Editing Genomics (section)

==== Shotgun sequencing ====
<!-- [[File:Sanger-sequencing.svg|thumb|upright=1.5|The Sanger (chain-termination) method for DNA sequencing.]] -->
[[Image:ABI PRISM 3100 Genetic Analyzer 3.jpg|left|thumbnail|An ABI PRISM 3100 Genetic Analyzer. Such capillary sequencers automated early large-scale genome sequencing efforts.]]
{{Main|Shotgun sequencing}}
Shotgun sequencing is a sequencing method designed for analysis of DNA sequences longer than 1000 base pairs, up to and including entire chromosomes.<ref name = "Staden_1979" /> It is named by analogy with the rapidly expanding, quasi-random firing pattern of a [[shotgun]]. Since gel electrophoresis sequencing can only be used for fairly short sequences (100 to 1000 base pairs), longer DNA sequences must be broken into random small segments which are then sequenced to obtain ''reads''. Multiple overlapping reads for the target DNA are obtained by performing several rounds of this fragmentation and sequencing. Computer programs then use the overlapping ends of different reads to assemble them into a continuous sequence.<ref name = "Staden_1979"/><ref name = "Anderson_1981a"/>  Shotgun sequencing is a random sampling process, requiring over-sampling to ensure a given [[nucleotide]] is represented in the reconstructed sequence; the average number of reads by which a genome is over-sampled is referred to as [[Shotgun sequencing#Coverage|coverage]].<ref name = "Pop_2008"/>

For much of its history, the technology underlying shotgun sequencing was the classical chain-termination method or '[[Sanger sequencing|Sanger method]]', which is based on the selective incorporation of chain-terminating [[dideoxynucleotide]]s by [[DNA polymerase]] during [[in vitro]] [[DNA replication]].<ref name = "Sanger_1977"/><ref name = "Sanger_1975"/> Recently, shotgun sequencing has been supplanted by [[Dna sequencing#Next-generation methods|high-throughput sequencing]] methods, especially for large-scale, automated [[genome]] analyses. However, the Sanger method remains in wide use, primarily for smaller-scale projects and for obtaining especially long contiguous DNA sequence reads (>500 nucleotides).<ref name=Mavro_2012/> Chain-termination methods require a single-stranded DNA template, a DNA [[primer (molecular biology)|primer]], a [[DNA polymerase]], normal deoxynucleosidetriphosphates (dNTPs), and modified nucleotides (dideoxyNTPs) that terminate DNA strand elongation. These chain-terminating nucleotides lack a 3'-[[hydroxyl|OH]] group required for the formation of a [[phosphodiester bond]] between two nucleotides, causing DNA polymerase to cease extension of DNA when a ddNTP is incorporated. The ddNTPs may be radioactively or [[fluorescence|fluorescently]] labelled for detection in [[DNA sequencer]]s.<ref name=Pevsner_2009/> Typically, these machines can sequence up to 96 DNA samples in a single batch (run) in up to 48 runs a day.<ref name = "illumina2012"/>