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

Goals of genomicsCompile 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 genomics:• Aims to determine

structure of every protein encoded by the genome.• Identify novel

protein folds and 3-D structures for better understanding the functions of proteins.

Functional genomics:

• Aims to collect and use data from sequencing for decribing gene and protein functions

• functions of genes and non-gene sequences in genomes

• Gena and protein interactions

• Genotype- phenotypes

Comparative Genomics

• Aims to compare genomic features between different species

• e,.g. for better understanding the evaloutionary relationships.

• to determine the function of each genome E.g studying genes in model organisms

• Yeast and human

Mutational Genomics:

• The study of genome in terms of mutations that occur in an individual’s DNA or genome

• One of the aspect of functional genomics

• Also referred as gene function determination

• 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.