What is a Genome?
- A genome is an organism’s complete set of DNA (deoxyribonucleic acid), 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.
What is Genome sequencing?
- Genome sequencing is figuring out the order of DNA nucleotides, or bases, in a genome—the order of adenine (A), cytosine (C), guanine (G), and thymine (T) that make up an organism’s DNA.
- The nucleotide sequence is the most fundamental level of knowledge of a gene or genome.
- No understanding of genetic function or evolution could be complete without obtaining this information.
First-Generation Sequencing Technology
- The so-called first-generation sequencing technologies, which emerged in the 1970s, included the Maxam-Gilbert method and the Sanger method (or dideoxy method).
- The Sanger method became the more commonly employed of the two approaches.
Next-Generation Sequencing Technology
- Next-generation (massively parallel, or second-generation) sequencing technologies have largely supplanted first-generation technologies.
- These newer approaches enable many DNA fragments (sometimes on the order of millions of fragments) to be sequenced at one time and are more cost-efficient and much faster than first-generation technologies.
- The utility of next-generation technologies was improved significantly by advances in bioinformatics that allowed for increased data storage and facilitated the analysis and manipulation of very large data sets, often in the gigabase range (1 gigabase = 1,000,000,000 base pairs of DNA).
Why in News?
- To speed up testing as well as improve the accuracy of testing for coronavirus (COVID-19) positive cases, the Council of Scientific and Industrial Research (CSIR) is working on developing “mega labs.”
- These labs will have large machines called Next Generation Sequencing machines (NGS).
News in Detail
- The NGS machines, which are also used for sequencing human genomes, will be repurposed to sequence 1,500-3,000 viral genomes at a go for detecting the SARS-CoV-2 novel coronavirus.
- The CSIR has partnered with the U.S.-based Illumina, a company that specialises in the manufacture of NGS machines.
- Five such sequencers, costing ₹4 crore each, are currently available in India.
Advantage over RT-PCR
- Used optimally and with appropriate modifications, these genome sequencing machines can substantially detect the possible presence of the virus even in several instances where the traditional RT-PCR (reverse transcription polymerase chain reaction) tests miss out.
About real-time PCR
- This is primarily because the RT-PCR test identifies the SARS-CoV-2 virus by exploring only specific sections of the virus whereas the genome method can read a bigger chunk of virus genome.
- Therefore genome method provides more certainty that the virus in question is indeed the particular coronavirus of interest.
- It can also trace the evolutionary history of the virus and track mutations more reliably.
- Unlike the RT-PCR that needs primers and probes — a key hurdle in operationalising such tests on a mass scale early on in the pandemic — the NGS does not need primers and probes, and only needs custom reagents.