What is a genome
A genome is a collective term for all the genetic material within an organism. In essence, the genome decides exactly what that organism will look and act like at birth – one huge, expansive instruction manual that tells cells their duties. Every living thing has a genome, from bacteria to plants to humans, and they are all different in size with various combinations of genes inside.
The human genome packs in 30,000 genes, but this is just 1% of the total genetic material contained within. Quite frankly, it’s a mess in there – much of the genetic material is duplicated DNA that (supposedly) does very little, and the vast majority of DNA simply doesn’t code for anything (these sections are called introns). That isn’t to say it does nothing. In fact, recent studies have shown us that non-coding DNA is essential to controlling whether our genes get switched on or not. However, most of the time it’s the actual genes that are the important bit.
Genome research
Studying the genome of humans and other organisms is vital for a number of reasons. Firstly, it helps us characterize each one – before genomics, scientists simply grouped animals and plants by what they looked like, but research into their genes now allows for accurate characterization of organisms into specific genera and species.
In humans, genomic research has allowed researchers to understand the underlying causes of many complex diseases and find possible targets for treatment. Currently, the best tool to do this is genome-wide association studies (GWAS).
The idea behind GWAS is relatively intuitive – simply take a group of people with the disease you wish to study, and compare their genomes for common genetic variants that could predict the presence of that disease. These studies have illuminated a huge number of variants linked with higher disease prevalence while also helping researchers to understand the role each gene plays in the human body. Although powerful, GWAS studies are purely a starting point. Following a large-scale GWAS, researchers must then analyze any variants that are highlighted in great depth, and many times such research will provide nothing of clinical relevance. However, it’s still our best way of identifying risk variants in genetic disease.
Genome mapping
So, we know the genome is packed to the brim with genes that code for proteins, separated by large strings of non-coding DNA. However, when cells replicate early in development they usually go through chromosomal recombination, in which chromosomes trade regions of their genetic code between each other. This spreads genes to many different positions (called loci) throughout the genome. If we can make a map of these genes, we can discover their function, how they are inherited, or target them with therapies.
Therefore, we want to create a genome map. There are two types of maps used in genomics: genetic maps and physical maps.
Physical maps are relatively straightforward, in which genomic loci are mapped based on the physical distance between them, measured in base pairs. The most common way to create a physical map of a human genome is by first breaking the DNA sequence into many fragments, before using a variety of different techniques to identify how those pieces fit back together. By understanding which pieces overlap and reconstructing the shattered genome, scientists can gain a decently accurate map of where each gene lies.
Genetic maps are slightly different, using specific marker regions within the DNA that are used as trackers. These maps require samples (usually saliva) from family members, which are then compared to identify how much recombination has occurred that includes markers of interest. The principle is that if two genes are close together on the chromosome, then they are more likely to travel together through the genome as it recombines. By using this data, scientists can get a rough idea of where specific genes lie on chromosomes. However, it is not as accurate as physical mapping and relies heavily on a decent population size and the number of genetic markers used.
Genome browser
A genome browser is any available database that allows a user to access and compare genomes in an intuitive way. When you map or sequence a genome, the data is pretty messy. Genomes are usually stored in huge files, called FASTA files, that contain extensive strings of letters that would look foreign to most users. Genome browsers take this data and make it accessible to scientists around the globe.
Many genome browsers are available online, containing bacterial, model organism, and human reference genomes.
Genomelink
Genomelink is one of the latest examples of public access and analysis of genomes. The industry took off in recent years, with the rapid rise of sites that provide ancestry and medical information based on genomic sequencing, including Ancestry and 23andMe. These sites work by comparing genetic markers associated with different populations – should you share specific regions of DNA that correspond with African populations, for example, you may have some relation to African ancestors. Each site uses its own markers, so information may vary between tests, and some have disputed the true accuracy of these tests, although advances in genomics have significantly improved them in recent years.
Genomelink goes further than most sites, claiming to provide information on a huge variety of genetic traits that a user may have. These include metabolism, sports performance, and even personality traits such as loneliness. Each trait is drawn from genome correlation studies, with each taking a specific trait and comparing the genomes of each carrier of that trait.
However, although both Genomelink and other sites use up-to-date reference genomes and are usually relatively accurate, they should never be substituted for medical information. If you believe you carry a pathogenic gene variant, you should seek advice from a genomic counselor.
