Maarg Manthan · Topic 10.4

Genome Sequencing and Its Practical Uses

Science & Technology › Biotechnology – Principles and Techniques · Topic 10.4

Genome sequencing is the process of finding the exact order of the four bases, adenine, thymine, guanine and cytosine, in the complete DNA of an organism. The first generation method of Frederick Sanger, developed in 1977, was used for the Human Genome Project, which ended in 2003. Next generation sequencing, from the mid 2000s, reads millions of fragments at once and cut the cost of a human genome from billions of dollars to a few hundred dollars. Long read methods and nanopore sequencing now give far longer reads. Uses include medicine, tracking of pathogens, crop breeding, conservation, and forensic work.

5 min read · UPSC Prelims · Science & Technology · Biotechnology – Principles and Techniques

At a Glance

First method Sanger, 1977
Modern method Next generation sequencing
Human project Completed 2003
Surveillance INSACOG for viruses
Indian project GenomeIndia
Exam link UPSC Prelims, Science & Technology: Biotechnology – Principles and Techniques

Where Does It Fit?

This topic follows the types of RNA. It explains how the order of bases is read and how that knowledge is used in daily practice. Previous topic: Types of RNA and Their Technological Applications. Next topic: DNA Sequencing and Nucleic Acid Probes.

How Has Sequencing Technology Developed?

Generation	Features
First generation (Sanger)	Chain termination method of 1977 that reads one fragment at a time with high accuracy. Used for the Human Genome Project
Second generation	Next generation sequencing that reads millions of short fragments in parallel, for example Illumina machines. Fast and cheap, though short reads are hard to assemble in repeat regions
Third generation	Long read methods such as PacBio and Oxford Nanopore that read very long single molecules, helping to complete gaps
Whole genome sequencing	Reads all of the DNA
Exome sequencing	Reads only the protein coding regions
Targeted sequencing	Reads chosen genes, for example cancer panels

What Are the Practical Uses?

Rare disease diagnosis: finding the single gene change behind an inherited illness
Cancer care: tumour sequencing shows mutations that guide the choice of targeted therapy
Newborn and carrier screening: early detection of inherited conditions
Pathogen surveillance: sequencing virus genomes shows variants and spread. India set up INSACOG, the Indian SARS-CoV-2 Genomics Consortium, in December 2020
Antimicrobial resistance: finding resistance genes in bacteria such as tuberculosis
Agriculture: reference genomes of rice, wheat, pigeon pea, chickpea and millets support breeding
Conservation and forensics: genomes identify species, track wildlife trade and identify individuals
Population studies: variation among communities helps to find disease risks and ancestry

What Else Should You Remember?

Reference genome: an assembled sequence used as a standard to compare other individuals of a species
Cost fall: the first human genome cost billions of dollars, and the cost is now a small fraction of that, which made large projects possible
GenomeIndia: a Department of Biotechnology project that has sequenced genomes of 10,000 Indians from diverse groups, announced as completed in January 2025 with data kept at the Indian Biological Data Centre. Check the latest figures before quoting
Ragi genome: India sequenced the finger millet genome, as in Genome Sequencing of Ragi (First in the World)
Indian cobra and other genomes: the Indian cobra genome has been sequenced by Indian scientists
Earth BioGenome Project: an international effort to sequence all eukaryotic species
Data and privacy: genome data identifies people, so consent, storage and sharing rules are needed
Interpreting results: finding a variant is easier than knowing what it does
Sanger sequencing: Frederick Sanger won a second Nobel Prize in Chemistry in 1980 for this chain termination method. He had received an earlier one in 1958 for the structure of insulin
Pooled and wastewater sequencing: sequencing sewage samples can track viruses in a city without testing individuals
Cancer panels: small sets of cancer related genes are sequenced from tumour tissue or blood to match patients to drugs
Coverage and depth: how many times each base is read. Higher depth gives more confident results
Bioinformatics: assembly, alignment and variant calling are done with computer programmes, so data skills are as important as laboratory skills
Mitochondrial genome: a small circular genome of about 16,500 base pairs inherited from the mother, widely used in ancestry and forensic work
Ancient DNA: sequencing of DNA from old bones and fossils, which earned Svante Paabo the 2022 Nobel Prize in Physiology or Medicine for work on Neanderthal genomes
Variant types: single base changes, small insertions or deletions and large structural changes can all be found by sequencing
Clinical use: a diagnosis from sequencing can end a long search for the cause of the illness of a child, and can guide family planning
Limits: sequencing shows risk, not certainty, and many variants are of unknown significance

Why Does It Matter for the Exam?

Methods: Sanger versus next generation sequencing
Projects: Human Genome Project, GenomeIndia, Earth BioGenome Project
Surveillance: INSACOG and virus genomes
Current affairs link: new genome sequences of Indian crops and animals
Common errors: confusing genome sequencing with gene editing

As an analytical point, cheap sequencing creates a flood of data. India benefits most when sequencing is linked to public health systems, with open science and strong privacy rules.

Why Is This Topic Important?

Methods Sanger and NGS
Projects Indian and global
Uses Health and farming

What Came Next?

The next topic covers DNA sequencing in detail and the use of nucleic acid probes. Next topic: DNA Sequencing and Nucleic Acid Probes.

Key People and Terms

Sequencing Reading the order of bases
NGS Parallel sequencing
Exome Coding regions of genome
Reference genome Standard sequence
INSACOG Indian virus sequencing network
Read length Size of fragment read

Exam Corner

Points to Remember

Sanger method: 1977.
Human genome: 2003.
INSACOG: formed December 2020.
Exome means coding regions.
Four bases: A, T, G, C.

Do Not Confuse With

Sequencing and editing Reading versus changing DNA
Genome and exome All DNA versus coding parts
Short read and long read Cheap and accurate versus long and gap-closing

Memory Hook

Sanger one at a time, NGS millions at once, long reads close the gaps.

Mains Angle

Questions ask about use of sequencing in health and surveillance. These points help.

Health Diagnosis and cancer
Surveillance Pathogens
Issues Privacy and cost

A Question You May Face

An original practice question, not a past paper question.

“Discuss the applications of genome sequencing in health care and disease surveillance and the ethical issues involved.”

How to Answer

Meaning Reading bases.
Uses Diagnosis, surveillance.
Issues Privacy, equity.
Way Rules and access.

GS Relevance

Prelims: sequencing methods, projects, applications, Indian initiatives. GS Paper 3: science and technology, biotechnology, health, agriculture.

Frequently Asked Questions

What is genome sequencing?

Genome sequencing is the method of determining the exact order of the four DNA bases, adenine, thymine, guanine and cytosine, across the entire DNA of an organism. It gives a complete genetic map that scientists use to find genes, variants linked to disease, and differences between individuals or species.

How is next generation sequencing different from Sanger sequencing?

Sanger sequencing reads one DNA fragment at a time with high accuracy and was used in the Human Genome Project. Next generation sequencing reads millions of fragments together, making it much faster and cheaper, though the short reads need computer assembly. Third generation methods read very long fragments.

What is INSACOG?

INSACOG is the Indian SARS-CoV-2 Genomics Consortium, a network of laboratories set up in December 2020 to sequence the virus that causes COVID-19 across India. It tracked variants and their spread, and the approach has served as a model for genomic surveillance of other pathogens.

What is the GenomeIndia project?

GenomeIndia is a project of the Department of Biotechnology that sequenced the genomes of 10,000 people from diverse Indian population groups to build a reference database. The data are stored at the Indian Biological Data Centre and are meant for research on disease risks and precision medicine.

What is the difference between whole genome and exome sequencing?

Whole genome sequencing reads all the DNA of a person, including the regions between genes. Exome sequencing reads only the protein coding regions, which make up a small part of the genome but contain many disease causing changes. Exome sequencing is cheaper, so it is often used for diagnosis.

PYQ Practice — Statement Analysis

1 The Human Genome Project was completed in 2003.

True

Using Sanger based methods.

2 Exome sequencing reads the entire genome including non-coding regions.

False

It reads only coding regions.

3 INSACOG was set up to sequence the SARS-CoV-2 virus.