What is meant by Genomic study?

Genomic studies (genomics) is the study of the whole genome of an organism. Using bioinformatics and high-performance computing, genomic researchers examined massive amounts of deoxyribonucleic acid (DNA)-sequence data to discover variations or mutations that affect drug response, health, or disease. Genomics is a much younger discipline than genetics, having only emerged in the last few decades as a result of technological advancements in DNA sequencing and computational biology.

What is the purpose of the Genomic study?

Identifying the sequence of DNA (deoxyribonucleic acid) that constitutes an organism’s genetic information is an important aspect of genomics. The term 'genomics' includes the study of human genes and chromosomes. The human genome is made up of 23 chromosome pairs and approximately 24,000 genes. The study of the human genome entails scanning through approximately 3 billion units of DNA across 24,000 genes. The Human Genome Project was an international scientific research project that attempted to identify the base pairs that constitute human DNA and identify and sequence all of the genes in the human genome from both a functional and physical (structure, shape, or size of the genome) perspective.

Next-generation genomic technology (NGS) can collect larger amounts of genetic information in medicine. When this data is merged with informatics, all of this information can be integrated. As a result, researchers will be able to analyze disease and therapeutic responses based on genetics, which will aid in the pursuit of precision medicine. Researchers are using genome studies to understand why some people suffer from certain infections, traits, and biological factors while others don’t. NGS enables researchers to:

• Sequence whole genome efficiently.
• Use RNA sequencing (RNA-Seq) to find new RNA variations and splice sites or to measure mRNAs for gene expression studies.
• Thoroughly sequence and analyze target regions.
• Discover new pathogens.
• Examine epigenetic factors, including genome-wide DNA methylation and DNA-protein interactions.
• Sequence cancer samples in order to analyze uncommon somatic mutations, tumour subclones, and other factors.
• Investigate the human microbiome.

Genomics is the study of the entire genome, which enables the study of gene interactions and the environment. Since complex diseases, including cancer, diabetes, and heart disease, are usually triggered by an interaction of genetic and environmental factors rather than by specific genes, genomics includes the research study of such diseases. Genomics helps to introduce new therapies and treatments for some of the most complex diseases and modern diagnostic tools. Genome sequencing and testing can determine disease risk (such as cancer), history, attributes, and drug response, and it is assisting in the creation of new personalized therapeutics, often known as precision medicines. Early disease detection increases the likelihood of successful therapy, and genomics can diagnose a disease long before symptoms appear. Genomics enables researchers to better understand the interactions between the environment and genes, which assists researchers in finding methods to prevent disease and improve health.

Type of Genomic studies

Structural genomics: The primary objective of structural genomics is to discover the structure of each protein encoded by the genes present in the genome.

Functional genomics: Functional genomics analyze the transcriptome (the whole range of transcripts present in a given organism) and the proteome (the whole arrangement of encoded proteins) and attempts to gather and use information from sequencing to characterize gene and protein functions.

Structural genomics

The detailed and reliable elucidation of the genomic DNA of a particular species is referred to as 'structural genomic studies.' When this sequence is identified, it opens up a world of possibilities. It is beneficial in the technique of altering the genes and DNA sequences of an organism. Structural genomics consists of a combination of experimental and simulation methodologies to characterize the three-dimensional framework of each protein encoded by the genome.

Apart from elucidating protein functions, structural studies can be used to detect protein folds and potential therapeutic targets. The structural study of the genome entails a variety of approaches to protein structure prediction, such as experimental procedures based on genomic sequences or modeling-based methods relying on sequence or structural similarity to a protein of known sequences.

Procedures

De novo methods: Using de novo methods, any open reading frame (ORF) in an entire genome sequence can be cloned and sequenced as a protein. Proteins that have been extracted and crystallized can be examined using X-ray crystallography. This enables the determination of the structure of any protein encoded by the genome.

Threading: It uses structural modeling and folding similarities between an unknown protein and a protein with a known sequence to characterize the structure of the new protein.

Sequenced-based modeling: It compares the protein's genetic code to other protein sequences of known structure. It employs protein structural similarity to build a model of the unidentified protein's structure.

Ab initio modeling: This method is used to predict the 3D structures of proteins using the necessary data from the amino acid interactions and protein sequence.

Functional genomics

Functional genomics analyzes gene and protein expression and function with a focus on translation, transcription, protein-protein interactions, and regulation of gene expression. The goal of genome functional studies is to determine the roles of genes or proteins, and finally, all elements of a genome. It investigates the genes and proteins of an organism using a variety of technological methods, including cellular, biochemical, and physiological properties of every protein. The functional study of the genome includes both functional aspects of the genome, such as polymorphism and mutagenesis, and the analysis of molecular activities.

Assays for DNA accessibility

Assays are available to recognize accessible regions of the genome. These open chromatin regions are potential regulatory domains. FAIRE-Seq (Formaldehyde-Assisted Isolation of Regulatory Elements), DNase-Seq, and ATAC-seq are examples of these assays.

DNase I hypersensitive sites sequencing (DNase-seq) is a method in molecular biology that uses genome-wide sequencing of regions sensitive to DNase I cleavage to determine the location of regulatory regions.

Assay for Transposase-Accessible Chromatin Using Sequencing (ATAC-seq) is a molecular biology method for determining genome-wide chromatin accessibility.

FAIRE-Seq is the equivalent of DNase-Seq for identifying accessible DNA regions in the genome at a genome-wide level.

DNA sequencing

The genomic study relies on DNA sequencing. Whole-genome sequencing is the process of identifying the entire DNA sequence and determining the order of nucleotides in the genome of an organism. DNA sequencing relies on molecule separation techniques and analytical chemistry.

DNA sequencing is carried out to determine the nucleic acid sequence and is the most convenient way to study gene expression and transcription. It refers to the method for determining the order of the four bases: adenine, cytosine, guanine, thymine, and cytosine. Rapid DNA sequencing methods have stimulated biological and biomedical research and innovation.

DNA sequencing can be used by researchers to look for genetic variations or mutations that can influence the development or occurrence of a disease. The disease-causing alteration could be as small as a deletion, a single base-pair substitution, or as large as a deletion of a large number of bases.

Mass spectrometry/Affinity purification (MS/AP)

Proteins that react with one another in complexes can be identified using mass spectrometry and affinity purification (MS/AP). Protein complexes are formed around a specific 'bait' protein. The bait protein is recognized by an antibody or a recombinant label, allowing it to be derived along with other proteins that have developed a complex with it. The proteins are then fragmented into smaller peptides, and the mass-to-charge ratios of fragmented peptides are used to recognize the proteins using mass spectrometry.

DNA microarray

Microarrays are used to determine the amount of messenger ribonucleic acid (mRNA) in a sample that belongs to a particular gene or probe DNA sequence. Immobilized probe sequences are allowed to hybridize with fluorescently labeled "target" mRNA on spots of a solid substrate. The amount of target sequence that has hybridized to that spot and the abundance of mRNA sequence is proportional to the intensity of fluorescence of that spot. Microarrays lead to the discovery of genes associated with a particular process based on differences in transcript levels and expression patterns compared with genes of known function.

Context and Applications

This topic is significant in the exams at school, graduate, and post-graduate levels, especially for

• Bachelors in Biology/Genetics
• Masters in Biology/Genetics

Practice Problems

Question 1: Study of all of a person’s genes is known as ________.

1. Genetics
2. Genomics
3. Population genetics
4. Phylogenetics

Answer: Option 2 is correct.

Explanation: Genomics is the study of an individual's entire genome. Genetics is the study of genes and the transmission of specific traits or conditions from generation to generation. The study of genetic variations within and between populations is known as population genetics. Phylogenetics is the study of the phylogenetic relationships between biological organisms.

Question 2: Genomic study relies on ________.

1. PCR
2. DNA sequencing
3. Electrophoresis
4. None of the above

Answer: Option 2 is correct.

Explanation: The genomic study relies on DNA sequencing. Genome sequencing is the process of identifying the entire DNA sequence and determining the order of the nucleotides in the genome of an organism.

Question 3: What is ATAC-seq used for?

1. To study protein interactions with DNA
2. To analyze genome-wide chromatin accessibility using sequencing.
3. To detect proteins that interact with one another in complexes.
4. None of the above

Answer: Option 2 is correct.

Explanation: ATAC-seq is a molecular biology method for determining genome-wide chromatin accessibility.

Question 4: What does functional genomics involve?

1. Determine the structure of each protein.
2. Analyse the function of proteins
3. Both 1 and 2
4. None of the above

Answer: Option 2 is correct.

Explanation: Functional genomics helps to gather and use data from sequencing to characterize gene and protein functions.

Question 5: The human genome project involves ____.

1. Identifying the base pairs that make up human DNA
2. Identifying and mapping all of the genes of the human genome
3. Both 1 and 2
4. None of the above

Answer: Option 3 is correct.

Explanation: The Human Genome Project was an international research project that attempted to identify and sequence all of the genes in the human genome from both a functional and physical standpoint.