OMICS

Omics refers to a field of study in biology ending with a suffix –omics. Another related suffix is

ome which is used to refer to a totality of some thing which is the basis of study in those fields

like; the genome.

Omic technology involves analysis of a large number of measurements in a short time period.

High-throughput analysis is essential considering data at the "omic" level, for example

considering all DNA sequences, gene expression levels, or proteins at once.

Tools are the protocols, procedures as well as the physical equipments used in the study of

omics. There are four major types of tools that are commonly performed or done in omics

technology;

Genomics

Proteomics

Transcriptomics

Metabolomics

Genomics

This is the quantitative study of genes, regulatory and non-coding sequences. It is described as

the comprehensive analysis of DNA structure and function. Genomics is the study not just of the

individual genes of an organism but of the whole genome, the entire complement of genetic

material of an individual. This also involves large-scale genotyping of Single Nucleotide

Polymorphisms (SNPs). Genomic SNP genotyping measures a person's genotypes for several

hundred thousand SNPs spread throughout the genome.

Tools, equipments and materials involved include;

A DNA microarray which is a collection of microscopic DNA spots attached to a solid

surface. DNA microarrays are used to measure changes in expression levels, to detect

single nucleotide polymorphisms (SNPs), or to genotype or resequence mutant genomes

DNA microarrays can be used to detect DNA (in comparative genomic hybridization), or

detect RNA (as cDNA after reverse transcription) that may or may not be translated into

proteins.

The molecular marker technologies which include use of Restriction Fragment length

polymorphisms (RFLP), Amplified Fragment Length Polymorphisms (AFLP), Simple

Sequence Repeats (SSR), e.t.c.

The sanger method for sequencing so as to identify the nucleotides that make up the

DNA strand.

The other essential tool is the computer soft wares to analyze the genomics data obtained.

The equipments involved are; thermocyclers, gel readers, eletrophoretic tanks and

centrifuges while the major physical materials are DNA template, primers, DNA markers,

dNTPS, enzymes, buffers, salts like MgCl, KCl, e.t.c.

Proteomics

Proteomics is the large-scale study of proteins, particularly their structures and functions. The

proteome is the entire complement of proteins expressed by a cell or tissue type. Proteomics

confirms the presence of the protein and provides a direct measure of the quantity present. It

focuses on the identification, localization, and functional analysis of the protein make-up of the

cell. It seeks to profile every protein being expressed in a cell or tissue. The proteins present in a

cell, together with their function, sub-cellular location, and perhaps even structure, change

dramatically with the organism, and the conditions faced by their host cells including: age,

checkpoint in the cell cycle, and external or internal signaling events.

Tools, equipments and materials include;

Classically, antibodies to particular proteins or to their modified forms have been used in

biochemistry and cell biology studies.

For more quantitative determinations of protein amounts, techniques such as ELISAs are

used.

Electrophoresis is used for separation of protein depending on either size or charge. The 2

dimensional protein gels separate proteins based on charge and size while the 1

dimensional protein gels separate basing on size alone.

PROTOMAP which combines SDS-PAGE with shotgun proteomics to enable detection

of changes in gel-migration such as those caused by proteolysis or post translational

modifications.

Other techniques used are; matrix-assisted laser desorption/ionization (MALDI) which

have been employed for rapid determination of proteins in particular mixtures and

increasingly electrospray ionization (ESI)

Protein microarrays have been developed to study the protein to protein interactions.

Protein Microarrays consist of protein fragments placed as small spots onto a slide, which

are then used as "miniaturized chemical reaction areas".

Transcriptomics

This is the study of RNA, gene expression and involves the measurement of all gene expression

values in a cell or tissue type simultaneously. It is also referred to as expression profiling since it

examines the expression level of mRNAs in a given cell using high-throughput techniques based

on DNA microarray technology. The use of next-generation sequencing technology to study the

transcriptome at the nucleotide level is known as RNA-Seq.

The key aims of transcriptomics are: to catalogue all species of transcript, including mRNAs,

non-coding RNAs and small RNAs; to determine the transcriptional structure of genes, in terms

of their start sites, 5′ and 3′ ends, splicing patterns and other post-transcriptional modifications;

and to quantify the changing expression levels of each transcript during development and under

different conditions.

Technologies that have been developed to deduce and quantify the transcriptome include;

Hybridization-based approaches that involve incubating fluorescently labelled cDNA

with custom-made microarrays or commercial high-density oligo microarrays.

Specialized microarrays have also been designed; for example, arrays with probes

spanning exon junctions can be used to detect and quantify distinct spliced isoforms.

Genomic tiling microarrays that represent the genome at high density have also been

constructed and allow the mapping of transcribed regions to a very high resolution, from

several base pairs to ~100 base pairs.

Sequence-based approaches have been employed which directly determine the cDNA

sequence. These include; Sanger sequencing of cDNA or EST libraries.

Tag-based methods were developed to overcome these limitations of using the above

technologies, including serial analysis of gene expression (SAGE), cap analysis of gene

expression (CAGE) and massively parallel signature sequencing (MPSS). These tag-

based sequencing approaches are high throughput and can provide precise, ‘digital’ gene

expression levels.

Metabolomics

Metabolomics is the systematic study of the unique chemical fingerprints that specific cellular

processes leave behind, the study of their small-molecule metabolite profiles. The metabolome

represents the collection of all metabolites in a biological cell, tissue, organ or organism, which

are the end products of cellular processes.

Metabolome refers to the complete set of small-molecule metabolites such as metabolic

intermediates, hormones and other signaling molecules, and secondary metabolites to be found

within a biological sample.

Typical metabolomics experiments involve using chemical techniques such as

chromatography and mass spectrometry.

Gas chromatography, especially when interfaced with mass spectrometry (GC-MS), is

one of the most widely used and powerful methods. It offers very high chromatographic

resolution, but requires chemical derivatization for many biomolecules: only volatile

chemicals can be analysed without derivatization.

High performance liquid chromatography (HPLC) though when compared to GC, HPLC

has lower chromatographic resolution, but it does have the advantage that a much wider

range of analytes can potentially be measured.

Capillary electrophoresis (CE) which is suitable for use with a wider range of metabolite

classes than is GC and is most appropriate for charged analytes.

Mass spectrometry (MS) is used to identify and to quantify metabolites after separation

by GC, HPLC (LC-MS), or CE.

Mass spectral fingerprint libraries have been developed that allow identification of a

metabolite according to its fragmentation pattern. It is both sensitive and can be very

specific.

The Nanostructure-Initiator MS (NIMS), a desorption/ ionization approach has been

developed and it does not require the application of matrix and thereby facilitates small-

molecule identification.

Desorption electrospray ionization (DESI) which is a matrix-free technique for analyzing

biological samples that uses a charged solvent spray to desorb ions from a surface.

Nuclear magnetic resonance (NMR) spectroscopy. NMR is the only detection technique

which does not rely on separation of the analytes, and the sample can thus be recovered

for further analyses.

Biomarkers can be objectively measured and evaluated as an indicator of normal biologic

or pathogenic processes or pharmacological responses to a therapeutic intervention.

ADVANTAGES AND DISADVANTAGES OF OMICS TECHNOLOGY

Advantages;

Omics technologies allow a fast and cost-effective screening of gene and protein

expression, characterization of new gene and protein functions, the classification of

genes, proteins and metabolites in pathways.

Omics technologies can be used in the identification of therapeutic targets in the

organisms.

Disasdvantages;

There are numerous manufacturers of genechips, protein- and antibody arrays that exist

which leads to different hybridization technologies of cDNA or oligonucleotides and

proteins or antibodies fixed on carrier material causing a direct comparison of results

from applications of different manufacturers is very difficult

ADVANTAGES AND DISADVANTAGES OF MICROARRAY TECHNOLOGY

Advantages

High throughput: It is able to study the behaviour of many genes simultaneously, hence

lots of information can be obtained with one test

Good coverage of the genome with the chips that have larger numbers of test spots.

cost effective because the arrays are cheap and can easily be replaced

Adaptable and comprehensive

It is very user-friendly because the technique is neither radioactive nor toxic

It provides semi-quantitative data.

It is sensitive enough to detect low abundance transcripts that are represented on a given

array.

Disadvantages

There is incomplete coverage, which can lead to false normal results.

Ability to test only for unbalanced rearrangements (duplications and deletions), and not

balanced translocations or inversions.