Genome Sequencing

Context: In a Boost to pathology services in the hill districts, a genome sequencing lab was opened at Srinagar Medical College in Pauri Garhwal district of Uttarakhand.
Probable Question: Q. Discuss the potential applications and benefits of genome sequencing in fields such as medicine, agriculture, and bioengineering.
About Genome Sequencing:
  • Genome sequencing is the process of determining the complete DNA sequence of an organism’s genome.
  • The DNA consists of a double-stranded molecule built up by four bases – Adenine (A), Cytosine (C), Guanine (G) and Thymine (T). 
  • The process of deciphering the order of base pairs, to decode the genetic fingerprint of a human is called genome sequencing.
Genome Sequencing Methods:
  • Clone-by-clone: This method requires the genome to have smaller sections copied and inserted into bacteria. The bacteria then can be grown to produce identical copies, or “clones,” containing approximately 150,000 base pairs of the genome that is desired to be sequenced.
  • Whole-Genome Shotgun: As the name implies, “shotgun” sequencing is a method that breaks DNA into small random pieces for sequencing and reassembly. The pieces of DNA are also cloned into bacteria for growth, isolation and subsequent sequencing.
How does whole Genome Sequencing Work? Scientists conduct whole genome sequencing by following these four main steps:
  • DNA Shearing: Scientists begin by using molecular scissors to cut the DNA, which is composed of millions of bases (A’s, C’s, T’s and G’s), into pieces that are small enough for the sequencing machine to read.
  • DNA Barcoding: Scientists add small pieces of DNA tags, or bar codes, to identify which piece of sheared DNA belongs to which bacteria.
  • DNA Sequencing: The bar-coded DNA from multiple bacteria is combined and put in a DNA sequencer. The sequencer identifies the A’s, C’s, T’s, and G’s, or bases, that make up each bacterial sequence. The sequencer uses the bar code to keep track of which bases belong to which bacteria.
  • Data Analysis: Scientists use computer analysis tools to compare sequences from multiple bacteria and identify differences. The number of differences can tell the scientists how closely related the bacteria are, and how likely it is that they are part of the same outbreak.
Applications of Genome Sequencing:
  • Medical research and Diagnosis: Genome sequencing can be used for genetic testing and diagnosis of hereditary diseases. For Example: The study of SARS-CoV-2 whole genome sequencing (WGS) data has led to many important findings about this pathogen.
  • Drug Development: Genome sequencing can be used to identify new drug targets, optimise drug efficacy, and develop personalised medicine.
  • Agriculture: Genome sequencing can help breed crops and livestock with desirable traits such as higher yield, disease resistance, and nutritional content. For Example: Bt Cotton
  • Forensics: Genome sequencing can be used for forensic analysis, such as identifying victims of crimes and natural disasters.
    • For Example: Forensic scientists can compare DNA found at a crime scene (from blood or hair, for example) to DNA samples taken from suspects.
  • Bioengineering: Genome sequencing can aid in the design and development of synthetic biological systems and biomolecules for various applications.
  • Provides an insight in evolution: Scientists studying the genome sequences of early and modern humans have shown that our ancestors interbred with other hominins like Neanderthals and Denisovans.
Ethical Issues Associated with Genome Sequencing:
  • Privacy: Genome sequencing involves the analysis of an individual’s DNA, which contains sensitive personal information that can reveal information about their ancestry, and other characteristics.
  • Informed consent: There are challenges in obtaining informed consent from individuals, particularly in cases where the sequencing is done as part of a larger research study.
  • Genetic Discrimination: Genetic information obtained through genome sequencing could be used to discriminate against individuals in various contexts, such as employment, insurance, and education.
  • Data Sharing and Access: Genome sequencing generates vast amounts of data which can be used for research purposes. However, striking a balance between sharing genomic data for research purposes and protecting individuals’ privacy poses a serious challenge.
  • Psychological Impact: Genome sequencing can reveal information about an individual’s susceptibility to certain diseases which may cause psychological distress.
  • Stigmatisation: Genetic information can be misused to discriminate against individuals based on their genetic predispositions or susceptibilities to certain diseases.
Efforts towards Genome Sequencing at:
  • International Level:
    • The BabySeq project funded by the U.S. the National Institutes of Health is one of the most comprehensive studies to evaluate sequencing of newborns for routine newborn care.
    • Recently, the U.K. National Health Services recently launched a nationwide programme to sequence 100,000 sick newborns.
    • Human Genome Project: It is a publicly funded international collaborative research project aimed at determining the sequence of chemical base pairs which make up human DNA, & identifying & mapping all of the genes of the human genome.
  • India Level:
    • IndiGen Program
      • Council of Scientific & Industrial Research (CSIR) initiated the IndiGen Program in 2019.
      • Under this program, the whole genome sequencing of 1029 self-declared healthy Indians drawn from across the country has been completed.
      • This has enabled benchmarking the scalability of genome sequencing at population scale in a defined timeline.
    • Genome India Project:
      • Aim: To collect 10,000 genetic samples across India, to build a reference genome.
      • This project is led by the Centre for Brain Research at Bengaluru-based Indian Institute of Science.
      • Utility: It will help to understand fully the type and nature of diseases and traits that comprise the diverse Indian population.
Challenges associated with Genome India Project:
  • Medical Ethics: In a project that aims to create a database of genetic information, it may be misused for gene modification.
  • Data Storage: After collection of the sample, anonymity of the data and questions of its possible use and misuse would need to be addressed.
  • Social Issue: Studying genes and heredity can reinforce harmful stereotypes and lead to a racial interpretation of politics and history.
  • Technical and logistical issues: Collecting and analysing large amounts of genetic data can be technically challenging and requires advanced laboratory facilities and expertise.
  • Cost: Genome sequencing is an expensive process, and the project requires significant funding to collect and analyse genetic data from a large number of individuals.
Way Forward:
  • Trained Manpower: Increasing the number of clinicians skilled in gene data interpretation and expanding the availability of labs for genome sequencing are crucial steps in the direction to boost research.
  • Security of Data: To ensure the security and integrity of genomic data, it is crucial to minimise the risk of data breaches and maintain public confidence in organisations responsible for collecting, storing, and utilising such data.
  • Policy Formulation: To ensure the responsible use of genomic information, it is imperative to have a comprehensive and effective policy in place that prioritises the privacy protection of research subjects.
  • Stakeholder Involvement: It is essential to establish a transparent framework involving stakeholders that clearly defines the purpose of collecting genomic data and specifies the duration for which it will be stored in the database.
Additional Information: About Genome:
  • A genome is defined as an organism’s complete set of Deoxyribose Nucleic Acid (DNA), including all of its genes.
  • Each genome contains all of the information needed to build and maintain that organism.
  • In humans, a copy of the entire genome — more than 3 billion DNA base pairs — is contained in all cells that have a nucleus.

Image Source: India Mart

Indian SARS-CoV-2 Genomics Consortium (INSACOG):
  • INSACOG is a network of 10 laboratories established in 2020.
  • Aim: To continuously monitor the genomic changes of SARS-CoV-2 in India.
  • Application: The knowledge generated through INSACOG will assist in developing diagnostics & potential therapeutics & vaccines in the future.
 News Source: The Hindu
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