UNIVERSITY INSTITUTE OF

BIOTECHNOLOGY

SUBJECT: Omics Technologies

22BTT215

DISCOVER . LEARN .
EMPOWER

Dr. Sonia Kumari

Assistant Professor
Course Objectives

1. To give an exposure to the students the basic

concepts of omics and their versatile applications.
2. To serve as a fundamental course to integrate
emerging omics approaches for improvement of life
3. To ensure that a student learns various skills and
versatile techniques in omics technologies
 Omics Technologies
Course Outcome
CO1 Understanding the basic concepts of genomics, transcriptomics and proteomics.

CO2 Understanding how the Prokaryotic and Eukaryotic Genomes are organized

CO3 Understanding and utilizing molecular markers for genome analysis

CO4 Expected to get a good idea on using computational resources to understand and resolve
biological problems.

CO5 Listing and discussing the use of genomics and proteomics in human health.

CO6 Suggesting and outlining solution to theoretical and experimental problems in Genomics,
Transcriptomics and Proteomics fields.

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 Syllabus
Unit-1 (Genome and Genomics) Contact Hours:15

Genome Basic concept and various branches of omics, Genome organization:

organization Organization of Prokaryotic and Eukaryotic Genomes; Coding and Non-coding
regions; Repeat sequences: Interspersed repeats, Tandem repeats, Transposons,
Microsatellites,
Mapping and Genetic mapping; Physical mapping (Contig maps, Restriction maps, DNA
Genome sequence maps, FISH), Open Reading Frame, Codon bias, challenges in
Annotation annotating a eukaryotic genome vs. prokaryotic genomes, in silico annotation
approaches – de novo, homology based annotation – gene finding algorithms
Genome Molecular markers for genome analysis: Dominant and codominant markers,
analysis RFLP, AFLP, CAPS, SSRs, RAPDs, SNPs,Copy number variations (CNVs),
EST, STS, DNAsequencing, Geenome Sequencing, Next Generation
Sequencing (NGS) methods
SELF STUDY Vectors, Genetic material and properties
TOPIC
Unit-2 (Genomics and Transcriptomics) Contact Hours:15
Second Second generation Sequencing techniques – Pyrosequencing, Virtual
generation Terminator Sequencing, Introduction to third generation Sequencing
Sequencing Techniques – Nanopore and Ion torrent, Applications - Personal Genomics,
techniques Metagenomics, Gene expression analysis, Transcript Sequencing vs.
Hybridization, Real Time analysis, Microarray, SAGE, RNASeq, ChIPSeq,
Regulatory RNAs: small or large, Functional Genomics
using RNAi Computational prediction of miRNA target genes
SELF STUDY NCBI, Blotting techniques
TOPIC
Unit-3 (Proteomics) Contact Hours:15
Proteome SDS PAGE, 2D PAGE, DIGE, Liquid chromatography, Mass Spectrometry,
characterization Peptide mass fingerprinting. Post Translational Modification: Protein Sorting,
techniques Proteolytic Cleavage, Glycosylation, Phosphorylation. Protein-protein
interaction assays - Twohybrid methods, TAP/ GFP tags, Phage Display;
Protein chips, Protein Engineering, Application of Proteomics, Concept of
metabolome and metabolomics, Basic concepts of Lipidomics, Basic concepts
of Pharmacogenomics.
 Omics

• “Omics” is derived from -ome, which means “whole.”

• Omics technologies are simultaneous, high-throughput biomolecular
analytical techniques primary includes genomics, transcriptome, proteome,
and metabolome to measure cellular level biomolecules such as gene,
transcript, protein, and metabolite respectively, and use of these multi-Omics
data in R&D to make informed decisions in disease understanding, drug
discovery and development.
• The Omics approach integrates all biological information in systematic ways by
using bioinformatics and computational modeling to understand end-to-end
biological pathways and identify potential biological molecules at the cellular
and tissue levels. Advanced Omics use high-throughput analytical techniques
combined with big data bioinformatics to predict the biological interpretation
at high speed, accuracy, and reliability.
 Omics

• “Omics” is derived from -ome, which means “whole.”

• Omics technologies are simultaneous, high-throughput
biomolecular analytical techniques primary includes genomics,
transcriptome, proteome, and metabolome to measure cellular
level biomolecules such as gene, transcript, protein, and
metabolite respectively, and use of these multi-Omics data in R&D
to make informed decisions in disease understanding, drug
discovery and development.
• The Omics approach integrates all biological information in
systematic ways by using bioinformatics and computational
modeling to understand end-to-end biological pathways and
identify potential biological molecules at the cellular and tissue
levels. Advanced Omics use high-throughput analytical techniques
combined with big data bioinformatics to predict the biological
interpretation at high speed, accuracy, and reliability.
 Genomics, ‘Omics & Technology
• Genomics = “analysis of genomes”: became
important science during 1990’s
• Analyses of various other biological molecules have
developed into their own scientific disciplines; e.g.
Metabolomics = “analysis of metabolites”, etc.
• Transcriptomics/Proteomics: developed during past
10-15 years
• Bioinformatics: has developed as major branch of
science - enables efficient analysis of data from
“omics” experiments
 Genomics & Technology
• Significance of “omics” coincides with dramatic
improvements in different technologies:
molecular biology: increased range of
approaches for purification and manipulation of
proteins and nucleic acids
computers: required for gathering and analysis
of data
internet: allows data to be shared, quickly and
easily
• All developments have increased speed and cost-
effectiveness - available to much wider audience
SYLICA 'Omic Technologies – Bowater Feb 2013
 “Omics” Overview
• Analyses of various biological molecules have
developed into their own scientific disciplines; e.g.
Metabolomics = “analysis of metabolites”, etc.
• Transcriptome: set of all mRNAs ("transcripts”)
produced from a genome
• Proteome: set of all proteins produced under a given
set of conditions
• Both can vary because they reflect genes that are
actively expressed at any given time
• Transcriptomics and proteomics are both powerful,
but are used differently: transcriptomics is cheaper
and more user friendly than proteomics
SYLICA 'Omic Technologies – Bowater Feb 2013
 Omics
• Omics technologies provide the tools needed to look at the
differences in DNA, RNA, proteins, and other cellular
molecules between species and among individuals of a
species. These types of molecular profiles can vary with cell
or tissue exposure to chemicals or drugs and thus have
potential use in toxicological assessments.
• Omics experiments can often be conducted in high-
throughput assays that produce tremendous amounts of
data on the functional and/or structural alterations within
the cell. “These new methods have already facilitated
significant advances in our understanding of the molecular
responses to cell and tissue damage, and of perturbations in
functional cellular systems”
 Genomics
• The first of the -omics technologies to be
developed, genomics has resulted in massive amounts of
DNA sequence data requiring great amounts of computer
capacity. Genomics has progressed beyond sequencing of
organisms (structural genomics) to identifying the function
of the encoded genes (functional genomics).
• The genome of each species is distinctive, but smaller
genomic differences are also observed between each
individual of a species. It was originally thought that
obtaining the sequence of the human genome would
immediately tell us the identity of the human genes. The
genome has proved to be much more complex.
 Genomics
• When a gene is expressed it results in the production of a
messenger RNA and ultimately a particular protein. Gene
expression is not fully understood, but involves regulatory
sequences within the DNA and the binding of specific
regulatory proteins to these sequences. The expression and
regulation of the regulatory proteins is another level of
control. Whether a particular gene is expressed in an
organism can be influenced by various genetic and
environmental factors.
 Genomics
• The DNA sequences of a gene that code for a protein are
called exons, and they are interspersed with DNA called
introns, which do not code for proteins. The intron
sequences, previously thought to be nonsense material, are
now known to also contain important information. Although
the sequencing of the human genome was completed in
2003 (HGP, 2003), the identification of all of the genes
within the human DNA sequence is not complete. Locating
the beginning and ends of genes within the DNA remains a
challenge.
 Gene annotation
• is “adding pertinent information such as gene
coded for, amino acid sequence or other
commentary to the database entry of raw sequence
of DNA bases”.
• This involves describing different regions of the
code, identifying which regions can be called genes,
and identifying other features such as exons and
introns, start and stop codons, and so on.
 Proteomics
• Proteins are the primary structural and functional molecules in the cell,
and are made up of a linear arrangement of amino acids. The linear
polypeptide chains are folded into secondary and tertiary structures to
form the functional protein. Unlike the static nature of the cell’s genes,
proteins are constantly changing to meet the needs of the cell.
• Characterizing the identity, function, regulation, and interaction of all of
the cellular proteins of an organism, the proteome, will be a major
achievement. Studies of changes in the proteome of cells and tissues
exposed to toxic materials, compared to normal cells, is being used to
develop an understanding of the mechanisms of toxicity. As proteomics
tools become more powerful and widely used, protein and proteome
changes in response to exposures to toxic substances (fingerprints or
response profiles) will be developed into databases that can be used to
classify exposure responses at various levels of organization of the
organism, thus providing a predictive in silico toxicology tool.
 Metabolomics
• Metabolomics refers to the comprehensive evaluation of the metabolic
state of a cell, organ or organism, in order to identify biochemical
changes that are characteristic of specific disease states or toxic insults.
Typical metabolomics experiments involve the identification and
quantitation of large numbers of endogenous molecules in a biological
sample (e.g., urine or blood) using chemical techniques such as
chromatography and mass spectrometry. The output from these
techniques is compared to computerized libraries of mass spectrometry
tracings to facilitate identification of the compounds that are present.
Environmental stresses such as exposure to chemicals or drugs alter the
metabolic pathways in cells, and metabolite profiling can be used to
assess toxic responses/exposures.
 Transcriptomics
• Transcriptomics uses high-
throughput techniques based
on DNA microarrays
• For further details about
microarrays see Lucchini et
al., Microbiology, 147, 1403-
1414 (2001)

Nelson & Cox, “Lehninger, Principles of

Biochemistry”, 4th edn, 2004, p. 328
 Assessment Pattern
• The students will be assessed on the basis of surprise tests
• The students will be assessed on the basis of quiz relating
the subject
• The students will be assessed on the basis of seminars after
completion of every topic
• Daily discussion of the subject will be done before
commencing of the lecture

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 Applications

• The students will learn about omics field and it’s various
sub branches.

• Students will be able to apply their knowledge for analyzing

biological information.

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 REFERENCES
• 1. David W.Mount Bioinformatics (2001) Cold Spring Harbor
Laboratory Press, ISBN 0-87969-608-7
• 2. Computational Molecular Biology by P. A. Pevzner, Prentice Hall of
India Ltd, (2004) ISBN81-203- 2550-8
• 3.Jin Xiong Essential Bioinformatics, Cambridge University Press.

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 TEXT BOOKS/REFERENCE
BOOKS
• TEXTBOOKS
• T1 Bauxevanis, A.D. and Ouellette, B.F.F. (2005). Bioinformatics: A Practical guide to
the Analysis of Genes and Proteins. Wiley-Interscience, USA.
• T2 Lesk, A.M. (2008). Introduction to Bioinformatics. Oxford University Press, UK.
• T3 Mount, D. (2012). Bioinformatics: Sequence and Genome Analysis. Cold Spring
Harbor Laboratory Press
• T4 Leech Andrew, 2001 Molecular Modelling: Principles and applications (2nd Edition)
Prentice Hall.

• REFERENCE BOOKS:
• R1 Introduction to Proteomics -Tools for the New Biology by Daniel C. Liebler, Humana
Press.
• R2 Mass Spectrometry for Biotechnology by Gary Siuzdak, Academic Press.
• R3 Proteomics for Biological Discovery by Timothy Veenstra and John Yates, Wiley.
THANK YOU

For queries
Email: sonia.e13673@cumail.in