DNA sequencing has gained wider adoption in recent years. In 2016, Australia began moving genomic sequencing into clinical practice, with national initiatives such as the Australian Genomics Health Alliance helping to establish genomic testing in clinical care. In 2019, Japan introduced national health insurance coverage for comprehensive cancer genomic profiling using next-generation sequencing.
Though sequencing has been increasingly utilized, the concept and value of sequencing can still be difficult to fully understand, especially for non-biologists. This article focuses primarily on the use of DNA sequencing in human health and medicine, explaining the core concept of sequencing, how the technology works, and its major applications, as an introduction to sequencing for non-biologists.
Basic Biology and the Core Concept of Sequencing
At the most fundamental level, all living organisms are made up of cells, and nearly every cell contains DNA. DNA carries the genetic information that provides the instructions for how living organisms function. These instructions are expressed through a process known as the central dogma of molecular biology: DNA is transcribed into RNA, and RNA is then translated into proteins. Proteins carry out most of the essential functions in life. The central dogma provides a framework for understanding how genetic information leads to biological functions.
DNA sequencing is the process of determining the exact sequence of nucleotides in a DNA molecule. DNA is made up of four building blocks called nucleotides: adenine (A), thymine (T), cytosine (C), and guanine (G). The order of these nucleotides provides the instructions for building and maintaining life. DNA sequencing allows us to understand the DNA, located at the start of the central dogma.
How Does DNA Sequencing Work?
There are many DNA sequencing technologies, each with its own characteristics and approach. However, most sequencing workflows follow a similar overall process. DNA sequencing follows these four steps: DNA extraction, library preparation, sequencing, and data analysis.
DNA must first be obtained from the organism. One of the most common sample sources of DNA is blood, as it is relatively non-invasive and easy to process. Once the sample is collected, DNA is separated from other cellular materials, resulting in purified DNA.
DNA will ultimately be sequenced by specialized machines, but purified DNA cannot be read by the machine without some preparation. This process of converting purified DNA into a machine-readable form is called library preparation, named so because DNA molecules are labeled and organized like books in a library. The processed DNA that is ready for sequencing is called a library. Each sequencing company uses different biochemical approaches to read DNA, and thus the library preparation process can vary considerably between sequencing platforms.
After library preparation, the library is loaded onto a specialized chip-like consumable, which is then placed into a sequencing machine. In general, the chip-like consumable is the stage where the biochemical sequencing reaction takes place, while the sequencing machine provides the reagents and detection technology needed to read the DNA sequence.
Sequencing data requires processing to draw meaningful insights. In human applications, the analyses that follow sequencing are called mapping and variant calling. These analyses are analogous to solving a jigsaw puzzle and playing a game of spot the difference.
DNA molecules are very long, but the raw data generated after sequencing is typically fragmented. In mapping, the DNA fragments are aligned to their original positions using a pre-constructed reference genome as a comparison. Variant calling then compares the aligned sequencing data with the reference genome to identify differences, known as variants. Some variants can be deleterious, and the goal of the analysis is typically to find the causative variant for a particular disease condition.
The Application and Value of DNA Sequencing
Two main applications of DNA sequencing in human health are oncology and rare diseases. When thinking about DNA and genetics, various applications such as forensic testing, paternity testing, and ancestry testing may come to mind. However, many of these genetic tests can be performed using simpler and less expensive assays. It is important to keep in mind that not all genetics-related tests require DNA sequencing. DNA sequencing is particularly valuable when a large region of DNA needs to be examined to draw meaningful conclusions, which is precisely the case in oncology and rare disease genomics.
Genetic sequencing approaches can generally be divided into three types: whole-genome sequencing (WGS), whole-exome sequencing (WES), and gene panel sequencing. These approaches become progressively more targeted and less expensive as the genomic region being examined becomes smaller. WGS aims to sequence the entire genome. WES focuses only on the protein-coding regions of the genome, known as the exome, which accounts for approximately 2% of the genome. Gene panel sequencing only examines a selected subset of genes that are known to be relevant to a condition.
Rare diseases are health conditions that affect a small percentage of the population. Precisely because these diseases are rare, there may not be enough prior research to identify the cause of the disease. As such, a wider scan of the genomic region is often needed to identify the causative variant, leading to greater use of WGS and WES approaches.
Cancer is a genetic disease that leads to uncontrolled cell proliferation. Sequencing is widely used in cancer diagnosis and research because different cancers can be driven by different causative variants, and the most effective treatment strategy depends on the specific variants present in a patient’s cancer. Because cancer has been extensively studied and the many genes associated with each cancer type are already known, a gene panel sequencing approach is commonly used.
Conclusion
DNA sequencing is likely to see wider adoption in the coming years. Understanding it now helps you prepare for what comes next. To summarize, DNA sequencing is a technology that allows us to determine the exact sequence of nucleotides in a DNA molecule. Sequencing helps us understand the starting point of the central dogma of biology. Although often buried in jargon and complexity, the core workflow of sequencing is simple: DNA is extracted, prepared, sequenced, and analyzed so that disease-causing variants can be identified. From rare disease diagnosis to cancer treatment, sequencing is becoming an increasingly important tool in human healthcare. I hope you find the information useful.