Multiomics, multi-omics, integrative omics, "panomics" or "pan-omics" is a biological analysis approach in which the data sets are multiple "
omes
The branches of science known informally as omics are various disciplines in biology whose names end in the suffix ''-omics'', such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collectiv ...
", such as the
genome,
proteome
The proteome is the entire set of proteins that is, or can be, expressed by a genome, cell, tissue, or organism at a certain time. It is the set of expressed proteins in a given type of cell or organism, at a given time, under defined conditions ...
,
transcriptome,
epigenome
An epigenome consists of a record of the chemical changes to the DNA and histone proteins of an organism; these changes can be passed down to an organism's offspring via transgenerational stranded epigenetic inheritance. Changes to the epigenome ...
,
metabolome, and
microbiome (i.e., a
meta-genome and/or
meta-transcriptome, depending upon how it is sequenced);
in other words, ''the use of multiple
omics
The branches of science known informally as omics are various disciplines in biology whose names end in the suffix ''-omics'', such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collective ...
technologies to study life in a concerted way''. By combining these "omes", scientists can analyze complex biological
big data
Though used sometimes loosely partly because of a lack of formal definition, the interpretation that seems to best describe Big data is the one associated with large body of information that we could not comprehend when used only in smaller am ...
to find novel associations between biological entities, pinpoint relevant
biomarkers
In biomedical contexts, a biomarker, or biological marker, is a measurable indicator of some biological state or condition. Biomarkers are often measured and evaluated using blood, urine, or soft tissues to examine normal biological processes, pa ...
and build elaborate markers of disease and physiology. In doing so, multiomics integrates diverse omics data to find a coherently matching geno-pheno-envirotype relationship or association. The OmicTools service lists more than 99 softwares related to multiomic data analysis, as well as more than 99 databases on the topic.
Systems biology approaches are often based upon the use of panomic analysis data. The
American Society of Clinical Oncology
The American Society of Clinical Oncology (ASCO) is a professional organization representing physicians of all oncology sub-specialties who care for people with cancer. Founded in 1964 by Fred Ansfield, Harry Bisel, Herman Freckman, Arnoldus Go ...
(ASCO) defines panomics as referring to "the interaction of all biological
functions within a cell and with other body functions, combining data collected by targeted tests ... and global assays (such as genome sequencing) with other patient-specific information."
Single-cell multiomics
A branch of the field of multiomics is the analysis of multilevel
single-cell data, called single-cell multiomics.
This approach gives us an unprecedent resolution to look at multilevel transitions in health and disease at the single cell level. An advantage in relation to bulk analysis is to mitigate confounding factors derived from cell to cell variation, allowing the uncovering of heterogeneous tissue architectures.
Methods for parallel single-cell genomic and transcriptomic analysis can be based on simultaneous amplification or physical separation of RNA and genomic DNA. They allow insights that cannot be gathered solely from transcriptomic analysis, as RNA data do not contain
non-coding genomic regions and information regarding
copy-number variation
Copy number variation (CNV) is a phenomenon in which sections of the genome are repeated and the number of repeats in the genome varies between individuals. Copy number variation is a type of structural variation: specifically, it is a type of ...
, for example. An extension of this methodology is the integration of single-cell transcriptomes to single-cell methylomes, combining single-cell
bisulfite sequencing
Bisulfite sequencing (also known as bisulphite sequencing) is the use of bisulfite treatment of DNA before routine sequencing to determine the pattern of methylation. DNA methylation was the first discovered epigenetic mark, and remains the mo ...
to single cell RNA-Seq. Other techniques to query the epigenome, as single-cell
ATAC-Seq ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) is a technique used in molecular biology to assess genome-wide chromatin accessibility. In 2013, the technique was first described as an alternative advanced method for MNase-s ...
and single-cell
Hi-C
Hi-C is a fruit juiceāflavored drink made by the Minute Maid division of The Coca-Cola Company. It was created by Niles Foster in 1946 and released in 1947. The sole original flavor was orange.
History
Niles Foster, a former bakery and ...
also exist.
A different, but related, challenge is the integration of proteomic and transcriptomic data.
One approach to perform such measurement is to physically separate single-cell lysates in two, processing half for RNA, and half for proteins.
The protein content of lysates can be measured by proximity extension assays (PEA), for example, which use DNA-barcoded antibodies. A different approach uses a combination of heavy-metal RNA probes and protein antibodies to adapt
mass cytometry
Mass cytometry is a mass spectrometry technique based on inductively coupled plasma mass spectrometry and time of flight mass spectrometry used for the determination of the properties of cells (cytometry). In this approach, antibodies are conjug ...
for multiomic analysis.
Multiomics and machine learning
In parallel to the advances in highthroughput biology,
machine learning applications to biomedical data analysis are flourishing. The integration of multi-omics data analysis and machine learning has led to the discovery of new
biomarker
In biomedical contexts, a biomarker, or biological marker, is a measurable indicator of some biological state or condition. Biomarkers are often measured and evaluated using blood, urine, or soft tissues to examine normal biological processes, pa ...
s. For example, one of the methods of th
mixOmicsproject implements a method based on sparse
Partial Least Squares
Partial least squares regression (PLS regression) is a statistical method that bears some relation to principal components regression; instead of finding hyperplanes of maximum variance between the response and independent variables, it finds a li ...
regression for selection of features (putative biomarkers).
Multiomics in health and disease
Multiomics currently holds a promise to fill gaps in the understanding of human health and disease, and many researchers are working on ways to generate and analyze disease-related data. The applications range from understanding host-pathogen interactions and infectious diseases, cancer, to understanding better chronic and complex
non-communicable diseases and improving personalized medicine.
Integrated Human Microbiome Project
The second phase of the $170 million
Human Microbiome Project was focused on integrating patient data to different omic datasets, considering host genetics, clinical information and microbiome composition. The phase one focused on characterization of communities in different body sites. Phase 2 focused in the integration of multiomic data from host &
microbiome to human diseases. Specifically, the project used multiomics to improve the understanding of the interplay of gut and nasal microbiomes with
type 2 diabetes, gut microbiomes and inflammatory bowel disease and vaginal microbiomes and pre-term birth.
Systems Immunology
The complexity of interactions in the human
immune system has prompted the generation of a wealth of immunology-related multi-scale omic data. Multi-omic data analysis has been employed to gather novel insights about the immune response to infectious diseases, such as pediatric
chikungunya
Chikungunya is an infection caused by the ''Chikungunya virus'' (CHIKV). Symptoms include fever and joint pains. These typically occur two to twelve days after exposure. Other symptoms may include headache, muscle pain, joint swelling, and a r ...
, as well as noncommunicable
autoimmune disease
An autoimmune disease is a condition arising from an abnormal immune response to a functioning body part. At least 80 types of autoimmune diseases have been identified, with some evidence suggesting that there may be more than 100 types. Nearly a ...
s. Integrative omics has also been employed strongly to understand effectiveness and side effects of
vaccines, a field called systems vaccinology. For example, multiomics was essential to uncover the association of changes in plasma metabolites and immune system transcriptome on response to vaccination against
herpes zoster
Shingles, also known as zoster or herpes zoster, is a viral disease characterized by a painful skin rash with blisters in a localized area. Typically the rash occurs in a single, wide mark either on the left or right side of the body or face. ...
.
List of softwares for multi-omic analysis
The
Bioconductor
Bioconductor is a free, open source and open development software project for the analysis and comprehension of genomic data generated by wet lab experiments in molecular biology.
Bioconductor is based primarily on the statistical R program ...
project curates a variety of R packages aimed at integrating omic data:
omicade4 for multiple co-inertia analysis of multi omic datasets
offering a bioconductor interface for overlapping samples
a package focused on using multi omic data for evaluating
alternative splicing
Alternative splicing, or alternative RNA splicing, or differential splicing, is an alternative splicing process during gene expression that allows a single gene to code for multiple proteins. In this process, particular exons of a gene may be i ...
bioCancer a package for visualization of multiomic cancer data
a suite of multivariate methods for data integration
a package for encapsulating multiple data sets
The OmicTools
database further highlights R packages and other tools for multi omic data analysis:
PaintOmics a web resource for visualization of multi-omics datasets
* SIGMA, a Java program focused on integrated analysis of cancer datasets
* iOmicsPASS, a tool in C++ for multiomic-based phenotype prediction
Grimon an R graphical interface for visualization of multiomic data
Omics Pipe a framework in Python for reproducibly automating multiomic data analysis
Multiomic Databases
A major limitation of classical omic studies is the isolation of only one level of biological complexity. For example, transcriptomic studies may provide information at the transcript level, but many different entities contribute to the biological state of the sample (
genomic variants,
post-translational modification
Post-translational modification (PTM) is the covalent and generally enzymatic modification of proteins following protein biosynthesis. This process occurs in the endoplasmic reticulum and the golgi apparatus. Proteins are synthesized by ribosom ...
s, metabolic products, interacting organisms, among others). With the advent of
high-throughput biology
High throughput biology (or high throughput cell biology) is the use of automation equipment with classical cell biology techniques to address biological questions that are otherwise unattainable using conventional methods. It may incorporate tec ...
, it is becoming increasingly affordable to make multiple measurements, allowing transdomain (e.g. RNA and protein levels) correlations and inferences. These correlations aid the construction or more complete
biological network
A biological network is a method of representing systems as complex sets of binary interactions or relations between various biological entities. In general, networks or graphs are used to capture relationships between entities or objects. A typi ...
s, filling gaps in our knowledge.
Integration of data, however, is not an easy task. To facilitate the process, groups have curated database and pipelines to systematically explore multiomic data:
*
Multi-Omics Profiling Expression Database (MOPED), integrating diverse animal models,
* The Pancreatic Expression Database, integrating data related to
pancreatic tissue,
LinkedOmics connecting data from
TCGA cancer datasets,
* OASIS, a web-based resource for general cancer studies,
* BCIP, a platform for
breast cancer
Breast cancer is cancer that develops from breast tissue. Signs of breast cancer may include a lump in the breast, a change in breast shape, dimpling of the skin, milk rejection, fluid coming from the nipple, a newly inverted nipple, or a r ...
studies,
* C/VDdb, connecting data from several cardiovascular disease studies,
* ZikaVR, a multiomic resource for
Zika virus
''Zika virus'' (ZIKV; pronounced or ) is a member of the virus family ''Flaviviridae''. It is spread by daytime-active ''Aedes'' mosquitoes, such as '' A. aegypti'' and '' A. albopictus''. Its name comes from the Ziika Forest of Uganda, wh ...
data
* Ecomics, a normalized multi-omic database for ''
Escherichia coli
''Escherichia coli'' (),Wells, J. C. (2000) Longman Pronunciation Dictionary. Harlow ngland Pearson Education Ltd. also known as ''E. coli'' (), is a Gram-negative, facultative anaerobic, rod-shaped, coliform bacterium of the genus '' Esc ...
'' data,
* GourdBase, integrating data from studies with
gourd,
* MODEM, a database for multilevel
maize data,
* SoyKB, a database for multilevel
soybean data,
ProteomicsDB a multi-omics and multi-organism resource for life science research
See also
*
DisGeNET
*
Pangenomics
*
Hologenomics
*
Omics
The branches of science known informally as omics are various disciplines in biology whose names end in the suffix ''-omics'', such as genomics, proteomics, metabolomics, metagenomics, phenomics and transcriptomics. Omics aims at the collective ...
**
List of omics topics in biology
Inspired by the terms genome and genomics, other words to describe complete biological datasets, mostly sets of biomolecules originating from one organism, have been coined with the suffix '' -ome'' and ''-omics''. Some of these terms are related ...
*
Systems Biology
*
Network Medicine
Network medicine is the application of network science towards identifying, preventing, and treating diseases. This field focuses on using network topology and network dynamics towards identifying diseases and developing medical drugs. Biological ...
References
{{reflist
Biology theories
Molecular biology