       Impact factor: 5.899

Review 3.  Predicting risk of type 2 diabetes mellitus with genetic risk models on the basis of established genome-wide association markers: a systematic review.

Authors:  Wei Bao; Frank B Hu; Shuang Rong; Ying Rong; Katherine Bowers; Enrique F Schisterman; Liegang Liu; Cuilin Zhang
Journal:  Am J Epidemiol       Date:  2013-09-05       Impact factor: 4.897

4.  The inheritance of liability to diseases with variable age of onset, with particular reference to diabetes mellitus.

Authors:  D S Falconer
Journal:  Ann Hum Genet       Date:  1967-08       Impact factor: 1.670

5.  Accuracy of reporting of family history of colorectal cancer.

Authors:  R J Mitchell; D Brewster; H Campbell; M E M Porteous; A H Wyllie; C C Bird; M G Dunlop
Journal:  Gut       Date:  2004-02       Impact factor: 23.059

6.  Advantages and pitfalls in the application of mixed-model association methods.

Authors:  Jian Yang; Noah A Zaitlen; Michael E Goddard; Peter M Visscher; Alkes L Price
Journal:  Nat Genet       Date:  2014-02       Impact factor: 38.330

7.  Potential usefulness of single nucleotide polymorphisms to identify persons at high cancer risk: an evaluation of seven common cancers.

Authors:  Ju-Hyun Park; Mitchell H Gail; Mark H Greene; Nilanjan Chatterjee
Journal:  J Clin Oncol       Date:  2012-05-14       Impact factor: 44.544

Review 8.  Net reclassification indices for evaluating risk prediction instruments: a critical review.

Authors:  Kathleen F Kerr; Zheyu Wang; Holly Janes; Robyn L McClelland; Bruce M Psaty; Margaret S Pepe
Journal:  Epidemiology       Date:  2014-01       Impact factor: 4.822

9.  Prediction of breast cancer risk based on profiling with common genetic variants.

Authors:  Nasim Mavaddat; Paul D P Pharoah; Kyriaki Michailidou; Jonathan Tyrer; Mark N Brook; Manjeet K Bolla; Qin Wang; Joe Dennis; Alison M Dunning; Mitul Shah; Robert Luben; Judith Brown; Stig E Bojesen; Børge G Nordestgaard; Sune F Nielsen; Henrik Flyger; Kamila Czene; Hatef Darabi; Mikael Eriksson; Julian Peto; Isabel Dos-Santos-Silva; Frank Dudbridge; Nichola Johnson; Marjanka K Schmidt; Annegien Broeks; Senno Verhoef; Emiel J Rutgers; Anthony Swerdlow; Alan Ashworth; Nick Orr; Minouk J Schoemaker; Jonine Figueroa; Stephen J Chanock; Louise Brinton; Jolanta Lissowska; Fergus J Couch; Janet E Olson; Celine Vachon; Vernon S Pankratz; Diether Lambrechts; Hans Wildiers; Chantal Van Ongeval; Erik van Limbergen; Vessela Kristensen; Grethe Grenaker Alnæs; Silje Nord; Anne-Lise Borresen-Dale; Heli Nevanlinna; Taru A Muranen; Kristiina Aittomäki; Carl Blomqvist; Jenny Chang-Claude; Anja Rudolph; Petra Seibold; Dieter Flesch-Janys; Peter A Fasching; Lothar Haeberle; Arif B Ekici; Matthias W Beckmann; Barbara Burwinkel; Frederik Marme; Andreas Schneeweiss; Christof Sohn; Amy Trentham-Dietz; Polly Newcomb; Linda Titus; Kathleen M Egan; David J Hunter; Sara Lindstrom; Rulla M Tamimi; Peter Kraft; Nazneen Rahman; Clare Turnbull; Anthony Renwick; Sheila Seal; Jingmei Li; Jianjun Liu; Keith Humphreys; Javier Benitez; M Pilar Zamora; Jose Ignacio Arias Perez; Primitiva Menéndez; Anna Jakubowska; Jan Lubinski; Katarzyna Jaworska-Bieniek; Katarzyna Durda; Natalia V Bogdanova; Natalia N Antonenkova; Thilo Dörk; Hoda Anton-Culver; Susan L Neuhausen; Argyrios Ziogas; Leslie Bernstein; Peter Devilee; Robert A E M Tollenaar; Caroline Seynaeve; Christi J van Asperen; Angela Cox; Simon S Cross; Malcolm W R Reed; Elza Khusnutdinova; Marina Bermisheva; Darya Prokofyeva; Zalina Takhirova; Alfons Meindl; Rita K Schmutzler; Christian Sutter; Rongxi Yang; Peter Schürmann; Michael Bremer; Hans Christiansen; Tjoung-Won Park-Simon; Peter Hillemanns; Pascal Guénel; Thérèse Truong; Florence Menegaux; Marie Sanchez; Paolo Radice; Paolo Peterlongo; Siranoush Manoukian; Valeria Pensotti; John L Hopper; Helen Tsimiklis; Carmel Apicella; Melissa C Southey; Hiltrud Brauch; Thomas Brüning; Yon-Dschun Ko; Alice J Sigurdson; Michele M Doody; Ute Hamann; Diana Torres; Hans-Ulrich Ulmer; Asta Försti; Elinor J Sawyer; Ian Tomlinson; Michael J Kerin; Nicola Miller; Irene L Andrulis; Julia A Knight; Gord Glendon; Anna Marie Mulligan; Georgia Chenevix-Trench; Rosemary Balleine; Graham G Giles; Roger L Milne; Catriona McLean; Annika Lindblom; Sara Margolin; Christopher A Haiman; Brian E Henderson; Fredrick Schumacher; Loic Le Marchand; Ursula Eilber; Shan Wang-Gohrke; Maartje J Hooning; Antoinette Hollestelle; Ans M W van den Ouweland; Linetta B Koppert; Jane Carpenter; Christine Clarke; Rodney Scott; Arto Mannermaa; Vesa Kataja; Veli-Matti Kosma; Jaana M Hartikainen; Hermann Brenner; Volker Arndt; Christa Stegmaier; Aida Karina Dieffenbach; Robert Winqvist; Katri Pylkäs; Arja Jukkola-Vuorinen; Mervi Grip; Kenneth Offit; Joseph Vijai; Mark Robson; Rohini Rau-Murthy; Miriam Dwek; Ruth Swann; Katherine Annie Perkins; Mark S Goldberg; France Labrèche; Martine Dumont; Diana M Eccles; William J Tapper; Sajjad Rafiq; Esther M John; Alice S Whittemore; Susan Slager; Drakoulis Yannoukakos; Amanda E Toland; Song Yao; Wei Zheng; Sandra L Halverson; Anna González-Neira; Guillermo Pita; M Rosario Alonso; Nuria Álvarez; Daniel Herrero; Daniel C Tessier; Daniel Vincent; Francois Bacot; Craig Luccarini; Caroline Baynes; Shahana Ahmed; Mel Maranian; Catherine S Healey; Jacques Simard; Per Hall; Douglas F Easton; Montserrat Garcia-Closas
Journal:  J Natl Cancer Inst       Date:  2015-04-08       Impact factor: 13.506

10.  Post-GWAS gene-environment interplay in breast cancer: results from the Breast and Prostate Cancer Cohort Consortium and a meta-analysis on 79,000 women.

Authors:  Myrto Barrdahl; Federico Canzian; Amit D Joshi; Ruth C Travis; Jenny Chang-Claude; Paul L Auer; Susan M Gapstur; Mia Gaudet; W Ryan Diver; Brian E Henderson; Christopher A Haiman; Fredrick R Schumacher; Loïc Le Marchand; Christine D Berg; Stephen J Chanock; Robert N Hoover; Anja Rudolph; Regina G Ziegler; Graham G Giles; Laura Baglietto; Gianluca Severi; Susan E Hankinson; Sara Lindström; Walter Willet; David J Hunter; Julie E Buring; I-Min Lee; Shumin Zhang; Laure Dossus; David G Cox; Kay-Tee Khaw; Eiliv Lund; Alessio Naccarati; Petra H Peeters; J Ramón Quirós; Elio Riboli; Malin Sund; Dimitrios Trichopoulos; Ross L Prentice; Peter Kraft; Rudolf Kaaks; Daniele Campa
Journal:  Hum Mol Genet       Date:  2014-05-08       Impact factor: 6.150

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  244 in total

Review 1.  Complex Trait Prediction from Genome Data: Contrasting EBV in Livestock to PRS in Humans: Genomic Prediction.

Authors:  Naomi R Wray; Kathryn E Kemper; Benjamin J Hayes; Michael E Goddard; Peter M Visscher
Journal:  Genetics       Date:  2019-04       Impact factor: 4.562

Review 2.  Polygenic Scores to Assess Atherosclerotic Cardiovascular Disease Risk: Clinical Perspectives and Basic Implications.

Authors:  Krishna G Aragam; Pradeep Natarajan
Journal:  Circ Res       Date:  2020-04-23       Impact factor: 17.367

Review 3.  A systems approach to clinical oncology uses deep phenotyping to deliver personalized care.

Authors:  James T Yurkovich; Qiang Tian; Nathan D Price; Leroy Hood
Journal:  Nat Rev Clin Oncol       Date:  2019-10-16       Impact factor: 66.675

4.  Genetic variants demonstrating flip-flop phenomenon and breast cancer risk prediction among women of African ancestry.

Authors:  Shengfeng Wang; Frank Qian; Yonglan Zheng; Temidayo Ogundiran; Oladosu Ojengbede; Wei Zheng; William Blot; Katherine L Nathanson; Anselm Hennis; Barbara Nemesure; Stefan Ambs; Olufunmilayo I Olopade; Dezheng Huo
Journal:  Breast Cancer Res Treat       Date:  2018-01-04       Impact factor: 4.872

5.  Determination of chemical-disease risk values to prioritize connections between environmental factors, genetic variants, and human diseases.

Authors:  Marissa B Kosnik; David M Reif
Journal:  Toxicol Appl Pharmacol       Date:  2019-07-16       Impact factor: 4.219

6.  iFunMed: Integrative functional mediation analysis of GWAS and eQTL studies.

Authors:  Constanza Rojo; Qi Zhang; Sündüz Keleş
Journal:  Genet Epidemiol       Date:  2019-07-22       Impact factor: 2.135

7.  SummaryAUC: a tool for evaluating the performance of polygenic risk prediction models in validation datasets with only summary level statistics.

Authors:  Lei Song; Aiyi Liu; Jianxin Shi
Journal:  Bioinformatics       Date:  2019-10-15       Impact factor: 6.937

Review 8.  African genetic diversity and adaptation inform a precision medicine agenda.

Authors:  Luisa Pereira; Leon Mutesa; Paulina Tindana; Michèle Ramsay
Journal:  Nat Rev Genet       Date:  2021-01-11       Impact factor: 53.242

9.  Breast Cancer-Related Low Penetrance Genes.

Authors:  Daehee Kang; Ji-Yeob Choi
Journal:  Adv Exp Med Biol       Date:  2021       Impact factor: 2.622

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

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