Introduction

Genomics is the study of these genes and how mutations (changes) in the DNA can change the proteins produced or the way they are made; this form of precision medicine and research into it can lead to life-changing, personalised treatment.¹ Although many people may associate genomics with only genetic counsellors or geneticists in a lab, it is beneficial for a medical/health professional to understand genetics well. This article will dive more into genomics and look at specific examples. 

The development of gene sequencing technologies

Let us look at a quick timeline of how genomics has evolved into the biotech giant.² In the 1950s, the basic double-helix structure of DNA was discovered. It was time-consuming (over 10 years!) to sequence the variety of genomes and to create the final draft of the human genome using Sanger sequencing. Sanger sequencing is a gel-based method combining DNA polymerase (building blocks) with a mixture of standard and chain-terminating nucleotides (ddNTPs-modified versions).

With this combination DNA synthesis abruptly stops during the polymerase chain reaction (PCR). PCR- is a widely used laboratory technique in molecular biology that amplifies a specific segment of DNA, creating millions of copies of a particular sequence. This method involves repeated cycles of heating and cooling the DNA to denature (separate) the strands, annealing primers to target specific sequences, and extending the primers with a DNA polymerase enzyme to generate new strands.

To sequence DNA, four reactions occur, each with a different type of modified nucleotide that prevents the chain. Then, gel electrophoresis allows the sequence to be read base by base. This was ground-breaking at the time as it allowed sequencing of 500-1,000bp fragments.

Variations of this method were developed. In 2003, this technology led to the completion of the Human Genome Project. The human genome project successfully identified, stored, and made available to the public, the sequences of the human genome, which allows researchers to have a large database of genetic information. However, they were not economical, especially large-scale projects. So the main aim was to find a more cost-effective method rather than relying on capillary electrophoresis. 

Second-generation methods include Emulsion PCR, Bridge amplification, and Ion Torrent. Emulsion PCR paved the way for the first few next-generation sequencing (NGS) technologies. Emulsion PCR is used in pyrosequencing. It may sound daunting but essentially during pyrophosphate synthesis luminescence is produced, this can be used to read sequences as each nucleotide passes the system.

Also, this method uses template DNA—a strand of DNA that acts as a guide in the production of new DNA or RNA molecules—fixed in a solid phase. Additional developments in this method included adding beads to which DNA can attach, allowing better amplification. 

Pyrosequencing technologies were licensed to 454 Life Sciences, later bought by Roche. This allowed it to evolve into the first major successful commercial NGS technology. This is because huge varieties of DNA molecules were attached to beads and underwent a water-in-oil emulsion PCR. This type of pyrosequencing results in smaller bead-linked enzymes and dNTPs washed over the plate. This is much more effective than previous methods by increasing the yield. 

Continuing from the success of 454, numerous parallel sequencing techniques emerged. One of the most notable is the Solexa method of sequencing (later acquired by Illumina). In this method, adapter DNA molecules (DNA sequences engineered or modified for genomic analyses) are passed over a surface of complementary oligonucleotides bound to a flow cell.

This is called bridge amplification and allows the formation of dense clusters of amplified fragments so a fluorescent signal can be detected every time a single dNTP is added sequentially as sequencing-by-synthesis proceeds. As the process continues, the number of clusters being read increases. Illumina instruments was the first to make this parallel sequencing technology commercially available.

Ion Torrent measures the pH difference during polymerisation and SOLiD (Sequencing by Oligonucleotide Ligation and Detection) which involves, as the name suggests, sequencing by ligation rather than synthesis. NGS platforms like Ion Torrent and SOLiD are the dominant type of sequencing technology used today since they enable large-scale sequencing while remaining cost-effective. That said, the reading length of these NGS platforms is limited, generally producing reads of ~50-500 bp in length.

Now onto the third-generation sequencing technology! Examples include SMRT and Nanopore. Single-molecule real-time (SMRT) platform from Pacific Bioscience is one of the most commonly used 3rd gen techs. This utilises miniaturised wells, called zero-mode waveguides, in which a single polymerase incorporates labelled nucleotides and light emission is measured in real-time. Unlike the previous methods, PacBio machines can produce incredibly long reads, up to and sometimes over 10 kb in length. These reads are especially valuable for de novo genome assemblies (building the sequence of an organism's genome from scratch).

Nanopore scientists have shown that single-stranded RNA or DNA could be driven across a lipid bilayer through large α-haemolysin ion channels via electrophoresis. This enables direct, real-time analysis of long DNA or RNA fragments. It monitors variations to an electrical current as nucleic acids are passed through a protein nanopore.

This is provided by Oxford Nanopore Technologies, the first company offering nanopore sequencers. With further developments, nanopore sequencers could transform the composition of the data produced, as well as where, when and who can produce it. 

Bringing it back into the clinic

Now all this information may have you wondering—but how does this complex bioinformatics affect me as a clinician? It is because genetics underpins everything. One of the categories under the umbrella of genomics is pharmacogenomics; this studies how variations in genes can affect how a person absorbs a drug.³

For instance, as a clinician prescribing antibiotics, you might question why the same antibiotics are not as effective for your current patient as they were for a previous one, even though all other factors remain the same. 

Although this was briefly touched upon, genomics in healthcare can lead to tailored treatments. Imagine a world where everyone’s genes could be easily sequenced and you could predict all the side effects you could have if you were to take a certain medication. Likewise, in preventative medication, if you were told your inherited genes make you highly likely to develop diabetes, you could incorporate lifestyle changes to prevent that health outcome. 

Also, you may encounter patients with complex genetic conditions who require education. ‘’Rare’’ genetic conditions, for example, an uncommon form of cancer, affects 1 in 17 of the population, making it more than likely that in your career as a health or medical professional, you will encounter them.⁴ Educating patients allows them to feel more empowered, to understand the impact certain lifestyles can have and the importance of screening. 

Why can’t this DNA-fuelled dream be a reality?

A huge barrier is the lack of education clinicians in primary care have regarding genomics. A study showed only 20% of physicians had moderate to extensive education on genomics so 80% of the others would not feel confident interpreting genetic results.⁵ Another factor is cost. In contrast to the early days of genome sequencing and gene testing when it would be a mind-blowing number, now it is more affordable and will continue to become so.‘’

On average one stroke costs the NHS approximately £30,000 over 5 years’’ For 25% of patients clopidogrel (antiplatelet medication that helps to prevent strokes) does not have the intended pharmacological effect.⁶ Knowing which of the patients this will be through genetic analysis could allow them to begin alternative, more effective treatment without trial and error. Surely the initial expense of research and equipment is more than worth it, considering the many lives which will be saved? 

Summary

The world of genomics gives a lot of hope for new treatments for a variety of conditions, as we saw with stroke. The technology used in genome sequencing is rapidly evolving. Hopefully, future generations of clinicians will be taught genomics to a more comprehensive level allowing them to understand the implications of their treatment due to the patient’s genes.