This document provides information on genomics, proteomics, and metabolomics. It discusses that genomics is the study of genomes through sequencing and analysis. It involves various types of genomics like structural, functional, and comparative genomics. Proteomics is the large-scale study of the structure and function of proteins in organisms. Key proteomics methods include antibody detection and mass spectrometry. Metabolomics is the study of small molecule metabolites within cells and biofluids, which make up the metabolome. These "omics" fields provide insights into cellular processes and are applied in areas like disease diagnosis and drug development.

1. ADITYA BANGALORE INSTITUTE OF PHARMACY
DEPARTMENT OF PHARMACOLOGY
CELLULAR & MOLECULAR PHARMACOLOGY
PRESENTATIONON:
GENOMICS, PROTEOMICS, METABOLOMICS
PREPARED BY:
RAJESH YADAV
DEPARTMENT OF PHARMACOLOGY

2. A. GENOMICS
• This term genomics was first introduced in 1986 by Tom Roderick ,a
geneticist at the Jackson Laboratory in Maine, during a meeting about
mapping of the human genome.
• Genomics is an area within genetics that concerns the sequencing and analysis of an
organism’s genome.
• The genome is the entire DNA content that is present within one cell of an organism.
• Genomics is a discipline in genetics that applies recombinant DNA, DNA sequencing
methods, and bioinformatics to sequence, assemble, and analyze the function and structure
of genomes.

3. • Genomics including genome projects, genome sequencing, and genomic
technologies and novel strategies.
• The promise of genomics is huge. It could someday help us maximize
personal health and discover the best medical care for any condition.

4. TYPES OF GENOMICS
1. Structural genomics : It is used to determine the 3- dimensional structure of
every protein encoded by the genome. It is used in drug discovery and in
protein engineering on large scale.
2. Functional genomics: It is the branch of genomics that determine the function
of genes and their products.
3. Mutational genomics: It is the field of genomics that characterizes mutation
associated genes. In this we basically focuses on genomic, epigenomic and
transcript alterations in cancer.
4. Comparative genomics: It is the field of genomic research in which the
genomic features of different organisms can be compared. The genomic
features may include the DNA sequence, genes gene order regulatory
sequences.

5. ROLES OF BIOINFORMATICS IN GENOMIC
• Genomics is a branch of genetics that studies large scale changes in genomes
of organisms.
• Bioinformatics is a hybrid field that brings together the knowledge of biology
and the knowledge of information science, which is a sub-field of computer
science.
• Genomics and its subfield of transcriptomics, which studies genome-wide
changes in the RNA that is transcribed from DNA, studies many genes are once.

6. • Genomics may also involve reading and aligning very long sequences of DNA
or RNA. Analysing and interpreting such large-scale, complex data requires
the help of computers. The human mind, superb as it is, is incapable of
handling this much information.

7. • Genomes of organisms are very large. The human genome is estimated to have
three billion base pairs that contain about 25,000 genes.
• For comparison, the fruit fly is estimated to have 165 billion base pairs that
contain 13,000 genes.
• Additionally, a subfield of genomics called transcriptomics studies which genes,
among the tens of thousands in an organism, are turned on or off at a given
time, across multiple time points, and multiple experimental conditions at each
time point.
• In other words, “omics” data contain vast amounts of information that the
human mind cannot grasp without the help of computational methods in
bioinformatics.

8. GENOME ANALYSIS
• DNA Sequencing
• Annotation

9. DNA SEQUENCING
• DNA sequencing approaches fall into two broad categories,
1. Shotgun
2. high-throughput (or next-generation) sequencing

10. SHOTGUN SEQUENCING
• Shotgun sequencing is a sequencing method designed for analysis of
DNA sequences longer than 1000 base pairs, up to and including entire
chromosomes.
• Since this method can only be used for fairly short sequences (100 to
1000 base pairs), longer DNA sequences must be broken into random
small segments which are then sequenced to obtain reads.

11. HIGH-THROUGHPUT SEQUENCING
• The high demand for low-cost sequencing has driven the
development of high-throughput sequencing technologies
that parallelize the sequencing process, producing thousands or
millions of sequences at once.

12. ANNOTATION
• Genome annotation is the process of attaching biological information
to sequences, and consists of three main steps:
1.identifying portions of the genome that do not code for proteins
2.identifying elements on the genome, a process called gene
prediction, and
3.attaching biological information to these elements.

13. APPLICATION OF GENOMICS
• Genetic epidemiology is the study of the role of genetics factors in determining
health and disease in families and in populations, and the interplay of such
genetic factors with environmental factors.
• It is closely allied to both molecular epidemiology and statistical genetics but
these overlapping fields each have distinct emphases, societies and journals.
• This traditional approach has proved highly successful in identifying monogenic
disorders and locating the genes responsible.
• These have led to the discovery of many genetic polymorphisms that influence
the risk of developing many common disease.

14. B. PROTEOMICS
• Proteomics is the large-scale study of proteins, particularly their structures
and functions. Proteins are vital parts of living organisms, as they are the
main components of the physiological metabolic pathways of cells.
• Proteomics is a rapidly growing field of that is concerned with the
systematic, high-throughput approach to protein expression analysis of a cell
or an organism.
• Typical results of proteomics studies are inventories of the protein content
of differentially expressed proteins across multiple conditions.

16. HISTORY OF PROTEOMICS
• The first protein studies that can be called proteomics began in 1975 with
the introduction of the two-dimensional gel and mapping of the proteins
from the bacterium Escherichia coli, guinea pig and mouse. Albeit many
proteins could be separated and visualized, they could not be identified.
• The terms “proteome” and “proteomics” were coined in the early 1990s by
Marc Wilkins, a student at Australia's Macquarie University, in order to
mirror the terms “genomics” and “genome”, which represent the entire
collection of genes in an organism

17. PROTEOME
• Proteome refers to the total sets of proteins expressed in a
given cell at a given time.
• Detailed analysis of the proteome permits the discovery of new
protein markers for diagnostic purposes and of novel molecular
targets for drug discovery

18. METHODS OF STUDYING PROTEINS
• Protein detection with antibodies (immunoassays)
• Mass spectrometry and protein profiling

19. PROTEIN DETECTION WITH ANTIBODIES
(IMMUNOASSAYS)
• There are several specific techniques and protocols that use antibodies for
protein detection.
• The enzyme-linked immunosorbent assay (ELISA) has been used for
decades to detect and quantitatively measure proteins in samples.
• The Western blot can be used for detection and quantification of individual
proteins, where in an initial step a complex protein mixture is separated
using SDS-PAGE and then the protein of interest is identified using an
antibody.

20. MASS SPECTROMETRY AND PROTEIN PROFILING
• There are two mass spectrometry-based methods currently used for
protein profiling.
• The more established and widespread method uses high resolution,
two-dimensional electrophoresis to separate proteins from different
samples in parallel, followed by selection and staining of differentially
expressed proteins to be identified by mass spectrometry

21. ROLE OF PROTEOMICS IN BIOINFORMATICS
• Proteomics is a branch of Bioinformatics that deals with the techniques of
molecular biology, biochemistry, and genetics to analyze the structure,
function, and interactions of the proteins produced by the genes of a
particular cell, tissue, or organism. This technology is being improved
continuously and new tactics are being introduced.
• In the current day and age it is possible to acquire the proteome data.
Bioinformatics makes it easier to come up with new algorithms to handle
large and heterogeneous data sets to improve the processes.

22. ROLE OF PROTEOMICS IN DRUG
DEVELOPMENT
• Proteins are the principal targets of drug discovery. Most large pharmaceutical
companies now have a proteomics-oriented biotech or academic partner or have
started their own proteomics division.
• Common applications of proteomics in the drug industry include target
identification and validation, identification of efficacy and toxicity biomarkers from
readily accessible biological fluids, and investigations into mechanisms of drug
action or toxicity.
• Proteomics technologies may also help identify protein–protein interactions that
influence either the disease state or the proposed therapy.

23. ROLE OF PROTEOMICS IN DISEASES
DIAGNOSIS
• Proteomics is widely envisioned as playing a significant role in the translation
of genomics to clinically useful applications, especially in the areas of
diagnostics and prognostics.
• In the diagnosis and treatment of kidney disease, a major priority is the
identification of disease- associated biomarkers. Proteomics, with its high-
throughput and unbiased approach to the analysis of variations in protein
expression patterns, promises to be the most suitable platform for
biomarker discovery.

24. C. METABOLOMICS
• Metabolomics is the systematic study of the metabolome, the unique
biochemical fingerprint of all cellular processes
• Metabolomics is the large-scale study of small molecules, commonly known
as metabolites, within cells, biofluids, tissues or organisms. Collectively,
these small molecules and their interactions within a biological system are
known as the metabolome

25. SMALL MOLECULES (METABOLITES)
• These are the chemical compounds that are vigorously found
inside the cell.
• A small molecule (or metabolite) is a low molecular weight organic
compound, typically involved in a biological process as a substrate or
product. Metabolomics usually studies small molecules within a mass range
of 50 – 1500 daltons (Da).
• Some examples of small molecules include: sugars, lipids, amino acids, fatty
acids, phenolic compounds, alkaloids etc.

26. METABOLOME
• The metabolome is the complete set of metabolites within a cell, tissue or biological
sample at any given time point. The metabolome is inherently very dynamic: small
molecules are continuously absorbed, synthesised, degraded and interact with other
molecules, both within and between biological systems, and with the environment.
• Many reactions take place continuously within cells, so concentrations of metabolites
are considered to be very dynamic, and may change rapidly from one time point to
the next.

27. METABOLIC REACTIONS
• Metabolic pathways are essentially a series of chemical reactions, catalyzed
by enzymes, whereby the product of one reaction becomes the substrate for
the next reaction.
• These reactions can be divided into anabolic and catabolic.

28. USE OF METABOLOMICS
• We benefit from metabolomics on various levels:
1. from product and stress testing in food industries, e.g. control of pesticides
and identification of potentially harmful bacterial strains
2. to research in agriculture (crop protection and engineering)
3. medical diagnostics in healthcare
4. future applications in personalized medicine resulting in personliased
treatment strategies

29. ANALYTICAL TECHNOLOGIES
• Separation methods
1. Gas chromatography
2. High performance liquid chromatography
3. Capillary electrophoresis
• Detection methods
Mass spectrometry (MS) is used to identify and to quantify metabolites after
optional separation by GC, HPLC (LC-MS), or CE.

30. SOME APPLICATIONS OF METABOLOMICS
• Toxicology
• Functional genomics
• Nutrigenomics
• Health and medical
• Environmental metabolomics
• Biomarker discovery
• Personalised medicine
• Agricultural

31. TOXICOLOGY
• Metabolic profiling of the urine or blood could be utilized for the assessment
of toxicity. Several techniques are able to detect physiological changes in the
physiological sample that result from the presence of a toxin or toxins.
• The information that is revealed by way of metabolic profiling can also be
related to a specific health condition or syndrome, such as a lesion in the liver
or kidney.

32. NUTRIGENOMICS
• Nutrigenomics combines the knowledge obtained from genomics,
transcriptomics, proteomics and metabolomics with nutritional principles for
humans.
• A metabolome of any body fluid depends on various endogenous factors
including the individual’s age, gender, body composition, genetic
susceptibilities, and concurrent health conditions, as well as exogenous
factors such as nutrients, other components of food and medications.
• Metabolomics can be applied in nutrigenomics to determine the metabolic
fingerprint of an individual, which portrays the effect of the endogenous and
exogenous factors in the body on the metabolism of the individual.

33. HEALTH AND MEDICAL
• Metabolomics also promises to help advance the current
understanding, diagnosis and treatment of several health conditions,
such as endocrine diseases and cancer. The field can help to identify
the pathophysiological processes of disease and mechanisms that
can be targeted to manage the disease.
• For example, metabolomics biomarkers in tissue samples or biopsies
can be used to categorize and stage the progression of cancers. The
information can then be used to guide the appropriate decisions for
treatment.

34. ENVIRONMENTAL METABOLOMICS
• Metabolomics can also be applied to characterize the ways in which
an organism interacts with its environment. Studying these
environmental interactions and assessing the function and health of
an organism at a molecule level can reveal useful information about
the effect of environment on an organism’s health. This can also be
applied to a wider population to provide data for other fields of
research, such as ecology.

35. BIOMARKER DISCOVERY
• Biomarker discovery is another area where metabolomics informs decision
making. Biomarkers are "objective indications of medical state observed from
outside the patient - which can be measured accurately and reproducibly"
• In metabolomics, biomarkers are small molecules (metabolites) that can be
used to distinguish two groups of samples, typically a disease and control
group. For example, a metabolite reliably present in disease samples, but not
in healthy individuals would be classed as a biomarker.
• Samples of urine, saliva, bile, or seminal fluid contain highly informative
metabolites, and can be readily analysed through metabolomics fingerprinting
or profiling, for the purpose of biomarker discovery.

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