Genome, Whole Genome Sequencing, Genome India Project

Genome

• A genome is the DNA, or sequence of genes, in a cell.
• Most of the DNA is in the nucleus and intricately coiled into a structure called the chromosome.
• The rest is in the mitochondria, the cell’s powerhouse, and some is chloroplast DNA.
• Every human cell contains a pair of chromosomes, each of which has three billion base pairs or one of four molecules – adenine (A), thymine (T), guanine (G), and cytosine (C) – that pair in precise ways.

• The order of base pairs & varying lengths of these sequences constitutes the “genes”.
• Genes are responsible for making amino acids, proteins and, thereby, everything that is necessary for the body to function.

• When these proteins do not function as intended, it leads to disease.

Genome Sequencing

• Sequencing a genome means deciphering the exact order of base pairs in an individual.
• This “deciphering” or reading of the genome is what sequencing is all about.

• In this particular piece of DNA, an adenine (A) is followed by a guanine (G), which is followed by a thymine (T), which in turn is followed by a cytosine (C), another cytosine (C), and so on.

How do you sequence a genome?

• Almost any biological sample containing a full copy of the DNA — even a very small amount of DNA or ancient DNA — can provide the genetic material necessary for full genome sequencing.
  • Such samples may include saliva, epithelial cells, bone marrow, hair (as long as the hair contains a hair follicle), seeds, plant leaves, etc.
  • The whole genome cannot be sequenced all at once because available methods of DNA sequencing can only handle short stretches of DNA at a time.
  • Scientists must break the genome into small pieces, sequence the pieces & then reassemble them in the proper order to arrive at the sequence of the whole genome.
  • One strategy, known as the “clone-by-clone” approach, involves first breaking the genome up into relatively large chunks.
  • The other strategy, called “whole-genome” method, involves breaking the genome up into small pieces, sequencing the pieces, & reassembling the pieces into the full genome sequence.

Whole Genome Sequencing

• Exome, the portion of the genes responsible for making proteins occupies just about 1% of the actual gene. Rather than sequence the whole gene, many geneticists rely on “exome maps”.
• However, the non-exome portions also affect the functioning of the genes.
• Hence to know which genes of a person’s DNA are “mutated” the whole genome sequencing is required.
• Whole genome sequencing is the process of determining the complete DNA sequence of an organism’s genome at a single time.
• This entails sequencing all of an organism’s chromosomal DNA as well as DNA contained in the mitochondria and, for plants, in the chloroplast.
• In practice, genome sequences that are nearly complete are also called whole genome sequences.
• The whole genome sequencing relies on new technologies that allow rapid sequencing of the entire genome in a matter of a few days.

  

Advantages of Whole Genome Sequencing

• It provides a high-resolution, base-by-base view of the genome.
• Captures both large & small variants that might be missed with targeted approaches.
• Identifies potential causative variants for further follow-up studies of gene expression & regulation.
• Delivers large volumes of data in a short amount of time to support the assembly of novel genomes.
• Whole genome sequencing data of a person can be analysed to determine if they carry genes for particular single genetic disorders (caused due to mutation). This will help usher in a new era of personalized medicine.

Human Genome Project

• Human Genome Project is a publicly funded international collaborative research project aimed at
• determining the sequence of chemical base pairs which make up human DNA, &
• identifying & mapping all of the genes of the human genome.
• A base pair (bp) is a unit consisting of two nucleobases bound to each other by hydrogen bonds.
• They form the building blocks of the DNA double helix & contribute to the folded structure of both DNA & RNA.
• Human Genome Project was formally launched in 1990, & finally declared complete in 2003.
• The mapping of the human genome involves sequencing multiple variations of each gene.
• The HGP has revealed that there are probably about 20,500 human genes.

Applications & Benefits of Human Genome Project

It can help us

1. understand diseases including genotyping of specific viruses to direct appropriate treatment,
2. in the identification of mutations linked to different forms of cancer,
3. understand the design of medication & more accurate prediction of their effects,
4. in the advancement of forensic applied sciences, biofuels, animal husbandry, etc.
5. understand evolution much more accurately.
6. Another proposed benefit is the commercial development of genomics research related to DNA based products, a multibillion-dollar industry.

Genome India Project

• Taking inspiration from the Human Genome Project, the Department of Biotechnology (DBT) initiated the ambitious Genome India Project” (GIP) in 2020.
• It aims to collect 10,000 genetic samples from citizens across India, to build a reference genome.
• Gene Mapping project involves 20 leading institutions of the country with the Centre for Brain Research of Indian Institute of Science (IISc) Bangalore as the nodal point.

IndiGen: India’s Genome Sequencing Project

• The Council of Scientific and Industrial Research (CSIR) concluded the six-month-long exercise of conducting a “whole-genome sequence” of a 1,008 Indians that beloged to diverse ethnicities.
• The project is part of a programme called “IndiGen” and is a precursor to Genome India Project” (GIP).
• The project involved the Hyderabad-based Centre for Cellular and Molecular Biology (CCMB) and the CSIR-Institute of Genomics and Integrative Biology (IGIB).

Indian SARS-CoV-2 Genomics Consortium (INSACOG)

• It is a network of 10 laboratories established in December 2020.
• It aims at continuously monitoring the genomic changes of SARS-CoV-2 in India.
• Monitoring is done through Whole Genome Sequencing (WGS).
• Knowledge generated through this research consortium will assist in developing diagnostics & potential therapeutics & vaccines in the future. 

Goals & Objectives of Genome India Project” (GIP)

• Whole-genome sequencing and subsequent data analysis of the genetic data of these 10,000 individuals would be carried out.
• It aims to aid understanding of the nature of diseases affecting the Indian population.
• It allows India to draw upon its tremendous genetic diversity, given the series of large migrations historically, and thus, add greatly to the current information about the human species.
• This initiative would help lay the foundation of personalized healthcare for a very large group of persons on the planet.

Priority Areas

• Some of the priority areas are:
• Precision health
• Rare genetic disorders
• Mutation spectrum of genetic and complex diseases in the Indian population
• Genetic Epidemiology of Multifactorial Lifestyle Diseases
• Translational Research.

Suggested Reading: PMF IAS NCERT Biology Compilation Chapter 12: Nucleic Acids – DNA & RNA

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