Genome Sequencing: How? What? Why?

Genome Sequencing
Genome Sequencing

What is Genome Sequencing?

Human body is made up of approximately 37 trillion cells that are basic units of body. DNA or Deoxyribonucleic acid, a molecule that contains our specific genetic code is present in all the cells. This DNA contains small sections called Genes which contain instructions for a molecule or commonly known as carrier or traits. A genome can be defined as a sequence of genes in a cell which contain hereditary information of a person. Genome can be called as the genetic material of an organism consisting of genes (coding DNA), non-coding DNA and also mitochondrial DNA.

Genomics is the study of genome. Each human cell consists of 23 pairs of chromosomes (DNA molecule) which further contains billions of base pairs. The arrangement of these base pairs and their lengths constitute genes which are responsible for functioning of the body. Genome sequencing is the process of determining exact order of the base pairs that is, the complete DNA sequence of an organism. Genome sequencing will help discover the functioning of genes.

Inception of Genome Sequencing

The seeds of genome sequencing were laid in 1865 when Gregor Mendel discovered Laws of Inheritance (Law of Segregation, Law of Independent Assortment, Law of Dominance). Later in 1953, James Watson, Francis Crick, Maurice Wilkins and Rosalind Franklin discovered the double helical structure of DNA. This was followed by Robert Holley’s work on tRNA sequencing which was completed during 1960’s. Following this in 1970’s, Federick Sanger developed a DNA Sequencing technique and finally in 1990’s Human Genome Project was launched. Further in the timeline, in 1995 the first bacterium genome sequencing was achieved and in 1996, 1st cloned animal that is a sheep was born. Subsequently genome sequencing was successfully for nematode worm and fruit fly. The result of Human Genome Project of 1990’s was the first draft of human genome sequence of 2001.

The Human Genome project was completed in 2003. This project completion was a turning point and it opened up new perspectives related to human genome and one which received maximum focus was the information about linkages between diseases and unique genetic makeup of organisms. This linkage provided a breakthrough because it had established that around 10,000 diseases like cancer, cystic fibrosis, thalassemia, etc. were a result of gene malfunctioning and genome sequencing was the key to understand the deal with the issue.

In this backdrop advances were made to completely understand human genome. This led to the discovery of new gene-editing techniques like CRISPR. The major achievement in this field was of Council of Scientific and Industrial Research (CSIR), which in 2009 sequenced the 1st Indian genome. The whole genome mapping was necessarily because in prior attempts exome (occupies about 1% of actual gene) maps were being used but later it was established that the non-exome portions of gene are also responsible for its functioning and simple exome maps were incapable to know which genes of DNA were mutated. With advancement in the field, tech giants like Google have also made their contributions to the field, for example in the year 2017, Google announced a new tool “Deep Variant” which would make use of Artificial Intelligence to further develop the understanding of genome.

CSIR, launched a project called “IndiGen” in order to decipher the extent of gene variation in India and to dive into the depths of genomics. As a part of this project an exercise of whole-genome sequencing of 1008 Indians was conducted and successfully concluded within a 6 months span which concluded in 2019. The project aims to complete sequencing of more than 10000 Indian genomes in next three years.

The project will prove to be essential in deciphering why certain genes linked to certain diseases as already has been discovered, do not always cause the disease. Under IndiGen candidates will get a card and access to an application through which they can access information on their genes which will help to correlate gene variations to diseases. This correlation will help in deciding which medicines would not respond efficiently in treating individual’s disease because certain gene variation decreases the effect of certain medicines on individuals. The project was conducted jointly by Centre for Cellular and Molecular Biology, Institute of Genomics and Integrative Biology of CSIR. In order to test different genomes, the project had selected representatives from all states, different ethnicities, different age, etc.

Benefits of Genome-Sequencing

Genes form the basis of human body cells and details about them will have a fair share of advantages. It will increase the spectrum of public knowledge with respect to information stored in genes. It will help to early diagnosis and treatment procedures for mutated or altered genes which do not function properly and cause diseases for example- cancer, rare genetic diseases, etc. It will also help to develop precise and targeted medicine. Genomics informed drugs/medicines for curing only specific genes will be a great improvement over present generalized approach and this will also reduce cost of treatment significantly.

Genome sequencing with a large base will help to compare genomes of different cases thereby can be used to single out genetic risk factors that will save many more individuals. At present around 7 crore Indians suffer from rare genetic disease. This huge population creates immense economic and medical burden that can be avoided by information on genome. Besides, sequencing will help uncover detailed basic biological functions of genes which are yet to be discovered. This will elevate India’s position in global medical and scientific field.

Sequencing will also help in editing genes to prepare personalized medicines, diet, fitness plan based on genomics of a person hereby helping in achieving a healthier lifestyle. As per USA based company ‘Grand View Research Inc’- ‘ global predictive genetic testing and consumer genomics market was valued at around 2.3 billion dollars in 2015 and expected to double to 4.6 billion dollars by 2025’. This can help Indian economy significantly. Specially, the Indian project has brought down the cost of genome sequencing and is expected to further decrease the cost. Genome sequencing can also be used to get details about a person’s ancestry and will decrease India’s dependence on other nations like USA, UK for gene data.

Problems in Genome Sequencing and Solutions

India’s gene database compared to its vast and diverse population is small and it needs to be increased by collecting more data from people and interpreting them. India has small number of hospitals and a lack of manpower required for improving research activities in the area. This issue needs to be addressed at central level and government must develop existing academic institutions, healthcare, IT industry, biotech industry. ICMR, apex Indian body for regulating clinical research has set no regulatory framework which results in exploitation of people by companies who sell underdeveloped genome data and also questions of data privacy and security are raised due to lack of regulations. There is need of proper governance and an efficient regulatory framework in order to protect the highly sensitive and personal data and to ensure proper development of the field.

Gene editing has two major issues which need to be eradicated – first is ‘off-target mutations’ where CRISPR misses target gene and attaches itself to another sequence thereby creating a different result then was intended. Second is ‘Mosaicism’- CRISPR attaches to target gene but alters only some DNA thereby creating a genetically different property which would defeat the purpose of treatment. There is a lack of awareness about Genome sequencing and government should address this issue by disseminating knowledge to general public. Government must also develop infrastructure in order to ensure proper data analysis government must form independent consultation and advisory groups and encourage feedback from public.

Genome Sequencing: Global Scenario

Globally, India has entered the elite club of countries using genome sequencing. A number of countries have adopted different means to develop sequencing. For example- Switzerland based CRISPR therapeutics have launched human trial experiment CRISPR-Cas9 therapy to eliminate b-thalassemia. In China, an oncologist in 2016 edited human cells to treat lung cancer. China also focused to contain spread of esophageal cancer by editing DNA in WBCs. Singapore adopted ‘Genome Asia Look’ initiative aimed to achieve a sequence of 1 lakh Asian genomes. Further USA and China at present are in process of completing genome mapping of over a million people whereas UK aims to compete mapping of 1 lakh people. Also, the Ashkenazi Jews have successfully treated Tay-Sachs disease by means of genome sequencing. Lastly, India as discussed has successfully completed 1st step of ‘IndiGen’ and now Dr Lal Path Labs and Lifecell etc. have started partnership with IndiGen. India is trying to significantly increase base of gene data. Also, India has taken few steps to address privacy issue by means of using well protected supercomputers for data storage, anonymous IndiGen card in order to avoid data compromise in case of card loss.

Conclusion

Genome sequencing is a game changer and will usher in a new era of development. India has huge potential in this area and its IndiGen project is a welcome step but its expenses needs to be increased exponentially. The use of genome sequencing for early diagnosis, low cost treatment etc. will be crucial for overall development of medical field. India can adopt techniques from other nations and modify them to suit its purpose. However, safety and privacy of data is of utmost importance. India’s diverse population will be beneficial to create gene data pool of a vast spectrum of gene variations. India should pick up pace in order to bring about genome revolution.

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