Our world here at Basepaws revolves around your pets’ DNA. In order to analyze feline and canine genes, we must first decode the information within them. Many labs still rely on microarray techniques for genotyping studies due to a number of advantages. We, however, employ whole genome sequencing, a type of Next Generation Sequencing, which gives us large amounts of data to use and analyze in all aspects of our work.
Here we summarize the key differences between these two approaches for genotyping studies. Microarrays vs Whole Genome Sequencing (WGS): which should you choose?
Microarrays
A DNA microarray is a collection of short DNA fragments attached to a solid surface. Think of it like a tiny checkerboard that has thousands of spots. Each spot is designed to pair with a specific pattern of DNA. When DNA is placed on the board, those that match a specific spot will light up, or create a signal, that scientists can use to analyze many different things. Microarrays can be used to measure the expression of many genes simultaneously and to genotype multiple regions of a genome.
The core principle of the method is based on hybridization, matching, between two complementary DNA strands. When DNA fragments are attached to a surface, they can be exposed to free floating fluorescently labeled target sequences. These target sequences will bind to their corresponding sequence on the surface. The surface is then washed, and all DNA fragments that didn't bind to the microarrays are washed away. The fluorescently labeled target sequences will produce a light, or signal, and the subsequent screening of the fluorescent signal identifies the sequences which were binded by the target fragments. Using DNA microarrays allows for the identification of previously determined sequences but doesn't allow the identification of unknown sequences.
The microarray technique has been used for decades, and it certainly has a number of advantages. However, it is also:
1. Slow to respond to the latest discoveries in genetics – There are large costs and long timelines associated with re-designing a microarray chip to include newly discovered genetic targets, which requires designing an initial screening array first, followed by a smaller array for routine use.
2. Difficult to design in the absence of pre-existing Next Generation Sequencing (NGS) data – The limited amount of publicly available cat and dog genomic data makes selecting microarray candidate gene variants difficult. In addition, not all selected variants will work in a microarray assay, as there are limitations associated with the hybridization efficiency of the array.
3. Unsuitable for discovery – Microarrays have potential for Genome Wide Association Studies (GWAS), but since the genetic targets on a microarray are pre-selected, new gene variants cannot be discovered.
Microarrays vs Next Generation Sequencing: DNA microarray (source)
Whole Genome Sequencing (WGS)
DNA sequencing is a technique which determines the order of nucleotides in a DNA sequence. As explained in the blog about Basepaws science, a DNA molecule consists of two chains containing multiple nucleotide molecules, called polynucleotides. To determine the precise order of these nucleotides in the DNA molecule, we have to sequence it. Different methods or technologies can be used for this. The most basic methods for DNA sequencing are Maxam-Gilbert and Sanger. More advanced and faster methods are also available. These are Next Generation Sequencing (NGS) and Third Generation Sequencing.
Next Generation Sequencing (NGS), also known as high-throughput sequencing, is an umbrella term for a number of modern sequencing technologies. Basepaws employs Whole Genome Sequencing (WGS), a type of NGS, using the Illumina DNA sequencing platforms – the most broadly used NGS DNA sequencers across labs today. The Illumina NGS method is based on DNA that has been modified by adding a fluorescent dye and a temporary molecular stop sign to prevent more DNA being added to the strand. A DNA building enzyme will only add one fluorescently labeled molecule at a time allowing a camera or scanner to determine which molecule has been added based on the color that appears. A chemical wash is used to remove the dye and the temporary molecular stop sign and allow for the next DNA molecule to be added on. Illumina platforms sequence a wide range of fragments, ideally around 300-350 base pairs. With Whole Genome Sequencing we are able to see your pet's entire genome, and use that for analysis.
The reason we opt for DNA sequencing rather than microarrays for our genotyping studies is related to the following advantages of WGS:
1. No prior data required − We are not limited by the scarcity of publicly available feline genomic data.
2. High discovery potential – NGS allows discovery of previously unknown gene variants.
3. The method has much greater flexibility than microarrays, since there is no need for hardware redesign every time a new gene variant is to be studied.
Microarrays vs Next Generation Sequencing: An overview of Illumina sequencing From Zhou, X., Li, Y., 2015 (source)
Basepaws is dedicated to new discoveries within feline and canine science and genetics. We want to learn more about pets and their health and ancestry. This is the perfect place for the creation of novel and more efficient tools for genomic analysis. We have an active Research & Development team that is continuously optimizing our processes to increase efficiency and develop new technologies. After intense optimization of lab processes, we have found that DNA sequencing works best for all the analyses conducted in our labs and it allows us to drive companion research forward faster than microarray technology would.
