Editing Genomics (section)

==== High-throughput sequencing ====
{{See also|Illumina dye sequencing|Ion semiconductor sequencing}}
The high demand for low-cost sequencing has driven the development of high-throughput sequencing technologies that [[multiplex (assay)|parallelize]] the sequencing process, producing thousands or millions of sequences at once.<ref name = "Hall_2007"/><ref name = "Church_2005"/> High-throughput sequencing is intended to lower the cost of DNA sequencing beyond what is possible with standard dye-terminator methods. In ultra-high-throughput sequencing, as many as 500,000 sequencing-by-synthesis operations may be run in parallel.<ref name = "tenBosch2008"/><ref name = "Tucker_2009"/>

[[File:Illumina Genome Analyzer II System.jpg|thumb|Illumina Genome Analyzer II System. Illumina technologies have set the standard for high-throughput massively parallel sequencing.<ref name = "Baker_2012_Blog"/>]]
The Illumina dye sequencing method is based on reversible dye-terminators and was developed in 1996 at the Geneva Biomedical Research Institute, by [[Pascal Mayer]] and Laurent Farinelli.<ref name = "DNA_colony_patents"/> In this method, DNA molecules and primers are first attached on a slide and amplified with [[polymerase]] so that local clonal colonies, initially coined "DNA colonies", are formed. To determine the sequence, four types of reversible terminator bases (RT-bases) are added and non-incorporated nucleotides are washed away. Unlike pyrosequencing, the DNA chains are extended one nucleotide at a time and image acquisition can be performed at a delayed moment, allowing for very large arrays of DNA colonies to be captured by sequential images taken from a single camera. Decoupling the enzymatic reaction and the image capture allows for optimal throughput and theoretically unlimited sequencing capacity; with an optimal configuration, the ultimate throughput of the instrument depends only on the [[Analog-to-digital converter|A/D conversion]] rate of the camera. The camera takes images of the [[Fluorescent labeling|fluorescently labeled]] nucleotides, then the dye along with the terminal 3' blocker is chemically removed from the DNA, allowing the next cycle.<ref name = "Mardis_2008"/>

An alternative approach, ion semiconductor sequencing, is based on standard DNA replication chemistry. This technology measures the release of a hydrogen ion each time a base is incorporated. A microwell containing template DNA is flooded with a single [[nucleotide]], if the nucleotide is complementary to the template strand it will be incorporated and a hydrogen ion will be released. This release triggers an [[ISFET]] ion sensor. If a [[homopolymer]] is present in the template sequence multiple nucleotides will be incorporated in a single flood cycle, and the detected electrical signal will be proportionally higher.<ref name = "Davies_2011" />