We know that our identities are shaped by the information stored in our DNA. However, we must learn to read information before completely comprehending it. Like the programs that teach a computer what to do, genes are segments of DNA that work together to form an instruction manual that governs our cells. We were unable to interpret these genetic codes for a long time. The ability to read DNA was made possible in the 1970s by the development of a technique called DNA sequencing. Scientists were able to read, comprehend, and compare genetic information thanks to DNA sequencing, which revolutionized our knowledge of biology.
What is DNA sequencing?
The process of sequencing DNA entails determining the arrangement of the four chemical “bases” that constitute the molecule. The sequencing of a DNA segment allows scientists to determine the sort of genetic information stored within it.
Principle of DNA sequencing:
The following is a general principle of DNA sequencing.
DNA becomes single-stranded after being denatured. The detector receives the signals from the sequence that the sequencer machine reads and sends them to the computer. Each read is transformed into a nucleotide sequence by computer software after the signals have been examined.
How new is DNA sequencing?
Even though the double helix structure of DNA was discovered in 1953, it would take many more years for scientists to be able to examine DNA fragments. The first attempt to sequence the nucleic acid was undertaken in 1964 by Richard Holley and colleagues who sequenced the tRNA. Scientists were able to read the genetic code for the first time in the 1970s when DNA sequencing started.
Two further generations of sequencing have been released in the past fifteen years, beginning with the first generation, Sanger sequencing, in the 1970s. Next Generation Sequencing (NGS), also known as second-generation sequencing, gained popularity in the late 2000s and early 2010s and offered a means for employing short-read technology to sequence a full genome. The majority of the world’s sequencing data is provided by Illumina, which is the primary supplier of this sequencing approach.
A few years later, third-generation, or long-read, sequencing techniques were introduced, resulting in technology that can perfectly sequence a genome and cover annoying repeating DNA portions by sequencing even longer DNA pieces.
DNA Sequencing Methods
DNA sequencing procedures are often divided into two categories: conventional sequencing techniques and high-throughput sequencing approaches. Here is the overview of some DNA sequencing methodologies:
What do improvements in DNA sequencing mean for human health?
Although standard DNA sequencing in doctor’s offices is still a long way off, certain major medical institutions have begun to use it to detect and treat some diseases. In cancer, for example, doctors are increasingly able to use sequence data to establish the type of malignancy a patient has. This enables the clinician to make more informed treatment recommendations. Such comparisons can reveal a lot of information on the role of inheritance in disease susceptibility and response to environmental influences. Furthermore, the ability to sequence the genome more swiftly and economically offers up new avenues for diagnosis and therapy.
Ongoing and prospective large-scale research use DNA sequencing to investigate the genesis of common and complex diseases, such as heart disease and diabetes, as well as inherited diseases that cause physical malformations, developmental delays, and metabolic disorders. Comparing the genome sequences of various animals and creatures, such as chimps and yeast, can shed light on the biology of development and evolution.
Common Types of Sequencing
Numerous sequencing techniques have been devised that compromise comprehension depth for speed and cost:
- Whole-genome sequencing involves sequencing an organism’s whole genome, including both coding and non-coding sections. The sequenced genome is then compared with a reference genome for that species.
- Whole-exome sequencing focuses on the protein-coding regions of the genome, known as exons. Exome sequencing and analysis is faster than whole genome sequencing, but it cannot detect mutations in non-coding DNA.
- RNA sequencing measures gene expression, providing insights on cell function. It accomplishes this by sequencing the complementary DNA (cDNA) of each mRNA molecule in tissues or single cells.
- SNP genotyping identifies characteristics associated with single nucleotide polymorphisms (called “snips”) in certain genetic loci. Businesses such as 23andMe employ this technology to provide information on genetic heritage and disease risk. Although this technology is faster and less expensive than whole-genome sequencing, it produces far less data.
The steps of DNA sequencing
1. Sample preparation
DNA is extracted from a sample, such as a cheek swab or a forensic specimen. To achieve sufficient amounts, certain sections are frequently replicated numerous times (also known as amplification).
2. Reading the sequence
Several methods can be used to identify the order of each base.
3. Compared to other sequences
To determine whether there are any differences, the new sequence is compared to a reference sequence (such as the Human Genome Project’s).
Bioinformatics’ Software Tools for Data Analysis
Base-calling and/or polymorphism identification, de novo, genome browsing and annotation, and sequence read alignment are the four broad categories into which the software features for next-generation sequencing data analysis can be divided. For every category, a number of software packages have been created. For example, there are many bioinformatics software tools available for short-read sequencing, which is used for de novo genome and transcriptome assembly. There have also been recent publications on the application of de novo genome assembly software approaches. New short-read sequencing classifications and software tools are continually being developed for commercial application all around the world, particularly in the United States, Europe, and Australia. Numerous for-profit sequencing companies, including Roche, Illumina, SOLiD, and others, offer software services to clients for various types of DNA and RNA sequencing analysis. It is important to remember that alignment software like BLAST or BLAT was built primarily for long reads produced by traditional first-generation sequencing, and hence it is not ideal for short-read sequencing analysis of next-generation sequencing.
Cost of DNA Sequencing
According to the most recent data given by the National Human Genome Research Institute of the United States National Institutes of Health, the cost per genome and raw megabase of DNA sequence reduced considerably between July 2001 and July 2013. First-generation sequencing techniques were used from 2001 to 2007, followed by the use of second-generation NGS platforms from 2008 to the present in 2013.
Between 2001 and 2007, the price per raw megabase of DNA sequence dropped from more than $8,000 to $700, and then to less than $0.1 by 2013. The cost of a genome DNA sequence likewise rose, from $100,000 in 2001 to $10,000,000 in 2007, and then to around $8,000 in 2013.
Refrences
Shendure, J., Balasubramanian, S., Church, G. M., Gilbert, W., Rogers, J., Schloss, J. A., & Waterston, R. H. (2017). DNA sequencing at 40: past, present and future. Nature, 550(7676), 345-353.
Mardis, E. R. (2017). DNA sequencing technologies: 2006–2016. Nature protocols, 12(2), 213-218.
Shendure, J., & Aiden, E. L. (2012). The expanding scope of DNA sequencing. Nature biotechnology, 30(11), 1084-1094.
Van Dijk, E. L., Jaszczyszyn, Y., Naquin, D., & Thermes, C. (2018). The third revolution in sequencing technology. Trends in Genetics, 34(9), 666-681.
Slatko, B. E., Gardner, A. F., & Ausubel, F. M. (2018). Overview of next‐generation sequencing technologies. Current protocols in molecular biology, 122(1), e59.
