Types of genome sequencing

Whole genome sequencing

Whole genome sequencing focuses on sequencing all of the DNA in an organism’s genome.

De novo sequencing (‘de novo’ = starting from the beginning)

• This is when the whole genome of an organism is sequenced and assembled for the first time, without the availability of a reference genome.
• If you imagine the genome is a jigsaw puzzle of fixed dimensions (for example, 1 m²), the smaller the pieces, the more pieces there are, the harder the puzzle is to complete. It is the same when assembling a genome for the first time.
• In genome assembly, a combination of short and long pieces of DNA are sequenced to cover as much of the genome as possible and minimise the risk of there being any gaps in the final sequence.

Resequencing

• Resequencing projects are when an organism’s genome is sequenced and assembly is done using the reference genome as a template (for example, with humans this would be the genome produced by the Human Genome Project).
• The key reason for carrying out resequencing is to compare differences between genomes from the same species.

Targeted genome sequencing

• Targeted sequencing means researchers can focus on sequencing specific areas of interest within the genome.
• One common use of targeted sequencing is to look for single nucleotide polymorphisms (SNPs). SNPs are single base changes in the DNA sequence. They are the most common type of genetic variation between us, and can be used to help scientists find genes associated with disease.
• During targeted sequencing, the DNA sequence being studied is amplified by a process called the polymerase chain reaction (PCR).
• After the sequence has been amplified, the DNA is sequenced by high-throughput sequencing.
• Targeted sequencing reduces the cost and time needed for sequencing projects and allows for a more in-depth study of specific regions of the genome.

Exome pulldown

• Exome sequencing is a type of targeted sequencing where researchers sequence only the genes in a genome.
• Genes make up less than two per cent of the human genome. Therefore, sometimes researchers focus their sequencing efforts only on the genes (the exome).
• The exome contains all the instructions needed to make proteins in your body.
• Due to the fact that exome sequencing is only looking at a very small section of the genome, it enables scientists to focus on the parts of the DNA sequence that are more likely to be linked to disease, the genes.
• Sequencing an exome is much quicker and cheaper than sequencing the whole genome.

During exome pulldown, magnetic beads are used to pull out DNA sequences of interest.
Image credit: Genome Research Limited