Types of genomics

Group
Hina zamir (04)
Mahnoor khan (02)
Rameen Nadeem (25)
Syeda iqra Hussain
(?05)
Maleeha Inayat (06)
Overview
• Genomics overview
• Goal of genomics
• Types of genomics overview
• Structural genomics
• Functional genomics
• Mutational genomics
• Comparative genomics
Genomics overview

Genome: entirety
of genetic material
coined by Winklen
1920
Genomics: field of
study where entire
genome is studied
Coined by Thomas
Rhodrick
als of genomics
Compile the genomic sequences of organisms
Search out the location of the genes for
analyzing spatial relationships and annotate the
gene set in a genome
Learn the function of genes and their influence
Establish how gene expression profiles of a
cell vary under different conditions.
Compare gene and protein profiles among
different organisms to learn about evalutionary
relationships.
Structural Functional genomics:
genomics: • Aims to collect and use
• Aims to determine data from sequencing
structure of every for decribing gene and
protein encoded by protein functions
the genome.
• Identify novel • functions of genes and
protein folds and 3- non-gene sequences in
D structures for genomes
better
understanding the • Gena and protein
functions of interactions
proteins. • Genotype- phenotypes
Comparative Genomics Mutational Genomics:
• Aims to compare
• The study of genome in
genomic features terms of mutations that
between different species occur in an individual’s
• e,.g. for better DNA or genome
understanding the
evaloutionary • One of the aspect of
relationships.
functional genomics
• to determine the function
of each genome E.g • Also referred as gene
studying genes in model function determination
organisms
• Yeast and human • Aim to determine
function of gene
• Or anonymous
sequence
Structural genomics
Definition

• Structural genomics helps to describe the 3-

dimensional structure of every protein encoded by
a particular genome.
• The principal difference between structural
genomics and traditional structural prediction is
that structural genomics attempts to determine the
structure of every protein encoded by the genome,
rather than focusing on oneparticular protein.
• It involves taking a large number of approaches to
structure determination, including
• experimental methods using genomic sequences or
• modeling-based approaches ....
• based on sequence or structural homology of a
protein of known structure or
• based on chemical and physical principles for a
protein with no homology to any known structure.
Goals
• Structural genomics has role in determination of
function of a protein.
• Used in drug discovery and
• in protein engineering On a large scale
• Interpretation of protein structure:
• The gene sequence of the target protein can also
be compared to a known sequence and structural
information can then be inferred from the known
protein’s structure.
Functional genomics
Functional genomics:

• Branch of genomics that determines biological

functions of genes and their products.
• Functional genomics (transcriptomics and
proteomics) is a global, systematic and
comprehensive approach for identification and
description of the processes and pathways
involved in the normal and abnormal state of
genes.
Why we need to study?

• It is estimated that approximately 30% of the open

reading frames in a fully sequenced organism have
unknown function at the biochemical level and are
unrelated to any known gene. This is why recently
the interest of researchers has shifted from
genome mapping and sequencing to determination
of genome function by using the functional
genomics approach.
Example:

• A single gene can give rise to multiple gene

products. RNA can be alternatively spliced or edited
to form mature mRNA. Besides, proteins are
regulated by additional mechanisms such as
posttranslational modifications,
compartmentalization and proteolysis. Finally,
biological function is determined by the complexity
of these processes.
Techniques of functional genomics:

• At the DNA level(Genetic interaction mapping, the

ENCODE project)
• Gene expression profiling at the transcript level
(differential display, expressed sequence tags, serial
analysis of gene expression and DNA microarrays)
• Proteome analysis (Protein microarray, 2D-PAGE)
Mutational genomics
Mutational genomics

• Mutational genomics is the field of genomics that

characterizes mutation associated genes.
• In this we basically focuses on genomic, epigenomic and
transcript alterations in cancer.
• Mutational genomics bears similarity to genetical
genomics, linking genotype to transcriptional state.
• In mutational genomics the difficult task is the finding of
genes that underlying transcriptional changes
Mutational genomics strategy
• There are three basic types of mutational genomics strategy
• First, the systematic approach of deliberately mutating every gene
in the genome, one at a time, and generating banks of specific
mutant strains.
• Second, the random approach in which genes are mutated
indiscriminately. Individual mutation are then catalogued by
obtaining flanking sequence tags, and genes are annotated by
matching the tags to entries in sequence databases.
• The third approach encompasses a group of techniques which
generate functional phenocopies of mutant allelles. i.e, the likeness
of a mutation without actually altering the DNA sequence of an
organism.
Oncogenomics

• Oncogenomics is a sub-field of mutational genomics that

characterizes cancer-associated genes.
• It focuses on genomic, epigenomic and transcript alterations in
cancer.
• Cancer is a genetic disease caused by accumulation of DNA
mutations and epigenetic alterations leading to unrestrained cell
proliferation and neoplasm formation.
• The goal of oncogenomics is to identify new oncogenes or tumor
suppressor genes that may provide new insights into cancer
diagnosis, predicting clinical outcome of cancers and new targets for
cancer therapies.
Goal of Oncogenomics
Comparative
genomics
Defination
• field of biological research in which the genomic
features of different organisms are compared The
genomic features may include the DNA sequence
genes gene order regulatory sequences
Purpose
• In this branch of genomics, whole or large parts of
genomes resulting from genome projects are
compared TO STUDY basic biological similarities
differences evolutionary relationships between
organisms The major principle of comparative
genomics is that common features of two
organisms will often be encoded within the DNA
that is evolutionarily conserved between them.
•
By comparing the sequences of genomes of
different organisms, researchers can understand
what, at the molecular level, distinguishes
different life forms from each other.
• Comparative genomics also provides a powerful
tool for
• 1: Studying evolutionary changes
• 2: Helping to identify genes that are conserved
or common among species
• 3: Genes that give each organism its unique
characteristics.
How are genomes compared?

• A simple comparison of the general features of

genomes such as genome size, number of genes,
and chromosome number presents an entry point
into comparative genomic analysis. The
comparisons highlight some striking findings. Finer-
resolution comparisons are possible by direct DNA
sequence comparisons between species.
Comparison of discrete segments of genomes is
also possible by aligning homologous DNA from
different species.
Tools

• Computational tools for analyzing sequences and

complete genomes are developed quickly due to
the availability of large amount of genomic data. At
the same time, comparative analysis tools are
progressed and improved.
Applications
•
Applying a comparative genomics approach by
analyzing the genomes of several related pathogens
can lead to the development of vaccines that are
multiprotective Identifying the loci of advantageous
genes is a key step in breeding crops that are
optimized for greater yield, cost-efficiency, quality,
and disease resistance.