Genomics- A Brief Overview.
Do you know that over 7 million people die from cancer and over 11 million new cases are diagnosed worldwide every year? Shocking right? You’d think that with treatments such as chemotherapy, radiotherapy, and surgery, the death rates from cancer should be decreasing. Rather, it seems to be skyrocketing every year. What if I told you that with one technology, you could cure cancer and therefore potentially decreasing the staggering death rates of cancer. This technology is Genomics.
Seems surreal right? If this technology already exists, why aren’t we utilizing it yet? Firstly, what is Genomics?
Genomics
Genomics is the study of analyzing and mapping the genome, that is all the genetic information contained in the DNA of an organism. Knowing the sequence of the billions of letters that make up your genome is the goal of genome sequencing. Our DNA plays an important role in determining our appearance, traits, and most importantly, our health.
A Genome is all the genes plus some extras in an organism. Genes are made up of DNA. Deoxyribose Nucleic Acid (DNA) is made up of a double helix and sequence of molecules that are called Adenine (A), Thymine(T), Cytosine(C), and Guanine (G) that form base pairs — creating a sort of code for human life. A binds to T and G to C. The DNA sequence is recorded by RNA molecules, which transport information around the cell. RNA helps make proteins from corresponding amino acids to the DNA sequence. These fold into proteins which are used to perform functions around the body.
Why is Genomics important?
Genomics can revolutionize healthcare by helping to cure genetic diseases such as sickle cell anemia, cancer, and Huntington's disease. Genetic diseases are caused by mutations in the sequence of genetic information. Previously, I mentioned that our DNA is a code for human life. Well, mutations are when the DNA sequence is not the way it’s coded and has changes in it. Mutations in the sequence of genetic information can cause alterations in the body like the wrong proteins being created and abnormal cell activity. Some mutations or variations are not harmful, like mutations changing brown eyes to blue eyes. However, some mutations can cause genetic diseases as mentioned above.
Examples of such mutations are:
Deletion- A deletion changes the number of DNA bases by removing a piece of DNA. Small deletions may remove one or a few base pairs within a gene, while larger deletions can remove an entire gene or several neighboring genes. The deleted DNA may alter the function of the resulting protein(s).
Insertion -An insertion changes the number of DNA bases in a gene by adding a piece of DNA. As a result, the protein made by the gene may not function properly.
Duplication- A duplication consists of a piece of DNA that is abnormally copied one or more times. This type of mutation may alter the function of the resulting protein.
Repeat Expansion — A repeat is a mutation that increases the number of times that the short DNA sequence is repeated. This type of mutation can cause the resulting protein to function improperly.
Frameshift Mutation — A frameshift mutation shifts the grouping of these bases and changes the code for amino acids. The resulting protein is usually nonfunctional. Insertions, deletions, and duplications can all be frameshift mutations.
Missense Mutation -This type of mutation is a change in one DNA base pair that results in the substitution of one amino acid for another in the protein made by a gene.
Nonsense Mutation-A nonsense mutation is also a change in one DNA base pair. Instead of substituting one amino acid for another, however, the altered DNA sequence prematurely signals the cell to stop building a protein. This type of mutation results in a shortened protein that may function improperly or not at all. With sequencing, mutations can be identified. Well, how do we go about sequencing?
How the genome is sequenced.
Throughout history, scientists have searched for the most effective and accurate method/process of sequencing the genome. Examples of previously used methods are Sanger sequencing, Applied Biosystems, and Genome Analyzer. Next-Generation Sequencing is currently the best and widely used technology to accurately sequence large portions of DNA.
Next-Generation Sequencing (NGS) perform sequencing of millions of small DNA fragments. There are 4 steps to DNA sequencing regarding this commonly used version of DNA sequencing.
These steps include:
Library Preparation- This step is where the long string of DNA is broken down into millions of fragments. Specialized adaptors are glued to the 2 sides of the DNA fragments. The DNA fragments are led to Polymerase Chain Reaction (PCR) or amplification. They are then gel purified.
Cluster Preparation- This is where a DNA library is placed into a flow cell. The DNA fragments attach to the top of the flow cell. Every DNA fragment goes through a Bridge Amplification Cycle.
Sequencing- Nucleotides are added to the flow cell and single bases are identified as they combine into each DNA strand. The nucleotides in this step are very special because they are fluorescently labeled. This helps the scientists identify each cluster and each cluster can be visualized due to fluorescent lights.
Data Analysis- Once the scientists are able to visualize the various DNA sequences, they are sequentially aligned using a reference DNA sequence also known as a reference genome. (A reference genome is a man-made DNA sequence that expresses a specific species’ set of genes. This phase is done using an advanced bioinformatics program. This program helps to distinguish any variances between the aligned reads and the “Reference” DNA sequence.)
Through this genetic mutations could be identified. Next-Generation Sequencing has become a popular process that can aid in various scientific fields. Millions of DNA sequences can be quickly processed at astonishingly low rates. So after sequencing, what could possibly come next? This is when the tool called gene editing comes in.
What is Gene editing?
Gene editing is a method of making specific alterations to DNA and modifying gene functions. CRISPR-cas9 is a gene-editing technology that allows for a faster and cheaper way of editing. CRISPR-cas9 which is short for Clustered Regularly Interspaced Palindromic Repeat and associated 9 is a naturally occurring gene editing process that occurs in bacteria. It works by cutting the DNA of the viral DNA and disables the virus. Scientists adopted the same method but in the laboratory.
CRISPR-cas9 allows scientists to make alterations to DNA in the cell. DNA is cut and after the DNA is cut, they could either add or insert genomic pieces. That could therefore cure genetic diseases. CRISPR enables cells to be protected from recorded viruses not only in one generation but over many generations as well. So if a mutation in your gene is edited, it will not be passed on to the next generation.
Why Gene editing is the most effective?
I’m very sure we’ve all heard someone say that a specific disease is prone to their family. For example, if their grandmother had cancer and so did their mum, there is a possibility that they could inherit it too. This is due to the fact that genetic mutations can be hereditary. Cancer is caused by changes (mutations) to the DNA within cells. The DNA inside a cell is packaged into a large number of individual genes, each of which contains a set of instructions telling the cell what functions to perform, as well as how to grow and divide.
Treatments for cancer include chemotherapy, radiotherapy, and surgery. However, these treatments have side effects, some devastating and some making you sicker. One common defect is that all these treatments cannot prevent the mutation in your genome that causes cancer from being passed on to the next generation. So why not target the root of the problem and instead edit the cancer-causing mutation.
Gene editing isn’t limited to humans. In fact, Genetically Modified Foods (GMOs) are also edited. And this an ongoing debate. Well, you’ve probably eaten a GMO food before. Well, except if you don’t like bananas. The banana that you eat had been genetically modified a long time ago.
Cost Of Gene Sequencing.
The first human genome was sequenced in 2003 and clearly, it was no easy task. It took two decades and required the effort of hundreds of scientists across dozens of countries and it cost over 3 billion dollars. The cost of sequencing has dramatically decreased from $100M to around $1000. The cost will decrease even further to $100 and will be less time-consuming. It has become more affordable for anyone to do so due to sequencing being more widely available. This is due to companies such as Illumina and deep genomics. However, editing the mutation in your genome is still not possible right now due to it being very expensive and is not feasible for most people. Also, this arises concerns due to ethical issues.
From personalized healthcare to detecting genetic diseases earlier and even produce more plants to feed our ever-growing population. The possibilities of genomics are endless.
Hey, my name is Sakeenah Ajayi. I am 15 years old and is passionate about biotech. I’ll be deep-diving into my focus on genomics. Can’t wait! In my next article, I’ll be discussing the role that Artificial Intelligence plays in Genomics. Let’s connect through my socials here. Twitter Linkedin Gmail Website
