The Human Phenome Project

@article{Freimer2003TheHP,
  title={The Human Phenome Project},
  author={Nelson B. Freimer and Chiara Sabatti},
  journal={Nature Genetics},
  year={2003},
  volume={34},
  pages={15-21}
}
A principal goal of genetic research is to identify specific genotypes that are associated with human phenotypes. It will soon be possible to conduct genome-wide genotyping on a massive scale. Our current approaches for defining and assaying phenotypes may be inadequate for making optimal use of such genotypic data. We propose an international effort to create phenomic databases, that is, comprehensive assemblages of systematically collected phenotypic information, and to develop new approaches… 

Figures from this paper

Unravelling the human genome–phenome relationship using phenome-wide association studies
TLDR
These studies reveal a number of challenges that will need to be overcome to unlock the full potential of PheWAS for the characterization of the complex human genome–phenome relationship.
Phenomics: the next challenge
TLDR
Phenomics should be recognized and pursued as an independent discipline to enable the development and adoption of high-throughput and high-dimensional phenotyping.
Clinical phenome scanning.
TLDR
A clinical phenome scanning approach to genotype-phenotype association studies is proposed, as this approach acknowledges the heterogeneous nature of common diseases and takes advantage of the unprecedented density of phenotypic data available in population-based DNA biobanks.
Phenomics: the systematic study of phenotypes on a genome-wide scale
Expression genetics and the phenotype revolution
TLDR
The authors have made enormous progress on the genotyping front, and it is now important to focus energy on devising ultrahigh-throughput methods to phenotype, and these models will be essential to test new treatments in a robust systems context that accounts for genetic variation.
Phenomics: Expanding the Role of Clinical Evaluation in Genomic Studies
TLDR
The components of phenomics are reviewed and examples of their application to genomic studies are provided, specifically for implicating novel disease processes, reducing sample heterogeneity, hypothesis generation, integration of multiple types of data, and as an extension of Mendelian randomization studies.
Phenomics: Expanding the Role of Clinical Evaluation in Genomic Studies
TLDR
The components of phenomics are reviewed and examples of their application to genomic studies are provided, specifically for implicating novel disease processes, reducing sample heterogeneity, hypothesis generation, integration of multiple types of data, and as an extension of Mendelian randomization studies.
Evaluating Phenotypic Data Elements for Genetics and Epidemiological Research: Experiences from the eMERGE and PhenX Network Projects
  • J. Pathak, Helen Pan, C. Chute
  • Biology
    AMIA Joint Summits on Translational Science proceedings. AMIA Joint Summits on Translational Science
  • 2011
TLDR
The results suggest that adopting multiple standards and biomedical terminologies will expose studies to a broader user community and enhance interoperability with a wider range of studies, in turn promoting cross-study pooling of data to detect both more subtle and more complex genotype-phenotype associations.
Mouse Phenome Project: understanding human biology through mouse genetics and genomics.
  • M. Bogue
  • Biology, Engineering
    Journal of applied physiology
  • 2003
TLDR
A new and powerful paradigm for biomedical research is created with the availability of a nearly complete, high-accuracy sequence of the mouse genome.
Phenotype Data: A Neglected Resource in Biomedical Research?
TLDR
The available phenotype resources are surveyed and different approaches to analyzing their content are reviewed and this review aims to assist researchers keen to understand and make effective use of these highly valuable data.
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 34 REFERENCES
Accessing genetic variation: genotyping single nucleotide polymorphisms
TLDR
The hope that single nucleotide polymorphisms will allow genes that underlie complex disease to be identified, together with progress in identifying large sets ofSNPs, are the driving forces behind intense efforts to establish the technology for large-scale analysis of SNPs.
Use of population isolates for mapping complex traits
TLDR
A large number of population isolates have been targeted for mapping genes for complex diseases using haplotype signatures and the past successes with Mendelian disorders have prompted unprecedented interest among medical researchers in both the public and private sectors.
Multifactorial genetics: Rat genetics: attachign physiology and pharmacology to the genome
TLDR
The Rat Genome Project has been rapidly gaining momentum, especially since the announcement in August 2000 of plans to sequence the rat genome, and this combined physiological and genomic information should facilitate the discovery of mammalian genes that underlie the physiological pathways that are involved in disease.
What exactly are genomes, genotypes and phenotypes? And what about phenomes?
TLDR
The goal is to clarify the situation by defining clearly and precisely the notions of genetic complement, genome, genotype, phenetic complement, and phenotype and analysing the logical structure of this family of concepts.
Blocks of Limited Haplotype Diversity Revealed by High-Resolution Scanning of Human Chromosome 21
TLDR
High-density oligonucleotide arrays are used in combination with somatic cell genetics to identify a large fraction of all common human chromosome 21 SNPs and to directly observe the haplotype structure defined by these SNPs.
HapMap Launched With Pledges of $100 Million
HUMAN GENOME A consortium of six nations is diving into a massive new genomics project it hopes will pinpoint the genes behind common diseases. After months of passing the hat among countries and
High-resolution haplotype structure in the human genome
TLDR
A high-resolution analysis of the haplotype structure across 500 kilobases on chromosome 5q31 using 103 single-nucleotide polymorphisms (SNPs) in a European-derived population offers a coherent framework for creating a haplotype map of the human genome.
Large-scale, high-throughput screening for coagulation and hematologic phenotypes in mice.
TLDR
The data show that considerable variation in many basic hematological and coagulation parameters exists among the inbred strains and allow investigators to knowledgeably select the most appropriate strain to meet their individual study designs and goals.
Minimum information about a microarray experiment (MIAME)—toward standards for microarray data
TLDR
The ultimate goal of this work is to establish a standard for recording and reporting microarray-based gene expression data, which will in turn facilitate the establishment of databases and public repositories and enable the development of data analysis tools.
A mouse phenome project
A community-wide effort to establish baseline phenotypic data on commonly used and genetically diverse inbred mouse strains and to provide the information through a publicly accessible database.
...
1
2
3
4
...