‘Omics is the study of particular types of information (such as, for example, genomics), typically on a complete or massive scale. We use the technologies of DNA sequencing and analysis to obtain genomic information about ourselves and other living things. However, genomics is but one sibling in this family of information and associated technologies. The information may be focused on classes of molecules (e.g., proteins in proteomics, metabolites in metabolomics) or systems (e.g., microbes in microbiomics). Born in basic research, ‘omics have become a powerful contributor across precision medicine.
Integration of ‘omics information into the knowledge network will illuminate new hypotheses to be tested in research labs, provide clinicians and researchers new and detailed insight into the molecular mechanisms of disease, and translate into advice for disease prevention and improved diagnostics and therapeutics.
In the future, newborns could be assessed from an ‘omic perspective, looking at genes, proteins, gut microbes, metabolic markers and the like. Beginning even before birth, practitioners would be able to see how these elements of health change as people progress through the course of their lives. These details would not only help the individual, but also provide a wealth of information for comparative analyses between individuals and groups, revealing patterns of risk and response to treatment for individuals and populations.
There’s much more to ‘omics technologies and medicine than simply sequencing and taking measurements. Collecting, analyzing, recording and using ‘omic data is no small feat, particularly because these processes include people. They also include patient consent and understanding, use of electronic medical records, obtaining and managing samples, ensuring accuracy of the data, maintaining a clinical lab, advancing bioinformatics hardware and software, and employing both computational learning and human judgment to interpret the massive amount of information these tools generate.
UCSF’s Genomic Medicine Initiative is aimed at creating a bridge between genomic technologies and medical practice to provide more precise patient diagnostics and care. GMI researchers apply genomics approaches to better understand cancer, as well as a range of other conditions. For instance, patients with rare, undiagnosed conditions often struggle with symptoms for which the cause is unknown, because there are no standard laboratory tests. With no clear answers, patients may experience a “diagnostic Odyssey,” taking one test or procedure after another in an attempt to understand and find treatment for their symptoms. With 'omic technologies and medicine woven into the knowledge network, researchers and clinicians may find an explanation for the individual’s disease and help provide an effective treatment plan.
‘Omic technologies are speeding up diagnosis of bacterial infections with next-generation sequencing (NGS). NGS techniques rapidly extract information about the genome and gene expression,, often in a matter of hours. Some UCSF clinicians are using these methods to deliver rapid and certain diagnoses.
- Clinical Cancer Genomics Laboratory (CCGL)
As part of the GMI, researchers have developed a working process to test patient samples using the “UCSF500,” a panel of more than 500 gene mutations implicated in cancer to provide more precise diagnosis and treatment plans for patients.
- Screening Pediatric Diseases:
Sequencing the exome (the coding regions of the genome) in infants to identify genetic conditions and undiagnosed diseases, and to assess whether this approach is a beneficial and feasible replacement for standard newborn testing.
- Diagnosing infectious disease:
Validating the use of next-generation sequencing for patients with encephalitis, meningitis, sepsis and pneumonia.
- Collaboration with Syapse – A collaboratively developed software platform that allows physicians to unite genomic testing and analysis, treatment regimens, clinical data, and outcomes data, and integrates them into UCSF’s electronic medical record system.
- Epilepsy Phenome/Genome Project:
UCSF has been a leader in an international effort to make sense of the multiple genetic mutations and clinical symptoms behind epilepsy. The project, which involves 4,000 epilepsy patients and family members from 40 medical institutions, has uncovered new genes never before associated with this debilitating disease. Among them was KCNT1, a gene also involved in heart disease, which has led to the successful use of a common, FDA-approved cardiovascular drug to treat children with a severe form of epilepsy that has resisted current treatments. Through these types of connections, ‘omics can not only expand our understanding of the pathways of disease, but also bring us closer to precise and effective therapies.