Understanding a human pangenome map

Context: Human Pangenome Reference Consortium has released a pangenome reference map built using genomes from 47 anonymous individuals (19 men and 28 women), mainly from Africa but also from the Caribbean, Americas, East Asia, and Europe.

What is a genome?

  • The genome is the blueprint of life, a collection of all the genes and the regions between the genes contained in our 23 pairs of chromosomes.
  • Each chromosome is a contiguous stretch of DNA string, i.e., the human genome consists of 23 different strings, each composed of millions of individual building blocks called nucleotides or bases [adenine (A), cytosine (C), guanine (G), and thymine (T)]. These bases or building blocks (A, T, G and C) are arranged and repeated millions of times in different combinations to make all of our 23 chromosomes.
  • Genome sequencing is the method used to determine the precise order of the four bases and how they are arranged in chromosomes. Sequencing individual genomes helps us understand human diversity at the genetic level and how prone we are to certain diseases
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What is a reference genome?

  • Human reference map or reference genome, represents a single, representative genome sequence for a given species or individual. The reference map is typically derived from the genome of an individual that is chosen as a representative of the species or a reference panel of individuals from the same population. 
  • When genomes are newly sequenced, they are compared to a reference genome, i.e., it serves as a standard or reference against which other genomes can be compared and aligned. This helps us to understand the regions of differences between the newly sequenced genome and the reference genome.
  • 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.
    • The reference genome of 2001 was 92% complete and contained many gaps and errors. Additionally, it was not representative of all human beings as it was built using mostly the genome of a single individual of mixed African and European ancestry.
    • Since then, the reference genome map has been refined and improved to have complete end-to-end sequences of all 23 human chromosomes and is still continuously evolving to fill the gaps.

What is a pangenome? 

  • The pangenome refers to the entire set of genes present in a species, including both the core genome (genes present in all individuals) and the accessory genome (genes present in only some individuals or strains).
  • A pangenome map typically involves the identification and annotation of genes and their genomic locations within a species. It provides insights into the genetic diversity and variability within a species, as well as the presence of specific genes or gene variants in different individuals or populations.
  • By comparing the genomes, researchers can identify shared genes and gene clusters as well as unique genes present in specific individuals. 

Importance of pangenome map:

  • Humans are more than 99% similar in their DNA, there is still about a 0.4% difference between any two individuals. This may be a small percentage, but considering that the human genome consists of 3.2 billion individual nucleotides, the difference between any two individuals is a whopping 12.8 million nucleotides.
  • A complete and error-free human pangenome map will help us understand those differences and explain human diversity better
  • It will also help us understand genetic variants in some populations, which result in underlying health conditions. E.g., The pangenome reference map has added nearly 119 million new letters to the existing genome map and has already aided the discovery of 150 new genes linked to autism.


  • The genomes from many populations are still not a part of it. E.g., In the current version of the pangenome map, genomes from people from the Indian sub-continent, indigenous groups in Asia and Oceania, and West Asian regions are not represented.     

To read more about ‘Genome Sequencing and the Genome India Project’, kindly click on the link given below: https://compass.rauias.com/current-affairs/genome-sequencing-and-the-genome-india-project/   

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