Literature DB >> 20497613

Likelihood ratios for genome medicine.

Alexander A Morgan1, Rong Chen, Atul J Butte.   

Abstract

Patients are beginning to present to healthcare providers with the results of high-throughput individualized genotyping, and interpreting these results in the context of the explosive growth of literature linking individual variants with disease may seem daunting. However, we suggest that results of a personal genomic analysis may be viewed as a panel of many tests for multiple diseases. By using well-established methods of evidence based medicine, these very many parallel tests may be combined using likelihood ratios to report a post-test probability of disease for use in patient assessment.

Entities:  

Year:  2010        PMID: 20497613      PMCID: PMC2887074          DOI: 10.1186/gm151

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


  24 in total

1.  Users' guides to the medical literature: XV. How to use an article about disease probability for differential diagnosis. Evidence-Based Medicine Working Group.

Authors:  W S Richardson; M C Wilson; G H Guyatt; D J Cook; J Nishikawa
Journal:  JAMA       Date:  1999-04-07       Impact factor: 56.272

2.  Clinical assessment incorporating a personal genome.

Authors:  Euan A Ashley; Atul J Butte; Matthew T Wheeler; Rong Chen; Teri E Klein; Frederick E Dewey; Joel T Dudley; Kelly E Ormond; Aleksandra Pavlovic; Alexander A Morgan; Dmitry Pushkarev; Norma F Neff; Louanne Hudgins; Li Gong; Laura M Hodges; Dorit S Berlin; Caroline F Thorn; Katrin Sangkuhl; Joan M Hebert; Mark Woon; Hersh Sagreiya; Ryan Whaley; Joshua W Knowles; Michael F Chou; Joseph V Thakuria; Abraham M Rosenbaum; Alexander Wait Zaranek; George M Church; Henry T Greely; Stephen R Quake; Russ B Altman
Journal:  Lancet       Date:  2010-05-01       Impact factor: 79.321

3.  The incidentalome: a threat to genomic medicine.

Authors:  Isaac S Kohane; Daniel R Masys; Russ B Altman
Journal:  JAMA       Date:  2006-07-12       Impact factor: 56.272

4.  Overcoming the winner's curse: estimating penetrance parameters from case-control data.

Authors:  Sebastian Zollner; Jonathan K Pritchard
Journal:  Am J Hum Genet       Date:  2007-02-16       Impact factor: 11.025

5.  Bias-reduced estimators and confidence intervals for odds ratios in genome-wide association studies.

Authors:  Hua Zhong; Ross L Prentice
Journal:  Biostatistics       Date:  2008-02-28       Impact factor: 5.899

6.  A navigator for human genome epidemiology.

Authors:  Wei Yu; Marta Gwinn; Melinda Clyne; Ajay Yesupriya; Muin J Khoury
Journal:  Nat Genet       Date:  2008-02       Impact factor: 38.330

Review 7.  Why most discovered true associations are inflated.

Authors:  John P A Ioannidis
Journal:  Epidemiology       Date:  2008-09       Impact factor: 4.822

8.  The complete genome of an individual by massively parallel DNA sequencing.

Authors:  David A Wheeler; Maithreyan Srinivasan; Michael Egholm; Yufeng Shen; Lei Chen; Amy McGuire; Wen He; Yi-Ju Chen; Vinod Makhijani; G Thomas Roth; Xavier Gomes; Karrie Tartaro; Faheem Niazi; Cynthia L Turcotte; Gerard P Irzyk; James R Lupski; Craig Chinault; Xing-zhi Song; Yue Liu; Ye Yuan; Lynne Nazareth; Xiang Qin; Donna M Muzny; Marcel Margulies; George M Weinstock; Richard A Gibbs; Jonathan M Rothberg
Journal:  Nature       Date:  2008-04-17       Impact factor: 49.962

9.  Two genome-wide association studies of aggressive prostate cancer implicate putative prostate tumor suppressor gene DAB2IP.

Authors:  David Duggan; Siqun L Zheng; Michele Knowlton; Debbie Benitez; Latchezar Dimitrov; Fredrik Wiklund; Christiane Robbins; Sarah D Isaacs; Yu Cheng; Ge Li; Jielin Sun; Bao-Li Chang; Leslie Marovich; Kathleen E Wiley; Katarina Bälter; Pär Stattin; Hans-Olov Adami; Marta Gielzak; Guifang Yan; Jurga Sauvageot; Wennuan Liu; Jin Woo Kim; Eugene R Bleecker; Deborah A Meyers; Bruce J Trock; Alan W Partin; Patrick C Walsh; William B Isaacs; Henrik Grönberg; Jianfeng Xu; John D Carpten
Journal:  J Natl Cancer Inst       Date:  2007-12-11       Impact factor: 13.506

10.  The diploid genome sequence of an individual human.

Authors:  Samuel Levy; Granger Sutton; Pauline C Ng; Lars Feuk; Aaron L Halpern; Brian P Walenz; Nelson Axelrod; Jiaqi Huang; Ewen F Kirkness; Gennady Denisov; Yuan Lin; Jeffrey R MacDonald; Andy Wing Chun Pang; Mary Shago; Timothy B Stockwell; Alexia Tsiamouri; Vineet Bafna; Vikas Bansal; Saul A Kravitz; Dana A Busam; Karen Y Beeson; Tina C McIntosh; Karin A Remington; Josep F Abril; John Gill; Jon Borman; Yu-Hui Rogers; Marvin E Frazier; Stephen W Scherer; Robert L Strausberg; J Craig Venter
Journal:  PLoS Biol       Date:  2007-09-04       Impact factor: 8.029

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  14 in total

Review 1.  Personalized medicine: hope or hype?

Authors:  Keyan Salari; Hugh Watkins; Euan A Ashley
Journal:  Eur Heart J       Date:  2012-06-01       Impact factor: 29.983

2.  OrderRex: clinical order decision support and outcome predictions by data-mining electronic medical records.

Authors:  Jonathan H Chen; Tanya Podchiyska; Russ B Altman
Journal:  J Am Med Inform Assoc       Date:  2015-07-21       Impact factor: 4.497

3.  Additive interactions between susceptibility single-nucleotide polymorphisms identified in genome-wide association studies and breast cancer risk factors in the Breast and Prostate Cancer Cohort Consortium.

Authors:  Amit D Joshi; Sara Lindström; Anika Hüsing; Myrto Barrdahl; Tyler J VanderWeele; Daniele Campa; Federico Canzian; Mia M Gaudet; Jonine D Figueroa; Laura Baglietto; Christine D Berg; Julie E Buring; Stephen J Chanock; María-Dolores Chirlaque; W Ryan Diver; Laure Dossus; Graham G Giles; Christopher A Haiman; Susan E Hankinson; Brian E Henderson; Robert N Hoover; David J Hunter; Claudine Isaacs; Rudolf Kaaks; Laurence N Kolonel; Vittorio Krogh; Loic Le Marchand; I-Min Lee; Eiliv Lund; Catherine A McCarty; Kim Overvad; Petra H Peeters; Elio Riboli; Fredrick Schumacher; Gianluca Severi; Daniel O Stram; Malin Sund; Michael J Thun; Ruth C Travis; Dimitrios Trichopoulos; Walter C Willett; Shumin Zhang; Regina G Ziegler; Peter Kraft
Journal:  Am J Epidemiol       Date:  2014-09-25       Impact factor: 4.897

4.  Big data opens a window onto wellness.

Authors:  Atul J Butte
Journal:  Nat Biotechnol       Date:  2017-08-08       Impact factor: 54.908

5.  The reference human genome demonstrates high risk of type 1 diabetes and other disorders.

Authors:  Rong Chen; Atul J Butte
Journal:  Pac Symp Biocomput       Date:  2011

6.  Interpretome: a freely available, modular, and secure personal genome interpretation engine.

Authors:  Konrad J Karczewski; Robert P Tirrell; Pablo Cordero; Nicholas P Tatonetti; Joel T Dudley; Keyan Salari; Michael Snyder; Russ B Altman; Stuart K Kim
Journal:  Pac Symp Biocomput       Date:  2012

7.  Interpretable Clinical Genomics with a Likelihood Ratio Paradigm.

Authors:  Peter N Robinson; Vida Ravanmehr; Julius O B Jacobsen; Daniel Danis; Xingmin Aaron Zhang; Leigh C Carmody; Michael A Gargano; Courtney L Thaxton; Guy Karlebach; Justin Reese; Manuel Holtgrewe; Sebastian Köhler; Julie A McMurry; Melissa A Haendel; Damian Smedley
Journal:  Am J Hum Genet       Date:  2020-08-04       Impact factor: 11.025

8.  Multiplex meta-analysis of RNA expression to identify genes with variants associated with immune dysfunction.

Authors:  Alexander A Morgan; Vasilios J Pyrgos; Kari C Nadeau; Peter R Williamson; Atul Janardhan Butte
Journal:  J Am Med Inform Assoc       Date:  2012 Mar-Apr       Impact factor: 4.497

9.  Clinical utility of sequence-based genotype compared with that derivable from genotyping arrays.

Authors:  Alexander A Morgan; Rong Chen; Atul Janardhan Butte
Journal:  J Am Med Inform Assoc       Date:  2012-06       Impact factor: 4.497

10.  Type 2 diabetes risk alleles demonstrate extreme directional differentiation among human populations, compared to other diseases.

Authors:  Rong Chen; Erik Corona; Martin Sikora; Joel T Dudley; Alex A Morgan; Andres Moreno-Estrada; Geoffrey B Nilsen; David Ruau; Stephen E Lincoln; Carlos D Bustamante; Atul J Butte
Journal:  PLoS Genet       Date:  2012-04-12       Impact factor: 5.917

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