Understanding a Human Pangenome Map

What’s in today’s article?

• Why in news?
• Genome
• What is a genome?
• Genome Sequencing
• What is a reference genome?
• Pangenome map
• What is a pangenome map?
• Why is a pangenome map important?
• Pangenome map and India

Why in news?

• A recent study published in the Nature journal presents a pangenome reference map. 
• The map was created using genetic information from 47 unidentified individuals, including 19 men and 28 women. 
• These individuals come from various regions such as Africa, the Caribbean, Americas, East Asia, and Europe.

Genome

What is a genome?

• The human genome is the entire set of deoxyribonucleic acid (DNA)residing in the nucleus of every cell of each human body. 
• It carries the complete genetic information responsible for the development and functioning of the organism. 
• Our genome consists of 23 different strings, each composed of millions of individual building blocks called nucleotides or bases.
• The DNA consists of a double-stranded molecule built up by four bases – adenine (A), cytosine (C), guanine (G) and thymine (T). 
• Every base on one strand pairs with a complementary base on the other strand (A with T and C with G).
• In all, the genome is made up of approximately 3.05 billion such base pairs.

Genome Sequencing

• Genome sequencing is the method used to determine the precise order of the four letters (A, T, G and C) and how they are arranged in chromosomes.
  • In other words, Genome sequencing is the process of determining the complete DNA sequence of an organism’s genome.
• Sequencing individual genomes helps us understand human diversity at the genetic level and how prone we are to certain diseases.
• The genome is an identity card like Aadhaar. As each of our Aadhar card is unique, so is our genome. 
• As sequencing individual genomes of all humans is expensive, we do not yet have all our genome identity cards. 
• To circumvent this, one can have a collective identity card. For example, we can have a single genome identity card for everyone living in a region.

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What is a reference genome?

• About
  • A reference genome is a complete, assembled set of genetic information for a particular species.
  • When genomes are newly sequenced, they are compared to a reference map called a reference genome. 
  • This helps us to understand the regions of differences between the newly sequenced genome and the reference genome.
• Significance
  • One of this century’s scientific breakthroughs was the making of the first reference genome in 2001. 
  • It helped scientists discover thousands of genes linked to various diseases; better understand diseases like cancer at the genetic level; and design novel diagnostic tests.

Pangenome map

What is a pangenome map?

• About
  • A pangenome map refers to the representation and analysis of the collective genetic information present in the genomes of a particular species or a group of related species. 
  • Unlike a reference genome, which represents a single individual or a consensus sequence, a pangenome map captures the genetic diversity and variation across multiple individuals or populations.
  • The earlier reference genome is a linear sequence. However, the pangenome is a graph.
• Principle
  • The concept of a pangenome recognizes that the genome of a species is not a fixed entity.
  • But it consists of a core set of genes shared by most individuals, along with a variable set of genes that are unique or present only in certain individuals or subpopulations. 
  • This genetic variation can contribute to differences in traits, disease susceptibility, and other biological characteristics.

Why is a pangenome map important?

• A comprehensive picture of the species’ genetic content
  • A pangenome map integrates genomic data from multiple individuals or strains of a species to construct a comprehensive picture of the species’ genetic content. 
  • It includes the identification and classification of core genes shared by all or most individuals, as well as the characterization of variable genes that are present in only a subset of individuals.
  • Hence, a complete and error-free human pangenome map will help us understand those differences and explain human diversity better.
• Helpful for researchers
  • By constructing a pangenome map, researchers can:
    • gain insights into the genetic diversity within a species, 
    • study the evolution and adaptation of genes, 
    • identify genes associated with specific phenotypes or diseases, and 
    • understand the overall genomic architecture of the species.

Pangenome map and India

• The current map does not contain genome sequences from Indians.
• Still, it will help map Indian genomes better against the error-free and complete reference genomes known so far.
• Future pangenome maps may include high quality genomes from Indians, including from many endogamous and isolated populations within the country.
• If this happens, it will shed light on disease prevalence, help discover new genes for rare diseases, design better diagnostic methods, and help discover novel drugs against those diseases.

Q1) What is genome sequencing?

Genome sequencing is the process of determining the complete DNA sequence, or genome, of an organism. The genome is the entire set of genetic material present in an organism, including all of its genes, non-coding DNA, and other functional elements. Genome sequencing involves decoding the order of nucleotide bases (adenine, thymine, cytosine, and guanine) within an organism’s DNA. 

Q2) What is DNA, or deoxyribonucleic acid?

DNA, or deoxyribonucleic acid, is a molecule that carries the genetic instructions for the development, functioning, growth, and reproduction of all living organisms. It serves as the hereditary material in most organisms, including humans. There are four types of nitrogenous bases in DNA: adenine (A), thymine (T), cytosine (C), and guanine (G).

Source: Explained | Understanding a human pangenome map | The Hindu