Incoming links: Single-nucleotide polymorphism
Can be seen as a cheap form of DNA sequencing that only test for a few hits. Some major applications:
- gene expression profiling
- single-nucleotide polymorphism: specificity is high enough to detect snips
Why Oxford Nanopore was used instead of Illumina for the sequencing Updated 2024-12-15 +Created 1970-01-01
At the time of the experiment, Illumina equipment was cheaper per base pair and dominates the human genome sequencing market, but it required a much higher initial investment for the equipment (TODO how much).
The reusable Nanopore device costs just about 500 dollars, and about 500 dollars (50 unit volume) for the single usage flow cell which can decode up to 30 billion base pairs, which is about 10 human genomes 1x! Note that 1x is basically useless for one of the most important of all applications of sequencing: detection of single-nucleotide polymorphisms, since the error rate would be too high to base clinical decisions on.
Compare that to Illumina which is currently doing about an 1000 dollar human genome at 30x, and a bit less errors per base pair (TODO how much).
Other advantages of the MinION over Illumina which didn't really matter to this particular experiment are:
- portability for e.g. to do analysis on the field near infections outbreaks. Compare that to the smallest Illumina sequencer currently available in 2019, the iSeq 100: Figure 1. "Illumina iSeq 100 DNA sequencer".
- long reads which can be necessary for long repetitive regions, see also: Section "Sequence alignment"
Sequence alignment is trying to match a DNA or amino acid sequence, even though the sequences might not be exactly the same, otherwise it would be a straight up string-search algorithm.
This is fundamental in bioinformatics for two reasons:
- when you sequence the DNA of a new species, you can guess what each protein does by comparing it with similar proteins in other species that you have already studied
- when doing DNA sequencing, and specially short-read DNA sequencing, you generally need to align the reads to reference genomes to know where you are inside the entire genome, and then be able to spot mutations, notably single-nucleotide polymorphisms