Literature DB >> 23358379

Genotype to phenotype: lessons from model organisms for human genetics.

Ben Lehner1.   

Abstract

To what extent can variation in phenotypic traits such as disease risk be accurately predicted in individuals? In this Review, I highlight recent studies in model organisms that are relevant both to the challenge of accurately predicting phenotypic variation from individual genome sequences ('whole-genome reverse genetics') and for understanding why, in many cases, this may be impossible. These studies argue that only by combining genetic knowledge with in vivo measurements of biological states will it be possible to make accurate genetic predictions for individual humans.

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Year:  2013        PMID: 23358379     DOI: 10.1038/nrg3404

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


  104 in total

1.  Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals.

Authors:  Benjamin R Carone; Lucas Fauquier; Naomi Habib; Jeremy M Shea; Caroline E Hart; Ruowang Li; Christoph Bock; Chengjian Li; Hongcang Gu; Phillip D Zamore; Alexander Meissner; Zhiping Weng; Hans A Hofmann; Nir Friedman; Oliver J Rando
Journal:  Cell       Date:  2010-12-23       Impact factor: 41.582

2.  Systematic pathway analysis using high-resolution fitness profiling of combinatorial gene deletions.

Authors:  Robert P St Onge; Ramamurthy Mani; Julia Oh; Michael Proctor; Eula Fung; Ronald W Davis; Corey Nislow; Frederick P Roth; Guri Giaever
Journal:  Nat Genet       Date:  2007-01-07       Impact factor: 38.330

3.  Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

Authors:  Lucia A Hindorff; Praveen Sethupathy; Heather A Junkins; Erin M Ramos; Jayashri P Mehta; Francis S Collins; Teri A Manolio
Journal:  Proc Natl Acad Sci U S A       Date:  2009-05-27       Impact factor: 11.205

4.  The chemical genomic portrait of yeast: uncovering a phenotype for all genes.

Authors:  Maureen E Hillenmeyer; Eula Fung; Jan Wildenhain; Sarah E Pierce; Shawn Hoon; William Lee; Michael Proctor; Robert P St Onge; Mike Tyers; Daphne Koller; Russ B Altman; Ronald W Davis; Corey Nislow; Guri Giaever
Journal:  Science       Date:  2008-04-18       Impact factor: 47.728

5.  Genetic dissection of the biotic stress response using a genome-scale gene network for rice.

Authors:  Insuk Lee; Young-Su Seo; Dusica Coltrane; Sohyun Hwang; Taeyun Oh; Edward M Marcotte; Pamela C Ronald
Journal:  Proc Natl Acad Sci U S A       Date:  2011-10-31       Impact factor: 11.205

Review 6.  Genomic imprinting: the emergence of an epigenetic paradigm.

Authors:  Anne C Ferguson-Smith
Journal:  Nat Rev Genet       Date:  2011-07-18       Impact factor: 53.242

Review 7.  Epistasis--the essential role of gene interactions in the structure and evolution of genetic systems.

Authors:  Patrick C Phillips
Journal:  Nat Rev Genet       Date:  2008-11       Impact factor: 53.242

8.  A nuclear Argonaute promotes multigenerational epigenetic inheritance and germline immortality.

Authors:  Bethany A Buckley; Kirk B Burkhart; Sam Guoping Gu; George Spracklin; Aaron Kershner; Heidi Fritz; Judith Kimble; Andrew Fire; Scott Kennedy
Journal:  Nature       Date:  2012-07-18       Impact factor: 49.962

9.  A genome-wide synthetic dosage lethality screen reveals multiple pathways that require the functioning of ubiquitin-binding proteins Rad23 and Dsk2.

Authors:  Chang Liu; Dewald van Dyk; Yue Li; Brenda Andrews; Hai Rao
Journal:  BMC Biol       Date:  2009-11-12       Impact factor: 7.431

10.  A critical assessment of Mus musculus gene function prediction using integrated genomic evidence.

Authors:  Lourdes Peña-Castillo; Murat Tasan; Chad L Myers; Hyunju Lee; Trupti Joshi; Chao Zhang; Yuanfang Guan; Michele Leone; Andrea Pagnani; Wan Kyu Kim; Chase Krumpelman; Weidong Tian; Guillaume Obozinski; Yanjun Qi; Sara Mostafavi; Guan Ning Lin; Gabriel F Berriz; Francis D Gibbons; Gert Lanckriet; Jian Qiu; Charles Grant; Zafer Barutcuoglu; David P Hill; David Warde-Farley; Chris Grouios; Debajyoti Ray; Judith A Blake; Minghua Deng; Michael I Jordan; William S Noble; Quaid Morris; Judith Klein-Seetharaman; Ziv Bar-Joseph; Ting Chen; Fengzhu Sun; Olga G Troyanskaya; Edward M Marcotte; Dong Xu; Timothy R Hughes; Frederick P Roth
Journal:  Genome Biol       Date:  2008-06-27       Impact factor: 13.583

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  103 in total

Review 1.  Random monoallelic expression of autosomal genes: stochastic transcription and allele-level regulation.

Authors:  Björn Reinius; Rickard Sandberg
Journal:  Nat Rev Genet       Date:  2015-10-07       Impact factor: 53.242

2.  Dynamic sensitivity and nonlinear interactions influence the system-level evolutionary patterns of phototransduction proteins.

Authors:  Brandon M Invergo; Ludovica Montanucci; Jaume Bertranpetit
Journal:  Proc Biol Sci       Date:  2015-12-07       Impact factor: 5.349

3.  Photoreceptor phagocytosis is mediated by phosphoinositide signaling.

Authors:  Debarshi Mustafi; Brian M Kevany; Christel Genoud; Xiaodong Bai; Krzysztof Palczewski
Journal:  FASEB J       Date:  2013-08-02       Impact factor: 5.191

Review 4.  Genetic approaches in comparative and evolutionary physiology.

Authors:  Jay F Storz; Jamie T Bridgham; Scott A Kelly; Theodore Garland
Journal:  Am J Physiol Regul Integr Comp Physiol       Date:  2015-06-03       Impact factor: 3.619

Review 5.  Pervasive robustness in biological systems.

Authors:  Marie-Anne Félix; Michalis Barkoulas
Journal:  Nat Rev Genet       Date:  2015-08       Impact factor: 53.242

Review 6.  Progress in data interoperability to support computational toxicology and chemical safety evaluation.

Authors:  Sean Watford; Stephen Edwards; Michelle Angrish; Richard S Judson; Katie Paul Friedman
Journal:  Toxicol Appl Pharmacol       Date:  2019-08-09       Impact factor: 4.219

7.  RiceNet v2: an improved network prioritization server for rice genes.

Authors:  Tak Lee; Taeyun Oh; Sunmo Yang; Junha Shin; Sohyun Hwang; Chan Yeong Kim; Hyojin Kim; Hongseok Shim; Jung Eun Shim; Pamela C Ronald; Insuk Lee
Journal:  Nucleic Acids Res       Date:  2015-03-26       Impact factor: 16.971

Review 8.  Edgotype: a fundamental link between genotype and phenotype.

Authors:  Nidhi Sahni; Song Yi; Quan Zhong; Noor Jailkhani; Benoit Charloteaux; Michael E Cusick; Marc Vidal
Journal:  Curr Opin Genet Dev       Date:  2013-11-26       Impact factor: 5.578

9.  Missense variants in CFTR nucleotide-binding domains predict quantitative phenotypes associated with cystic fibrosis disease severity.

Authors:  David L Masica; Patrick R Sosnay; Karen S Raraigh; Garry R Cutting; Rachel Karchin
Journal:  Hum Mol Genet       Date:  2014-12-08       Impact factor: 6.150

Review 10.  Systems genetics approaches to understand complex traits.

Authors:  Mete Civelek; Aldons J Lusis
Journal:  Nat Rev Genet       Date:  2013-12-03       Impact factor: 53.242

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