Omics

Since the sequencing of the human genome in 2003, a multitude of omics disciplines have developed to explain the complex inter-relationships of system-wide molecular biology. Traditionally molecular biology was performed on a molecule by molecule basis. Each molecule was purified and characterised. Omics technologies collectively identify and characterise thousands of molecules simultaneously. There is a local network of core facilities and academic laboratories that provide access to state of the omics services at competitive prices. 

Since the sequencing of the human genome in 2003, a multitude of omics disciplines have developed to explain the complex inter-relationships of system-wide molecular biology. Traditionally molecular biology was performed on a molecule by molecule basis. Each molecule was purified and characterised. Omics technologies collectively identify and characterise thousands of molecules simultaneously.

 

The omics revolution of biology started with Genomics, the complete sequencing of all the DNA of an organism. These genomic sequences have been assembled and annotated to identify genes and control regions. The genome of an organism is largely static, it only changes slightly due to mutations occurring due to damage or replication errors. While the genome may provide us with information about an organism, it does nothing to tell us about the current state of the organism. DNA is translated into mRNA. Cells in the body have different gene expression patterns, thus conferring identity to those cells. Response to a stimulus may also alter gene expression patterns. Sequencing and quantitating mRNA allows us to determine which genes are being expressed, thus developed the field of transcriptomics. mRNA is translated into proteins. Control mechanisms between transcription and translation may affect proteins abundance. Identifying and quantifying proteins allows us to determine which of the expressed genes are translated and function as proteins. Proteomics is the large scale identification and quantification of proteins. Measuring post-transnational modification on proteins furthermore enables us to determine the state of these proteins. There are numerous subfields of proteomics focused on specific post-translational modifications, such as phospho-proteomics and glycoproteomics. In Metabolomics the metabolites of body fluids and cellular conditions are measured, allowing us to determine metabolic fluxes. Measuring the composition of lipids (Lipidomics) allows us to observe changes in cellular membranes.

 

Omics data generation produces a vast array of data. This data needs to be collected, stored and functionally annotated to deduce meaningful information from it. The field of Bioinformatics has produced tools to make sense of this data. This information portal will catalogue omics data generation resources and the tools used in omics data analysis. Through the help centre we offer expert guidance and assistance for omics research.

Genomics

 

The study of genomics has revolutionised the field of biology. The genome of an organism is the complete sequence of all its DNA. The information within DNA directs the development and maintenance of living organisms, and sequencing it enables the identification and comparison of organisms and individuals.
 
Thousands of species have now been sequenced. The genetic distance between organisms determines the diversity within a population or the evolutionary divergence between species. Determining genetic distances through genomic sequencing has resulted in a refinement of the phylogenetic tree, illustrating a high degree of relatedness among similar species. Studying the sequence properties of coding regions has established rules for predicting gene sequences, leading to the functional annotation of novel genes. The high degree of homology among genes enables the inference of information about genes found in one species to those found in another. Genomics has, therefore led to an increase in the interconnected study of biology.
 
In humans, there are roughly 20 000 protein-coding genes. These genes have mostly been functionally annotated, enabling an in-depth understanding of the processes occurring within cells expressing these genes. Mutations in genes generate population diversity, occasionally resulting in genetic disorders. In humans identification of mutations causing hereditary diseases enables informed family planning and targetted treatment of these disorders. With the thousands of human genomes sequenced, Genome-Wide Associations Studies (GWAS) can predict genetic risk factors for common diseases, without needing first to identify candidate genes.
 
Furthermore, sequencing the genomes of cancers has enabled the specific characterisation of the mutations causing these cancers. Determining the molecular cause of a tumour allows for the determination of precise treatment as the tumour develops. The field of precision medicine is currently mainly making use of genomics, but in time the other omics fields will contribute heavily as well to the development of personalised treatments.
 
There is a considerable drive to sequence a more significant proportion of the African population due to the broad genetic diversity within the African people. African genomes significantly increase the diversity within the genomics repositories. Spearheading this initiative is H3Africa. They aim to empower African researchers through nurturing collaboration on the African continent. The uniqueness of African genomic data will improve both African and global health. To ensure the quality of this data; they have established rigorous workflows for genomic analysis.

Proteomics

 

DNA contains the information of life, while proteins do the work, that makes life possible. Proteins catalyse chemical reactions, interact to form structural components and transduce signals within cells.  A proteome is the set of proteins produced by an organism in a specific biological context. Measuring protein abundance and state provides information on the current state of a biological system.  Proteomics is the large scale study of proteomes.

Proteins are more complicated to work with than nucleic acids, which have uniform chemistry. Amino acid side chains have different chemical properties, making extraction of the whole proteome complex. Proteins can not be amplified like genetic material, and the large dynamic ranges across the proteome make detection of low abundance proteins problematic.

Fortunately, developments in extraction techniques, liquid chromatography and mass spectrometry have made much of the proteome accessible for measurement. Development in proteomics has made it robust enough to be used in clinical settings. It is possible to identify thousands of proteins and determine their abundance. Through enrichment techniques, it is possible to focus on specific post-translational modifications and thereby gather information on the state of proteins.

Proteomics is actively used to understand the mechanisms underlying development and disease, identify biomarkers and evaluate the effectiveness of treatments. Clinically proteomes of tissue cultures, biopsies and biological fluids, such as cerebral spinal fluid, serum and urine, are studied. Proteomics is going to be fundamentally important in determining the progression of disease in precision medicine as the field develops.

Bioinformatics

Bioinformatics is the analysis and functional annotation of biological datasets. As the omics fields have developed, they have generated larger and larger quantities of data. This big data cannot be analysed, processed and viewed as text files or even in spreadsheets. To address the complexity and size of data being generated by omics research, the field of bioinformatics emerged. Researchers have developed tools to managing, analysing omics data. These tools are often open source and freely available but have also been bundled into commercial software packages. While it is possible to learn how to analyse you own data, the process may be very challenging, and it is often best to recruit a dedicated bioinformatician to assist with data management. This portal will undertake to catalogue bioinformatics tool, resources and experts avaialble locally to assist with solving data analysis.

 

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