Genomics – types and applications

 

Genomics – types and applications

History of Genomics :- 

• History of genomics dates back to the 1970s when the scientists determined the DNA sequence of simple organisms.

• The greatest breakthrough in the field of genomics occurred in the mid- 1990s when the scientists sequenced the entire genome of Haemophilus influenzae, a free-living organism which, however, does not cause influenza.

• The bacterium was thought to be the cause of flu until 1933 when it was proven that influenza is caused by a virus.

• In 2001, the scientists sequenced most of the human genome.

• Since then, genomes are being sequenced with relative ease.

• By the end of 2011, scientists sequenced genomes of over 2,700 viruses, more than 1,200 bacteria and archaea and 36 eukaryotes about 50 percent of which are fungi.

• Scientists get a number of highly useful information from sequenced DNA of organisms.

• But what is most important of all, they allow the scientists to determine the relationships between the genes and different sections of DNA which in turn allows them to determine which areas could offer benefits to science as well as make the knowledge useful for medical applications.

Types of Genomics

• Structural genomics:

Aims to determine the structure of every protein encoded by the genome.

• Functional genomics:

 Aims to collect and use data from sequencing for describing gene and protein functions.

• Comparative genomics:

 Aims to compare genomic features between different species.

1) Structural genomics :-

• Structural genomics is a field of genomics that involves the characterization of genome structures.

• This knowledge can be useful in the practice of manipulating the genes and DNA segments of a species.

• As an example, it is important to understand the locus of a gene within the genome before it is possible to clone the gene successfully.

• Likewise, knowledge about the composition of the gene is useful when attempting to understand its function and how it can be altered for practical purposes, such as to ultimately improve health.

• Structural genomics describes the 3-dimensional structure of each and every protein that may be encoded by a genome – when specifically analyzing proteins, this is more commonly referred to as structural proteomics.

• The study is aimed to study the structure of the entire genome, by utilizing both experimental and computational techniques.

• Whilst traditional structural prediction focuses on the structure of a particular protein in question, structural genomics considers a larger scale by aiming to determine the structure of every constituent protein encoded by a genome.

• Objectives of structural genomics :- 

• It is hoped that more extensive knowledge of the structure of genomes, and comparing different examples, could lead to the deduction of principles that govern overall genomic structure.

• As the protein structure and function are closely linked, the importance of structural genomics in understanding the function of proteins is paramount.

• Structural genomics can also provide insight in dynamic properties such as protein folding and identify possible targets that may be used for drug discovery.

2) Functional genomics:-

• The aim of functional genomics studies is to understand the complexmrelationship between genotype and phenotype on a global (genome-wide) scale.

Technologies used in functional genomic studies :-

• Microarrays

• Expression-profiling - used to measure the expression of thousands of genes at once, using oligonucleotide probes (usually ≤50 basepairs in length) designed from transcript cDNA or exon sequences across the genome.

• Tiling microarrays - often used for mapping transcription factor binding sites or locations of epigenetic marks (e.g. histone modifications). They use overlapping oligonucleotide probes (usually ≤50bp) covering several megabases of genomic sequences.

• HTS

• RNA sequencing (RNA-Seq) - is used to sequence cDNA in order to get information about a sample's RNA content.

• ChIP sequencing (ChIP-Seq) - uses Chromatin ImmunoPrecipitation (ChIP) with DNA sequencing to identify proteinbinding sites on DNA.

3) Comparative genomics :-

• Comparative genomics is a field of biological research in which the genomic features of different organisms are compared.

• 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.

• Therefore, comparative genomic approaches start with making some form of alignment of genome sequences and looking for orthologous sequences (sequences that share a common ancestry) in the aligned genomes and checking to what extent those sequences are conserved.

Methods :-

• Computational approaches to genome comparison have recently become a common research topic in computer science.

• A public collection of case studies and demonstrations is growing, ranging from whole genome comparisons to gene expression analysis.

• This has increased the introduction of different ideas, including concepts from systems and control, information theory, strings analysis and data mining.

• It is anticipated that computational approaches will become and remain a standard topic for research and teaching, while multiple courses will begin training students to be fluent in both topics.

Tools :-

• UCSC Browser: This site contains the reference sequence and working draft assemblies for a large collection of genomes.

• Ensembl: The Ensembl project produces genome databases for vertebrates and other eukaryotic species, and makes this information freely available online.

• MapView: The Map Viewer provides a wide variety of genome mapping and sequencing data.

• VISTA is a comprehensive suite of programs and databases for comparative analysis of genomic sequences. It was built to visualize the results of comparative analysis based on DNA alignments. The presentation of comparative data generated by VISTA can easily suit both small and large scale of data.

• BlueJay Genome Browser: a stand-alone visualization tool for the multi-scale viewing of annotated genomes and other genomic elements.

Applications of genomics :-

• Medical application

• Oral immunization with plants: Oral plant vaccines, which use DNA and transgenes to create surface antigens that stimulate immunity when consumed, show promise in the quest to immunize humans against hepatitis B.

• Heterologous prime-boost vaccine for malaria: Two-part vaccines with DNA from P. falciparum followed by modified Ankara virus are expected to reduce the risk of malaria infection by up to 80%.

• Anti-malarial drugs: The chemicals fosmidomycin and FR-900098 are being tested for their targeted effects in inhibiting DOX reductoisomerase in the body, which is involved in the lifecycle of P. falciparum, the most dangerous of the parasites that can cause malaria.

• Screening for thalassemias: Tests have been evolved that use the polymerase chain reaction to observe the gene mutations that are responsible for creating the structure of the hemoglobin molecule. Genetic counseling as a result of the screening test has reduced rates of thalassemia in Sardinia from 1 in 250 to 1 in 4000 live births.

Biotechnology applications :-

• There are several applications of genomic knowledge in the field of synthetic biology and bioengineering.

• Some scientific research has demonstrated the creation of a partially synthetic species of bacteria. For example, the genome of Mycoplasma genitalium was used to synthesize the bacterium Mycoplasma laboratorium, which has distinct characteristics from the original bacteria.

Social science applications :-

• Conservationists have made use of the genomic sequencing data to evaluate key factors that are involved in the conversation of a species.

• For example, the genetic diversity of a population or the heterogeneity of an individual for a hereditary condition with a recessive inheritance pattern can be used to predict the health and conservation of the population.

• This data can also be useful in determining the effects of evolutionary processes and picking up genetic patterns of a specific population, including human and animal life. Insights into these patterns can help to devise plans to aid the species and enable it to thrive into the future.