Genetics and Your Genome
Genetics, the scientific study of DNA has revealed important insights about processes in the human body, how it becomes susceptible to diseases as well as how it responds to medications when suffering from a disease. To recall, genes which are the basic physical and functional unit of heredity are made up of DNAs (deoxyribonucleic acid). DNA plays the major role in passing the characteristics of parents to the offspring when it starts to develop during the early stage of reproduction. DNA is made of two pairs of strands that are twisted together. Each strand is made of four chemical units, called nucleotide bases namely adenine (A), thymine (T), guanine (G) and cytosine (C). A specifically pair with a T (adenine-thymine pair) while C always pairs with a G (cytosine-guanine pair). The complete set of DNAs in an organism is called a genome. The whole human genome is estimated to have more than 3 billion bases consisting of about 30,000 genes.
How Do We Study the Genome?
The genome is carefully studied to understand the complexity and try to explain differences and similarities among individuals. This can further be a basis to group patients with genetic similarities to a common drug treatment that will benefit them the most with less side effects. In the study of melanoma, we are using genomics to further understand this disease. Different genomic tools are used to gather as many information as we can get from the DNA samples from the patients. How the genomic information in a tumour differ from that of a normal cell may help us understand how it developed and potentially how it might be treated. Here are some forms of data that are useful in understanding melanoma and other diseases:
- Transcriptomic Data – This information tells us the relative expression or concentration of genes extracted from biological samples from the patients. Higher concentration of a gene may impact processes in the human body or may indicate that an unusual process is happening in the body. For example, lack of expression of the gene called CDKN2A (Cyclin Dependent Kinase Inhibitor 2A) may decrease our body’s ability to protect itself from growth of cancer cells.
- Copy Number Data – This tells us the estimated copy of different parts or regions in the genome of the patient. Humans have 23 pairs of chromosomes having two copies of each except for sex chromosomes where males have one copy for each X and Y and females have 2 copies of X chromosome and no copy of Y. Deviating from the expected copy (deletion or amplification) of some regions in the genome, termed as copy number variation (CNV), may or may have no effect on one’s health. An example of harmful CNV is the deletion of CDKN2A located in the chromosome 9 (9p21.3). This is the commonest form of deletion in both primary and metastatic melanoma and leads to lack of expression of this gene.
- Mutation Data – This tells us whether or not a change in the DNA sequence has occurred in any part of region of the genome of a patient. Common mutation observed in melanoma are NRAS, BRAF, and NF1 mutations. Medicine has been developed to target some of these mutations to enhance the treatment potential.
- Methylation Data – Methylation is a process that can regulate the activity of a DNA segment without changing the sequence. This has the ability to switch on/off a gene. It may explain lack or excessive expression of a gene even if a normal copy number is observed.
Application of advance technology paves the way to collection of more information from the genome. This is very promising towards better understanding of melanoma and other diseases. More and more important information about the genome are being discovered as we strive to understand it better. I and my colleague Rohit, has previously written a blog on Multi-omics approach which talks about importance of integrating different forms of data in scientific research.
Biology of Genomes Meeting 2018
Recently, I attended the Biology of Genomes 2018 meeting from May 8 – 12, 2018 in Cold Spring Harbor Laboratory in New York, USA. I presented a poster about my PhD project dealing with copy number variation in primary melanoma.
Researchers and scholars from all over the world discussed their research to understand the genomes of different organisms including humans. The meeting addressed the DNA sequence variation and its role in molecular evolution, population genetics and complex diseases, comparative genomics, large-scale studies of gene and protein expression, and genomic approaches to ecological systems using different technologies and applications. Different genetic data either generated or downloaded from public databases were used to understand different topics in genomics. There was a special session that tackled the ethical, legal and social implications (ELSI) of genome research. Indeed our genome is very complicated and we still have a long way to go to fully understand it.