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Pangenome Reference Map


A recent publication in the Nature journal has introduced a Pangenome Reference Map, which was constructed using genomes obtained from 47 anonymous individuals. These individuals, comprising 19 men and 28 women, were primarily from Africa, but also included participants from the Caribbean, Americas, East Asia, and Europe.


GS III: Science and Technology

Dimensions of the Article:

  1. About Genome
  2. About Reference Genome
  3. About Pangenome Map
  4. Genome India Project

About Genome:

  • It refers to the complete set of genetic instructions or information that an organism possesses.
  • It is made up of DNA, which carries the instructions for the development, functioning, growth, and reproduction of all living organisms.
  • The study of genomics involves the analysis of genomes and has led to many breakthroughs in various fields, including medicine and biotechnology.

Genome Sequencing

  • Genome sequencing is figuring out the order of DNA nucleotides, or bases, in a genome—the order of adenine (A), thymine (T), cytosine (C), and guanine (G), that make up an organism’s DNA.

About Reference Genome

  • Reference genome serves as a standard map for scientists to compare and analyze newly sequenced genomes.
  • It helps scientists understand genetic differences and variations in newly sequenced genomes by comparing them to the reference genome.
  • The first reference genome, created in 2001, was a significant scientific achievement.
  • It facilitated the discovery of disease-related genes and advancements in understanding genetic aspects of diseases like cancer.
  • It aided in the development of new diagnostic tests.
Limitations of the First Reference Genome:
  • The first reference genome had some limitations and imperfections.
  • It was primarily based on the genome of one individual with mixed African and European ancestry.
  • There were gaps and errors in the initial reference genome.
Improvements with the Pangenome:
  • The new reference genome, known as the Pangenome, is more comprehensive and error-free compared to the first reference genome.
  • However, even with the Pangenome, there is still a lack of representation of the full diversity of human genetics.
  • The Pangenome includes a wider range of genetic variations but may not capture the entire spectrum of human genetic diversity.

About Pangenome Map

  • The pangenome map represents the genome as a graph, unlike the linear reference genome used previously.
  • Each chromosome in the pangenome is depicted as a bamboo stem with nodes.
  • Nodes represent sequences that are similar among all 47 individuals, while the internodes between the nodes indicate genetic variations among individuals from different ancestries.
  • Long-read DNA sequencing technology was employed to create complete and continuous chromosome maps in the pangenome project.
Understanding Genetic Differences and Diversity:
  • Despite humans sharing over 99% of their DNA, there is still approximately a 0.4% difference between any two individuals.
  • This seemingly small difference amounts to around 12.8 million nucleotides considering the vast size of the human genome (3.2 billion nucleotides).
  • A comprehensive and accurate pangenome map aids in understanding these genetic differences and explaining the diversity among individuals.
  • It facilitates the study of genetic variations that contribute to underlying health conditions.
Benefits and Future Applications:
  • The current pangenome map, although lacking Indian genomes, still holds value in comparing and mapping Indian genomes against existing accurate reference genomes.
  • Future pangenome maps incorporating high-quality Indian genomes, including those from diverse and isolated populations within the country, will provide valuable insights.
  • These insights include disease prevalence, discovery of new genes related to rare diseases, improved diagnostic methods, and development of novel drugs for these diseases.
Limitations and Representation Gaps:
  • The current pangenome map does not adequately represent diverse populations such as Africa, the Indian subcontinent, indigenous groups in Asia and Oceania, and West Asian regions.
  • Efforts should be made to include genomes from these populations to ensure a more comprehensive understanding of human genetic diversity and its implications.

Genome India Project

  • India’s population consists of over 4,600 diverse population groups, many of which are endogamous.
  • These groups have unique genetic variations and disease-causing mutations that cannot be compared to other populations.
  • The Genome India Project aims to create a database of Indian genomes to learn about these unique genetic variants and use the information to create personalized drugs and therapies.
  • The project was started in 2020 and is inspired by the successful decoding of the entire human genome in the Human Genome Project (HGP).
  • The project seeks to better understand the genetic variations and disease-causing mutations specific to the Indian population, which is one of the most genetically diverse in the world.
  • By sequencing and analyzing these genomes, researchers hope to gain insights into the underlying genetic causes of diseases and develop more effective personalized therapies.
  • The project involves the collaboration of 20 institutions across India and is being led by the Centre for Brain Research at the Indian Institute of Science in Bangalore.
  • Other countries, such as the United Kingdom, China, and the United States, also have similar programs to sequence their genomes.
Significance of the Genome India Project:

The Genome India Project (GIP) has significant implications in various fields, including healthcare, agriculture, and global science. Here are the key points of its significance:

  • Personalized Medicine: The GIP aims to develop personalized medicine based on patients’ genomes to anticipate and modulate diseases. By mapping disease propensities to genetic variations, interventions can be targeted more effectively, and diseases can be anticipated before they develop.
  • Understanding Disease Propensities: GIP can help understand the genetic basis of disease propensities in different populations. For example, variations across genomes may explain why cardiovascular disease leads to heart attacks in South Asians but to strokes in most parts of Africa.
  • Agriculture: The GIP can benefit agriculture by understanding the genetic basis of the susceptibility of plants to pests, insects, and other issues hampering productivity. This can reduce dependence on chemicals.
  • Global Science: The project is said to be among the most significant of its kind in the world because of its scale and the diversity it would bring to genetic studies. Global science will also benefit from a mapping project in one of the world’s most diverse gene pools.

-Source: The Hindu

February 2024