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Decoding Life’s Blueprint: An Introduction to Genomics

Opemipo Oduntan
14 min readSep 25, 2023

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If you’ve heard of DNA editing tools like CRISPR-Cas9, you’re likely familiar with their potential to revolutionize medicine. This technique is widely adopted globally, applied in various fields, from genetically modifying crops to researching cancer and HIV. Gene editing is a prominent buzzword in hackathons and healthtech, often used without a full grasp of its complexity. Hackathon judges love it, investors love it, and scientists and conspiracy theorists don’t love it.

Well, that isn’t entirely true, but on a general note, it’s sparked a lot of controvercial discussions surrounding what can or cannot be done to our genetics. While the ethics surrounding gene editing aren’t the focus of this article, the way in which gene editing is conducted and how our entire being revolves around pretty simple biochemistry is truly fascinating and something that makes for good discussion and thoughts in spite of the grey area surrounding its ethics.

Another thing you’ve likely heard of is the concept of sequencing. Sequencing, in it’s simplest and most basic form, is just the act of taking a sequence of any sort of thing and and arranging it in a specific order, whether it be in the order it came, or some other order that can be identified as a seperate sequence.

Sequencing in the context of genetics and, more specifically, genomics, is the act of taking the data gathered through experimentation with our DNA (Deoxyribonucleic Acid), and presenting it in a specific order. That sequence usually looks something like this…

Fig. 1 | https://pin.it/2nzkEXr

Though it looks incomprehensible, a collection of C’s, A’s, G’s, and T’s is what makes us who we are physically. In a single gene, which is a small portion of a genome, it would have hundreds if not thousands or more of these different characters to represent its sequence.

Now, by this point, you probably have a number of questions like “what do the different letters represent?” and “how come they’re color coded?”. Or even questions like “what is genomics?” and “how does gene editing work?”. All of these questions, along with many more, will be answered throughout this article.

The following is a highlight of the topics covered in this article:

  • Details on genomics: what genomics is; some key concepts/vocabulary involved.
  • Existing tools/technology that pertain to genomics
  • Details on applications of genomics: how genomics is used; what industries are affected; the future.
  • Ethical, Legal, and Social Implications (ELSI)
  • Current challenges and future trends

Before we dive deep into the topic of gene editing and genomics, first let’s take a moment to understand what exactly genomics is how it connects with our health and existence.

Genetics

The foundation of what makes us unique humans with specific traits is genetics. Genetics is the collection of all the organic molecular compounds stored within each and everyone of our cells telling it what to do and some of the characteristics it should develop.

The simplest example of this is a unicellular pond organism known as an Amoeba. This eukaryotic creature doesn’t exist within our body, but it is an independent creature with its own genetic encoding that tells it how to behave and how to look.

Fig. 2| Animal-like, Fungus-like, and Plant-like Protists | Biology Dictionary

Here are some of the unique characteristics that amoeba’s have:

  1. Pseudopodia: Genetics control flexible, temporary projections for movement.
  2. Phagocytosis: Genes regulate engulfing and digesting food particles.
  3. Asexual Reproduction: Genetics govern asexual cell division.
  4. Heterotrophic Lifestyle: Genes dictate organic matter uptake.
  5. Flexible Shape: Genetics maintain adaptable cell membrane.
  6. Cyst Formation: Genetics enable dormancy in adverse conditions.
  7. Genomic Flexibility: High mutation rates and lateral gene transfer enhance adaptability.
  8. Symbiotic Relationships: Genetics establish partnerships with other microorganisms.
  9. Resilience: Genetics provide resilience to extreme environments.
  10. Phylogenetic Diversity: Genetic diversity leads to varied behaviors and niches.

In all these cases, their genome, as well as how different genes are expressed enables them to develop these characteristics/abilities.

In the case of an amoeba’s ability to engulf and digest food particles (phagocytosis), genes related to phagocytosis in amoebas encode proteins involved in the formation of pseudopodia and the engulfment of particles. For example, the expression of actin genes plays a crucial role in the dynamic cytoskeletal changes required for pseudopod extension.

The field of study that encompasses genetics is called genomics. The text book definition of genomics is: “an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes”.

Genomics allows us to understand why certain organisms have specific traits and through an understanding of genomics, we can also understanding some of the things that factor into different health concerns of the 21st century.

Genome

Modern genomics is centered around this thing called a genome. In its simplest form, a genome is simply a collection of all of what makes up a living creatures DNA instructions. This collection of DNA instructions determines many things about the creature, including what sort of characteristics it will develop, the abilities it will naturally show greater proficiency in, and many more things. This is why so many things are based around our genetic make up because in the human body, every single one of our cells has the entire human genome in its nucleus. This means, all 3.2 billion base pairs of our genetics is wrapped up in a helix structure and stuffed into the nucleus of every single cell in our bodies.

Because of how common DNA is within our body, scientists have commited to sequencing the human genome for the past 30–40 years. In 2003, an organization known as the human genome project achieved what was thought to be impossible several years before their deadline. The achievement of sequencing a human genome up to 90% was a monumental point in human history that many gene editing and genomics scientists take pride in.

A single portion of DNA itself isn’t entirely the instructions our cells follow during development and evolution, but rather, the nitrogenous bases that are attached to the singular nucleotide structures within DNA. In a diagram, a single DNA nucleotide looks something like the following.

Phosphate Group (orange); Sugars (blue); Nitrogenous Base (yellow)

DNA nucleotides are composed of 3 basic structures:

  1. Phosphate Group — made up of one phosphorus and four oxygens, two of which, in some cases, hold a negative charge.
  2. Sugars — made up of a collection of hydrogen and oxygen atoms which connect to the phosphate group through a methelene molecule (CH₂).
  3. Nitrogenous Base — made up of a collection of nitrogen which form aromatic rings that connect to hydrazine (NH₂) which can refer to a number of chemical compounds.

The phosphate group and the sugars form the structural backbone of a DNA sequence and allow for any given portion of our DNA to kind of act like a lego piece. In short, they allow for DNA nucleotides to concatinate and form larger, more complex structures of DNA.

The bases, on the other hand, determine what our actual gene sequences look like through a combination of up to four different chemical nitrogenous bases:

  1. Cytosine (C)
  2. Guanine (G)
  3. Adenine (A)
  4. Thymine (T)

It’s truly fascinating how an abundance of diversity and beauty in nature arises from the simple combination of these four different bases. The hold a few basic properties, the most notable of which includes which base combinations work and which base combinations don’t work.

Cytosine (C) can chemically bond with Guanine (G) in a double helix structure, but cannot bond with Adenine (A) or Thymine (T) without falling apart. The same goes for Guanine, but vise versa. It can connect with Cytosine but can’t connect with Adenine and Thymine.

Cytosine pairs with Guanine but is unstable and can become uracil through spontaneous deamination. If not repaired by DNA enzymes like uracil glycosylase, it can cause a point mutation.

A single strand of this combination of nucleotides with different nitrogenous bases is known as RNA (Ribonucleic Acid). Below is a diagram showing what single strand of RNA looks like

Fig. 4 | Pin on DNA and Genetic Genealogy (pinterest.com)

Figure 5 diagrams the basic nitrogenous base pairs that make up a simple double helix structure formed by pairing two RNA on a spiral to form DNA.

Fig. 5 | https://www.toppr.com/ask/en-ch/question/is-the-correct-pairing-of-nitrogenous-bases/

Now that you have a bit of an idea on what DNA is, what the field of genomics is about, and how your genetics defines you as a person, let’s dive into a quick study of a few tools that exist in this industry.

Genome Sequencing

Earlier, we mentioned the concept of genome sequencing — where you “scan and print” a sequence of genetic information. This concept is absolutely fundamental to genomics and forms the foundation of a lot of research in this area.

A lot of the modern technological solutions revolve around this ability to transcribe the code that makes us humans and turn it into soething that can be easily analysed and compared. An example of one of these technologies is Next-Generation Sequencing (NGS).

Next-Generation Sequencing (NGS)

NGS, also known as high-throughput sequencing, is a revolutionary technology that has transformed the field of genomics. It allows for rapid and cost-effective sequencing of DNA and RNA, enabling researchers to decode the genetic information contained in an organism’s genome. In a sentence or two, it can be explained as follows:

It is a DNA sequencing technology that has largely replaced traditional Sanger sequencing. It can generate massive amounts of DNA sequence data in a single run, making it a cornerstone of modern genomics research and clinical applications.

How Does It Work?

NGS works by breaking the DNA or RNA sample into small fragments, then simultaneously sequencing millions of these fragments in parallel. The process involves the following key steps:

  1. Library Preparation: DNA or RNA is fragmented, and adapters are attached to the ends of these fragments. These adapters contain sequences that are necessary for sequencing machines to recognize and amplify the fragments.
  2. Clonal Amplification: The DNA fragments are amplified or copied using a process called polymerase chain reaction (PCR). This step creates clusters of identical DNA fragments, simplifying the sequencing process.
  3. Sequencing: The DNA clusters are sequenced in a massively parallel fashion. Various NGS platforms (e.g., Illumina, Oxford Nanopore, and Pacific Biosciences) use different methods to determine the sequence of nucleotides in each cluster.
  4. Data Analysis: The generated sequences are then analyzed using specialized bioinformatics software to reconstruct the original DNA sequence.
Fig. 6 | NGS Workflow and Fundamentals of Sample Preparation — Enzo Life Sciences

Inventor and Development:

NGS technology has been a collaborative effort involving multiple scientists and institutions over several decades. Key contributors include Frederick Sanger, who pioneered sequencing techniques, and Craig Venter, who led efforts in genomic sequencing. However, the development of modern NGS platforms, like Illumina’s Solexa sequencing and 454 Life Sciences’ pyrosequencing, emerged in the 2000s.

Why NGS?

NGS offers several advantages over traditional sequencing methods:

  1. Speed: NGS is significantly faster, allowing researchers to sequence entire genomes in a fraction of the time required by older techniques.
  2. Cost-Effective: It’s cost-effective because it can generate a vast amount of data in a single run, reducing the cost per base pair.
  3. High Throughput: NGS can simultaneously sequence multiple DNA fragments, enabling researchers to study complex genetic landscapes comprehensively.
  4. Applications: NGS has transformed various fields, including genomics, personalized medicine, cancer research, microbiology, and evolutionary biology, by enabling large-scale sequencing projects and uncovering genetic variations, mutations, and functional elements within genomes.

Bioinformatics and computational tools are the backbone of modern genomics research, playing a pivotal role in processing and deciphering the wealth of genetic information discovered/gathered by technologies like Next-Generation Sequencing (NGS).

Bioinformatics and Computational Tools

Bioinformatics is an interdisciplinary field that combines biology, computer science, mathematics, and statistics to manage, analyze, and interpret biological data, particularly large datasets generated by various biological experiments and technologies. It focuses on understanding the structure, function, and evolution of biological molecules, such as DNA, RNA, proteins, and their interactions. Bioinformatics plays a crucial role in genomics, proteomics, structural biology, and other branches of life sciences by providing tools and methods to extract meaningful insights from biological information.

Computational tools in the context of bioinformatics refer to software programs, algorithms, and databases specifically designed to address biological questions and analyze biological data. These tools are used to perform various tasks, including:

  1. Sequence Analysis: Tools for DNA, RNA, and protein sequence alignment, identification of motifs, and prediction of secondary structures.
  2. Structural Biology: Software for predicting and visualizing protein structures, simulating molecular dynamics, and analyzing protein-ligand interactions.
  3. Genome Analysis: Tools for genome assembly, gene prediction, annotation, and comparative genomics.
  4. Transcriptomics: Software for analyzing gene expression data from technologies like RNA-Seq, including differential expression analysis and functional enrichment.
  5. Proteomics: Tools for protein identification, quantification, and post-translational modification analysis.
  6. Phylogenetics: Algorithms for reconstructing evolutionary trees and inferring relationships among species based on genetic data.
  7. Metagenomics: Software for studying complex microbial communities and characterizing their taxonomic and functional profiles.
  8. Data Visualization: Programs for visualizing biological data, including genomic tracks, phylogenetic trees, and protein structures.
  9. Biostatistics: Statistical methods and software for hypothesis testing, data normalization, and statistical analysis of biological datasets.
  10. Databases: Repositories of biological data, such as nucleotide sequences, protein structures, and functional annotations, which serve as valuable resources for researchers.
  11. Pathway and Functional Analysis: Tools for exploring biological pathways, functional enrichment analysis, and interpreting the biological significance of gene sets.
  12. Machine Learning and Artificial Intelligence: Techniques for pattern recognition, predictive modeling, and classification in biological data analysis.

These computational tools are essential in handling the vast and complex biological data generated by experiments in genomics, structural biology, proteomics, and other life sciences disciplines. They enable researchers to extract knowledge, make predictions, and gain deeper insights into biological processes, ultimately advancing our understanding of the natural world and its intricacies.

Now with an understanding of some of the basic concepts that form the foundation of genomics as a field, let’s take a look at some of the existing applications of genomics.

Applications

Genomics isn’t an extremely new field in terms of science. However, in terms of its introduction to our modern economy as a commercial science, it’s generally in its elementary stages. Most of the existing gene therapies are heavily monitored and regulated, and it’s difficult to get most modern gene editing solutions through national health organizations like the FDA.

All this doesn’t mean that there aren’t applications outside of human medicine where it’s being applied. Genomics is a transformative field with a wide range of applications that span across various domains, from human health to environmental conservation. These applications showcase the profound impact of genomics on our understanding of life and the world around us.

A. Human Genomics

  • Genomic Medicine and Personalized Healthcare: Genomics has revolutionized the field of medicine by enabling personalized healthcare. It allows clinicians to tailor treatments and therapies to an individual’s genetic makeup, improving efficacy and minimizing side effects. From pharmacogenomics to cancer genomics, it has transformed the way we approach medical care.
  • Disease Genetics and Risk Assessment: Genomic studies have unraveled the genetic basis of numerous diseases. By identifying disease-associated genetic variants, researchers and healthcare providers can assess an individual’s genetic risk for certain conditions, offering opportunities for early intervention and preventive measures.

B. Agriculture and Biotechnology

  • Crop Improvement and Genetic Engineering: In agriculture, genomics plays a pivotal role in crop improvement. By deciphering the genetic code of plants and crops, scientists can develop varieties that are more resistant to pests and diseases, produce higher yields, and possess desirable traits like drought tolerance. Genetic engineering techniques, guided by genomics, enable the creation of genetically modified organisms (GMOs) with improved characteristics.

C. Evolutionary Biology

  • Studying Evolutionary Relationships: Genomics provides a powerful tool for unraveling the intricate web of evolutionary relationships among species. Comparative genomics allows scientists to trace the genetic similarities and differences across diverse organisms, shedding light on the tree of life and the processes that have driven evolution.

D. Environmental Genomics

  • Environmental Monitoring and Conservation: Genomics aids in monitoring and preserving our environment. By studying the genetic diversity of species in various ecosystems, scientists can assess the health of ecosystems and track the impact of environmental changes. Conservation genomics assists in the protection of endangered species and the preservation of biodiversity.

These applications represent just a fraction of the vast potential of genomics in addressing complex challenges and advancing our knowledge of biology and the natural world. As genomics continues to evolve and expand, it promises to shape the future of medicine, agriculture, ecology, and many other fields, ultimately contributing to a better understanding of life on Earth.

Another important thing to consider when discussin the topic of genomics is the issue of ethics and the implications of genetically profiling an individual. This makes for many good questions that need answers. This next section will discuss some of the problems in ethics we haven’t found a solution for.

Ethical, Legal, and Social Implications (ELSI)

The field of genomics presents numerous ethical, legal, and social challenges, which must be addressed to ensure responsible and equitable use of genetic information. Some of the key ELSI issues include:

A. Privacy and Data Security

Genomic data is highly sensitive and can reveal not only an individual’s health risks but also information about their family members. Therefore, protecting privacy and ensuring data security are crucial. Medical record segmentation, encryption, and secure data storage are some approaches to address these concerns.

B. Genetic Discrimination

The fear of genetic discrimination, such as denial of health insurance or employment based on genetic information, has been a significant concern. Legal principles protecting against discrimination and policies on the appropriate use and interpretation of genetic information can help mitigate these risks.

C. Informed Consent

Obtaining informed consent for genetic testing and research is essential, given the potential implications of the results. Research has been conducted to examine issues surrounding informed consent in genetics research, aiming to improve the understanding and protection of individuals participating in such studies.

D. Ethical Considerations in Genetic Research

Genetic research raises various ethical questions, including the responsible collection and use of samples, the involvement of underrepresented minorities, and the appropriate balance between data utility and privacy. Addressing these considerations requires a combination of legal, policy, and technological approaches.

The ongoing efforts to address these ELSI challenges are crucial for the responsible advancement of genomics. By incorporating ethical principles, protecting privacy, and ensuring equitable access to genetic information, we can maximize the benefits of genomics while minimizing potential harms.

Conclusion

One of the major things that will advance the human race as a whole is the introduction of biological evolution alongside our technological aspirations. The future of the eradication of disease, the enhancement of the human race. Maybe before we can solve the worlds biggest problems, we need to become hightened beings that can think beyond our current capabilities. What if we could unlock the genius in the masses, and those that were geniuses were beyond extraordinary? What if we could set the bar of expectations for 10 times as high and empower everyone to collectively cooperate to make the world a better place? This dream might not be so far away, which is all the more the reason to understand genomics and the future of the field. The future is near and the next 10 years are going to be hectic.

References

Genomics
Genetics
Science
Biology

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Opemipo Oduntan

Written by Opemipo Oduntan

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