What is Genome Sequencing

Context: Recent scientific studies have observed that Genome sequencing has helped scientists to discover key moments in human history, like population bottlenecks and genetic disease origins.

Key Observations of the Study

• Genomic analysis has provided valuable insights into the evolution and history of the human species.
• Molecular Clock of Human Evolution:
  • Genome sequencing technology allows scientists to rapidly sequence human genomes and analyze the data using computational tools.
  • The genome sequences provide a snapshot of the molecular clock of human evolution. The molecular clock concept suggests that genetic variations accumulate at a relatively constant rate over time.
  • By examining genetic variations within genomes, researchers can estimate the rate at which these variations accumulate. This rate helps create a timeline of human evolution, revealing when specific genetic changes occurred.
  • Additionally, the exchange of genetic material during the formation of gametes (sperm and ovum) contributes to the molecular clock, and genome sequencing helps capture this information.
• Population Bottlenecks:
  • Genome sequencing has enabled scientists to study the genetic diversity within human populations.
  • The study revealed that there was a significant bottleneck in human evolution about 900,000 years ago, which may have had a big impact on how humans developed.
  • Population bottlenecks occur when a population is reduced to a small number of individuals, resulting in a loss of genetic diversity.
  • With genome sequencing, researchers can analyze the genetic makeup of present-day populations and identify patterns of shared genetic material.
  • When a population goes through a bottleneck, the genomic contributions of the few individuals who survive become more pronounced in the subsequent generations. This phenomenon is known as the founder effect.
  • Genome sequencing helps detect founder effects by revealing more shared genetic material among individuals of a population that has gone through a bottleneck.
    • Examples of well-studied founder populations: Ashkenazi Jews and endogamous groups in India, where genome sequencing has revealed the genetic consequences of historical population bottlenecks.
• Determining the Age of Genetic Diseases:
  • By studying genome sequences from present-day populations and analyzing the genetic variations associated with specific diseases, researchers can estimate when these diseases likely originated.
  • For instance, genome sequences were used to conclude that sickle cell anaemia arose approximately 7,300 years ago.

What is Genome?

• A genome is all of the genetic material in an organism.
• It is made of DNA (or RNA in some viruses) and includes genes and other elements that control the activity of those genes.
• Genome v/s Gene: Genome is the entire set of genetic material or DNA, while gene is a specific segment of DNA that codes for a particular protein or RNA molecule.
• Human genome:
  • The human genome is the entire set of deoxyribonucleic acid (DNA) residing in the nucleus of every cell of each human body.
  • 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.

What is Genome Sequencing?

• Genome sequencing is figuring out the order of DNA nucleotides, or bases, in a genome—the order of Adenine, Cytosine, Guanines, and Thymine that make up an organism’s DNA.
• While the sequence or order of base pairs is identical in all humans, compared to that of a mouse or another species, there are differences in the genome of every human being that make them unique.

Methods of Genome Sequencing

• Major genome sequencing methods are the clone-by-clone method and the whole genome shotgun sequencing.
• The clone-by-clone method:
  • It involves constructing a physical map of the genome by cutting the DNA into small fragments, cloning these fragments into bacterial or yeast artificial chromosomes (BACs or YACs), and then mapping the location of each fragment within the genome.
  • The DNA in each BAC or YAC clone is then sequenced, and the sequences are assembled to reconstruct the entire genome.
  • It works well for larger genomes like eukaryotic genomes, but it requires a high-density genome map.
• The whole genome shotgun sequencing method:
  • It involves randomly fragmenting the genome into small pieces, sequencing each piece, and then using computational algorithms to assemble the sequences into a complete genome.
  • This method was made possible by the development of high-throughput sequencing technologies, such as next-generation sequencing, which can generate large amounts of sequence data rapidly and inexpensively.
  • It is a faster method of sequencing but is not suitable for larger genomes like eukaryotic genomes as they have several repetitive DNA sequences in which the assembling process is challenging.

Applications of Genome Sequencing

• Disease risk assessment: Genomic sequencing can identify genetic variants associated with increased risk of certain diseases, such as breast cancer or Alzheimer’s disease.
  • Genome sequencing has been used to evaluate rare disorders, preconditions for disorders, even cancer from the viewpoint of genetics, rather than as diseases of certain organs.
  • Nearly 10,000 diseases — including cystic fibrosis and thalassemia — are known to be the result of a single gene malfunctioning.
• Ancestry tracing: Genomic sequencing can provide information about an individual’s ancestry and genetic heritage.
• Cancer diagnosis: Liquid biopsies, where a small amount of blood is examined for DNA markers, could help diagnose cancer long before symptoms appear.
• Halting disease transmission: In public health, however, sequencing has been used to read the codes of viruses—
  • For Example: One of its first practical usages was in 2014, when a group of scientists from M.I.T and Harvard sequenced samples of Ebola from infected African patients to show how genomic data of viruses could reveal hidden pathways of transmission, which might then be halted, thus slowing or even preventing the infection’s spread.
  • Also, during the COVID-19 pandemic, genomic sequencing helped to identify the virus, track its spread, identify new variants, understand how the virus spreads, and develop vaccines.
• Pharmacogenomics: Genomic sequencing can identify genetic variants that affect an individual’s response to certain medications.

Concerns associated with Genome Sequencing

• Privacy concerns: As genomic sequencing involves the collection and analysis of genetic data, there are concerns about privacy and the potential misuse of this information.
• High Costs: Genomic sequencing can be expensive, which can limit access to this technology for some patients or researchers.
• Misuse: There is a risk that genomic sequencing data could be used for nefarious purposes, such as genetic discrimination or targeting of individuals based on their genetic profile.
• Psychological impact: Knowing one’s genetic risk factors can have a psychological impact, including increased anxiety or depression. Individuals may also face stigma or discrimination based on their genetic risk factors.
• Data interpretation and accuracy: Errors in data interpretation or analysis could lead to incorrect diagnoses or treatment decisions.

About the Genome India Project

• It is a government-led initiative launched in 2019 that aims to sequence the genomes of over 10,000 Indians from diverse socio-economic, geographical and linguistic backgrounds to create a comprehensive genomic database of the Indian population.
• The project involves about 20 institutions across India and with analysis and coordination done by the Centre for Brain Research at IISc, Bangalore.
• Significance of the project:
  • India’s 1.3 billion-strong population consists of over 4,600 population groups, many of which are endogamous. Thus, the Indian population harbours distinct variations, with disease-causing mutations often amplified within some of these groups. Creating a database of Indian genomes allows researchers to learn about genetic variants unique to India’s population groups and use that to customize drugs and therapies.
  • The project will also help “unravel the genetic underpinnings of chronic diseases currently on the rise in India, (for) example, diabetes, hypertension, cardiovascular diseases, neurodegenerative disorders, and cancer”.

Other Initiatives by the government

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