Key Points
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Genotype–phenotype databases contain data on genetic variants and associated phenotypes. In medical contexts, such databases are focused on disease-causing mutations and resulting diseases or phenotypic abnormalities.
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A major goal of genotype–phenotype databases is to provide assistance in assigning pathogenicity to genetic variants.
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As the focus shifts from the investigation of single genes by Sanger sequencing towards the determination of variants in tens, hundreds or thousands of genes or even the entire genome by next-generation sequencing, databases are becoming ever more essential for the interpretation of variants in diagnostic and research contexts.
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Numerous online databases of human variability exist, which differ with respect to the type of data stored, the amount of phenotypic information provided, the degree of accessibility of the data, and the number of diseases or genes covered.
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Increasingly, the focus of genotype–phenotype databases has shifted to support data discovery as a critical underpinning for data provision.
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Currently, the volume and the quality of phenotype data compared with genotype data held in genotype–phenotype databases is lower, possibly owing to practical, financial, ethical, legal and organizational challenges that must be overcome to produce good phenotypic data on large numbers of individuals.
Abstract
Genotype–phenotype databases provide information about genetic variation, its consequences and its mechanisms of action for research and health care purposes. Existing databases vary greatly in type, areas of focus and modes of operation. Despite ever larger and more intricate datasets — made possible by advances in DNA sequencing, omics methods and phenotyping technologies — steady progress is being made towards integrating these databases rather than using them as separate entities. The consequential shift in focus from single-gene variants towards large gene panels, exomes, whole genomes and myriad observable characteristics creates new challenges and opportunities in database design, interpretation of variant pathogenicity and modes of data representation and use.
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Acknowledgements
Preparation of this article was facilitated by funding from the European Union Seventh Framework Programme (FP7/2007-2013; 'BioShaRE' grant no. 261433, 'SYBIL' grant no. 602300, 'EMIF' IMI-JU grant no. 115372), the National Institutes of Health Office of the Director (grant no. 5R24OD011883), and the Bundesministerium für Bildung und Forschung (BMBF; project no. 0313911). The authors also acknowledge the many key insights provided by attendees of an IRDiRC workshop dedicated to this topic, and expert suggestions made by colleague R. Dalgleish (University of Leicester, UK).
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DATABASES
FURTHER INFORMATION
Glossary
- Genotype
-
In biology, genotype refers to the genetic makeup of an organism with reference to either a single nucleotide, a larger genetic locus or the entire genome. In the current context, genotype refers to a genetic sequence variant being assessed for potential causality of a disease, as well as its status as heterozygous, homozygous or hemizygous.
- Phenotype
-
In biology, phenotype refers to the observable characteristics of an organism, but in medicine, the word is usually used to describe clinically relevant abnormalities, including signs, symptoms and abnormal findings of laboratory analyses, imaging studies, physiological examinations, as well as behavioural anomalies.
- Variants
-
Genetic variants describe any deviations from a normal or reference sequence. For example, a substitution of one nucleotide for another at a certain chromosomal position, an insertion or deletion of one or more nucleotides, a chromosomal microdeletion encompassing several million nucleotides or a trisomy of an entire chromosome.
- Pathogenicity
-
The tendency of a genetic variant in a person's genome to produce disease. The term is most often used in the context of cancer or inherited disease, when a genetic variant has a substantial deleterious effect on the function of the gene product that leads to, or substantially contributes to, the development of disease.
- Effect sizes
-
The percentages of genetic variance explained by a specific locus, ranging from less than 1% for many common traits up to 100% for some Mendelian diseases.
- Multiple testing
-
The process of using bioinformatics analysis to assess potential pathogenicity of a variant is often formulated as a statistical hypothesis test. As tens of thousands of such tests may be performed in the analysis of diagnostic next-generation sequencing data, adjustments of the P values resulting from assessments of individual variations are required to avoid numerous false positive results, a procedure known as multiple testing correction.
- Whole-exome sequencing
-
(WES). A sequencing technique that seeks to selectively enrich and assay only the sequences belonging to the ~ 1.5% of the human genome consisting of the exons of protein-coding genes (called the exome) because the majority of causative variations identified in Mendelian diseases to date have been located in or very close to these exons.
- Big data
-
This term is used to describe collections of data that are characterized by features such as being large in size, complex and heterogeneous in type, rapidly produced or frequently changing, and of uncertain veracity, such that analysis requires high-performance computing resources and sophisticated algorithms. In biomedicine, especially high-throughput omics data such as whole-genome sequencing, as well as ever increasing amounts of clinical data available in electronic health care records, are often regarded as big data.
- Standards
-
In the present context, a formal set of specifications about the format and contents of data records of variants or diseases that are to be exchanged between databases.
- Metadata
-
Metadata, literally 'data about data', refers to information that accompanies other data and explains their context or provenance.
- Array-CGH
-
Array-comparative genomic hybridization (CGH) enables the gain or loss of genetic material to be detected in the range of as little as 40 kilobases up to entire chromosomes. Array-CGH has become a standard diagnostic tool for the identification of copy number variants.
- Web services
-
Databases, data processing or analytical functions that can be accessed by another computer program over the worldwide web.
- Penetrance
-
The proportion of persons who carry a pathogenic germline variation and also show signs of a disease irrespective of the clinical severity.
- Expressivity
-
The degree of clinical expression and severity of a disease in individuals who have inherited a given germline variation.
- Stratified medicine
-
An approach to patient care that subdivides patients into groups that are defined on the basis of expected risk of developing disease or the expected response to a certain treatment.
- Personalized medicine
-
This concept is synonymous with individualized medicine, and is used in varying ways to convey the idea of health or medical care being in some way tailored and optimized for a person. This typically means going beyond shaping care for groups of similar patients to the ultimate of uniquely customizing interventions for each separate individual.
- Probabilistic modelling
-
A class of computational algorithms that describe data observed from a system in a way that takes uncertainty and noise associated with the model into account. It is one method for making predictions about disease onset or severity on the basis of genetic and other data.
- Federation
-
A software strategy that allows data from disparate databases and other sources to be aggregated ad hoc as a virtual database that can be used for analysis. In the present context, federation involves connecting genotype–phenotype databases across networks to allow combined searches for information about variations or diseases.
- Cloud
-
Remote servers that are accessed via the Internet and provide data storage and analysis resources.
- Informed consent
-
An agreement on the part of a patient to take part in a clinical study and allow the results of the study to be used in some way, such as for additional research or health care activities or for sharing with others in a publication or database. Consent can only reasonably be given after the subject is informed and given the opportunity to discuss the purpose of the research and any potential harms and benefits.
- Biobanks
-
Collections of biological (often medically relevant) specimens such as blood, saliva or tissue, associated with data annotations that describe the subjects from whom the specimens were obtained, such as age, gender, environmental exposures, phenotypic features, molecular test results or clinical diagnosis. Biobanks are used by researchers to obtain sets of data and specimens from subjects with the same diagnosis or with similar characteristics to undertake research investigations.
- Registry
-
A registry comprises a collection of information about individuals affected by a specific disease or who share other similarities. Many registries collect information about individuals over time or are used to track information regarding the response of patients to treatments. A registry may, but does not necessarily, include genetic information.
- International Rare Diseases Research Consortium
-
(IRDiRC). This consortium comprises rare disease researchers and funding organizations and promotes the goal of developing 200 new therapies for rare diseases and a means to diagnose most rare diseases by the year 2020.
- Global Alliance for Genomics and Health
-
(GA4GH). This alliance comprises more than 200 institutions working in health care, research, disease advocacy, life science and information technology with the goal of creating a common framework of harmonized approaches to enable the responsible, voluntary, and secure sharing of genomic and clinical data.
- Human Variome Project
-
An umbrella organization that intends to help coordinate efforts to integrate the collection, curation, interpretation and sharing of information on variation in the human genome into routine clinical practice and research.
- Stakeholder
-
In the present context, a person or organization with an interest or role in medical databases, including patients and families, physicians, researchers, public and private research institutions, and funding agencies.
- Phenotype term cross-mapping
-
A computational link between equivalent or related terms in two or more different phenotype ontologies. For instance, the Medical Dictionary for Regulatory Activities (MedDRA) term Platyspondylia (10068629) is mapped to the Human Phenotype Ontology term Platyspondyly (HP:0000926).
- ORCID
-
ORCID provides a persistent digital identifier (for example, orcid.org/0000-0002-0736-9199) for each researcher that can be used to streamline workflows such as manuscript and grant submission and to unambiguously identify researchers in databases.
- APIs
-
(Application programming interfaces). A specification of a software component in terms of functionalities, formats and data types. In the current context, an API is a framework that allows exchange and processing of data and contents between different websites and databases.
- Ontologies
-
Ontologies are computational resources that combine catalogues of the relevant entities of a domain (a conceptualization) with a description of the interrelationships among those entities (a specification).
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Brookes, A., Robinson, P. Human genotype–phenotype databases: aims, challenges and opportunities. Nat Rev Genet 16, 702–715 (2015). https://doi.org/10.1038/nrg3932
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DOI: https://doi.org/10.1038/nrg3932
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