Literature DB >> 19858477

Colloquium papers: Numbering the hairs on our heads: the shared challenge and promise of phenomics.

David Houle1.   

Abstract

Evolution and medicine share a dependence on the genotype-phenotype map. Although genotypes exist and are inherited in a discrete space convenient for many sorts of analyses, the causation of key phenomena such as natural selection and disease takes place in a continuous phenotype space whose relationship to the genotype space is only dimly grasped. Direct study of genotypes with minimal reference to phenotypes is clearly insufficient to elucidate these phenomena. Phenomics, the comprehensive study of phenotypes, is therefore essential to understanding biology. For all of the advances in knowledge that a genomic approach to biology has brought, awareness is growing that many phenotypes are highly polygenic and susceptible to genetic interactions. Prime examples are common human diseases. Phenomic thinking is starting to take hold and yield results that reveal why it is so critical. The dimensionality of phenotypic data are often extremely high, suggesting that attempts to characterize phenotypes with a few key measurements are unlikely to be completely successful. However, once phenotypic data are obtained, causation can turn out to be unexpectedly simple. Phenotypic data can be informative about the past history of selection and unexpectedly predictive of long-term evolution. Comprehensive efforts to increase the throughput and range of phenotyping are an urgent priority.

Entities:  

Mesh:

Year:  2009        PMID: 19858477      PMCID: PMC2868290          DOI: 10.1073/pnas.0906195106

Source DB:  PubMed          Journal:  Proc Natl Acad Sci U S A        ISSN: 0027-8424            Impact factor:   11.205


  44 in total

1.  Complexity in biological signaling systems.

Authors:  G Weng; U S Bhalla; R Iyengar
Journal:  Science       Date:  1999-04-02       Impact factor: 47.728

2.  Orientation of the genetic variance-covariance matrix and the fitness surface for multiple male sexually selected traits.

Authors:  Mark W Blows; Stephen F Chenoweth; Emma Hine
Journal:  Am Nat       Date:  2004-03-09       Impact factor: 3.926

Review 3.  Genomic rearrangements and sporadic disease.

Authors:  James R Lupski
Journal:  Nat Genet       Date:  2007-07       Impact factor: 38.330

Review 4.  Tilting at quixotic trait loci (QTL): an evolutionary perspective on genetic causation.

Authors:  Kenneth M Weiss
Journal:  Genetics       Date:  2008-08       Impact factor: 4.562

5.  A novel 3-D image-based morphological method for phenotypic analysis.

Authors:  Erika Kristensen; Trish E Parsons; Benedikt Hallgrímsson; Steven K Boyd
Journal:  IEEE Trans Biomed Eng       Date:  2008-12       Impact factor: 4.538

6.  Many sequence variants affecting diversity of adult human height.

Authors:  Daniel F Gudbjartsson; G Bragi Walters; Gudmar Thorleifsson; Hreinn Stefansson; Bjarni V Halldorsson; Pasha Zusmanovich; Patrick Sulem; Steinunn Thorlacius; Arnaldur Gylfason; Stacy Steinberg; Anna Helgadottir; Andres Ingason; Valgerdur Steinthorsdottir; Elinborg J Olafsdottir; Gudridur H Olafsdottir; Thorvaldur Jonsson; Knut Borch-Johnsen; Torben Hansen; Gitte Andersen; Torben Jorgensen; Oluf Pedersen; Katja K Aben; J Alfred Witjes; Dorine W Swinkels; Martin den Heijer; Barbara Franke; Andre L M Verbeek; Diane M Becker; Lisa R Yanek; Lewis C Becker; Laufey Tryggvadottir; Thorunn Rafnar; Jeffrey Gulcher; Lambertus A Kiemeney; Augustine Kong; Unnur Thorsteinsdottir; Kari Stefansson
Journal:  Nat Genet       Date:  2008-04-06       Impact factor: 38.330

7.  Genomic sister-disorders of neurodevelopment: an evolutionary approach.

Authors:  Bernard Crespi; Kyle Summers; Steve Dorus
Journal:  Evol Appl       Date:  2009-01-07       Impact factor: 5.183

8.  Large recurrent microdeletions associated with schizophrenia.

Authors:  Hreinn Stefansson; Dan Rujescu; Sven Cichon; Olli P H Pietiläinen; Andres Ingason; Stacy Steinberg; Ragnheidur Fossdal; Engilbert Sigurdsson; Thordur Sigmundsson; Jacobine E Buizer-Voskamp; Thomas Hansen; Klaus D Jakobsen; Pierandrea Muglia; Clyde Francks; Paul M Matthews; Arnaldur Gylfason; Bjarni V Halldorsson; Daniel Gudbjartsson; Thorgeir E Thorgeirsson; Asgeir Sigurdsson; Adalbjorg Jonasdottir; Aslaug Jonasdottir; Asgeir Bjornsson; Sigurborg Mattiasdottir; Thorarinn Blondal; Magnus Haraldsson; Brynja B Magnusdottir; Ina Giegling; Hans-Jürgen Möller; Annette Hartmann; Kevin V Shianna; Dongliang Ge; Anna C Need; Caroline Crombie; Gillian Fraser; Nicholas Walker; Jouko Lonnqvist; Jaana Suvisaari; Annamarie Tuulio-Henriksson; Tiina Paunio; Timi Toulopoulou; Elvira Bramon; Marta Di Forti; Robin Murray; Mirella Ruggeri; Evangelos Vassos; Sarah Tosato; Muriel Walshe; Tao Li; Catalina Vasilescu; Thomas W Mühleisen; August G Wang; Henrik Ullum; Srdjan Djurovic; Ingrid Melle; Jes Olesen; Lambertus A Kiemeney; Barbara Franke; Chiara Sabatti; Nelson B Freimer; Jeffrey R Gulcher; Unnur Thorsteinsdottir; Augustine Kong; Ole A Andreassen; Roel A Ophoff; Alexander Georgi; Marcella Rietschel; Thomas Werge; Hannes Petursson; David B Goldstein; Markus M Nöthen; Leena Peltonen; David A Collier; David St Clair; Kari Stefansson
Journal:  Nature       Date:  2008-09-11       Impact factor: 49.962

9.  Mouse phenome database.

Authors:  Stephen C Grubb; Terry P Maddatu; Carol J Bult; Molly A Bogue
Journal:  Nucleic Acids Res       Date:  2008-11-05       Impact factor: 16.971

10.  Reduced body weight is a common effect of gene knockout in mice.

Authors:  Danielle R Reed; Maureen P Lawler; Michael G Tordoff
Journal:  BMC Genet       Date:  2008-01-08       Impact factor: 2.797

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  43 in total

Review 1.  Phenomics: the next challenge.

Authors:  David Houle; Diddahally R Govindaraju; Stig Omholt
Journal:  Nat Rev Genet       Date:  2010-12       Impact factor: 53.242

2.  Evolution in health and medicine Sackler colloquium: Making evolutionary biology a basic science for medicine.

Authors:  Randolph M Nesse; Carl T Bergstrom; Peter T Ellison; Jeffrey S Flier; Peter Gluckman; Diddahally R Govindaraju; Dietrich Niethammer; Gilbert S Omenn; Robert L Perlman; Mark D Schwartz; Mark G Thomas; Stephen C Stearns; David Valle
Journal:  Proc Natl Acad Sci U S A       Date:  2009-11-16       Impact factor: 11.205

3.  New experiments for an undivided genetics.

Authors:  Michael R Rose; Laurence D Mueller; Molly K Burke
Journal:  Genetics       Date:  2011-05       Impact factor: 4.562

4.  Evolution in health and medicine Sackler colloquium: Evolutionary perspectives on health and medicine.

Authors:  Stephen C Stearns; Randolph M Nesse; Diddahally R Govindaraju; Peter T Ellison
Journal:  Proc Natl Acad Sci U S A       Date:  2010-01-26       Impact factor: 11.205

5.  Uneven Distribution of Mutational Variance Across the Transcriptome of Drosophila serrata Revealed by High-Dimensional Analysis of Gene Expression.

Authors:  Emma Hine; Daniel E Runcie; Katrina McGuigan; Mark W Blows
Journal:  Genetics       Date:  2018-06-08       Impact factor: 4.562

6.  A simple developmental model recapitulates complex insect wing venation patterns.

Authors:  Jordan Hoffmann; Seth Donoughe; Kathy Li; Mary K Salcedo; Chris H Rycroft
Journal:  Proc Natl Acad Sci U S A       Date:  2018-09-17       Impact factor: 11.205

Review 7.  Q(ST)-F(ST) comparisons: evolutionary and ecological insights from genomic heterogeneity.

Authors:  Tuomas Leinonen; R J Scott McCairns; Robert B O'Hara; Juha Merilä
Journal:  Nat Rev Genet       Date:  2013-02-05       Impact factor: 53.242

8.  Pleiotropic mutations are subject to strong stabilizing selection.

Authors:  Katrina McGuigan; Julie M Collet; Scott L Allen; Stephen F Chenoweth; Mark W Blows
Journal:  Genetics       Date:  2014-05-02       Impact factor: 4.562

Review 9.  Whole-Organism Cellular Pathology: A Systems Approach to Phenomics.

Authors:  K C Cheng; S R Katz; A Y Lin; X Xin; Y Ding
Journal:  Adv Genet       Date:  2016-07-29       Impact factor: 1.944

10.  Quantification of facial skeletal shape variation in fibroblast growth factor receptor-related craniosynostosis syndromes.

Authors:  Yann Heuzé; Neus Martínez-Abadías; Jennifer M Stella; Eric Arnaud; Corinne Collet; Gemma García Fructuoso; Mariana Alamar; Lun-Jou Lo; Simeon A Boyadjiev; Federico Di Rocco; Joan T Richtsmeier
Journal:  Birth Defects Res A Clin Mol Teratol       Date:  2014-02-27
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