Systems genetics approaches for understanding complex traits with relevance for human disease
- Departments of Population & Public Health Sciences, University of Southern California, United States
- Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, United States
- Center for Public Health Genomics, University of Virginia School of Medicine, United States
- Departments of Biochemistry & Molecular Genetics, University of Virginia School of Medicine, United States
- Public Health Sciences, University of Virginia School of Medicine, United States
- Department of Biological Chemistry, University of California, Irvine, United States
- Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Luxembourg
- School of Life and Environmental Sciences, University of Sydney, Australia
- Faculty of Medicine and Health, University of Sydney, Australia
- Charles Perkins Centre, University of Sydney, Australia
- Departments of Human Genetics, University of California, Los Angeles, United States
- Medicine, University of California, Los Angeles, United States
- Microbiology, Immunology, & Molecular Genetics, David Geffen School of Medicine of UCLA, United States
Figures
Figure 1
Systems genetics strategy for integration of clinical (and other complex) traits with molecular traits.
In this cartoon, individuals in a cohort are examined for clinical or other complex traits of interest. Tissues from the same individuals are also examined using various omics technologies that quantitate to molecular traits. Genetic and environmental variations among the individuals will perturb the clinical and molecular traits. The relationships among the traits can then be statistically modelled using genetic mapping, correlation structure, causal inference, and network modelling. Figure adapted from Civelek and Lusis, 2014.
Figure 2
How networks can be used in systems genetics studies of disease.
Tables
Table 1
Commonly used genetic reference populations (GRPs) and outbred populations in mice and rats.
| GRPs | Species | Inbred or outbred | # of strains | Description | Data repository |
|---|---|---|---|---|---|
| BXD | Mouse | Inbred | 140 | Recombinant inbred lines generated from C57BL/6J and DBA/2J founders | https://genenetwork.org/ |
| HMDP | Mouse | Inbred | ~100 | A set of ~100 classical laboratory inbred strains and multiple recombinant inbred line panels | http://systems.genetics.ucla.edu |
| CC | Mouse | Inbred | ~50–75 | A panel of ~75 recombinant inbred lines derived from eight genetically diverse inbred founders | http://csbio.unc.edu/CCstatus/index.py |
| HRDP | Rat | Inbred | 99 | A set of ~100 classical laboratory inbred strains and recombinant inbred line panels | http://phenogen.org https://genenetwork.org/ |
| HXB/BXH | Rat | Inbred | 30 | Recombinant inbred lines generated from the spontaneously hypertensive rat (SHR/OlaIpcv) and Brown Norway (BN.Lx/Cub) founders | http://phenogen.org https://genenetwork.org/ |
| DO | Mouse | Outbred | An outbred population derived from eight genetically diverse inbred founders | https://genenetwork.org/ |
Table 2
Commonly used human biobanks for epidemiological and genetics studies.
| Cohort | Ancestry (N) | Disease traits | Biomarkers | Genomics | Transcriptomics | Proteomics | Metabolomics | Data repository |
|---|---|---|---|---|---|---|---|---|
| UK Biobank | European, Asian, African, Other (502,492) | ✓ | ✓ | ✓ | ✓ | ✓ | https://www.ukbiobank.ac.uk/ | |
| FinnGEN | European (500,000*) | ✓ | ✓ | https://www.finngen.fi/en | ||||
| Biobank Japan | Asian (260,000) | ✓ | ✓ | ✓ | ✓ | ✓ | https://biobankjp.org/en/ | |
| China Kadoorie Biobank | Asian (512,000) | ✓ | ✓ | ✓ | ✓ | ✓ | https://www.ckbiobank.org/ | |
| TOPMed | European, African, Hispanic, Asian (205,092) | ✓ | ✓ | ✓ | ✓ | ✓ | ✓ | https://topmed.nhlbi.nih.gov/ |
| BioVU | European (300,000†) | ✓ | ✓ | ✓ | https://victr.vumc.org/biovu-description/ | |||
| Millions Veteran Program | European, African, Hispanic, Asian (950,000†) | ✓ | ✓ | ✓ | https://www.mvp.va.gov/pwa/ | |||
| Geisinger MyCode | European (300,000†) | ✓ | ✓ | https://www.geisinger.org/precision-health/mycode |
-
*
Indicates goal of subject recruitment.
-
†
Recruitment still ongoing. Citations for the studies are provided in the text.
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Systems genetics approaches for understanding complex traits with relevance for human disease
eLife 12:e91004.
https://doi.org/10.7554/eLife.91004
