DNA sequencing

DNA sequencing is the determination of the order of nucleotide bases that make up a DNA molecule, or the ‘reading’ of the DNA sequence.

Methods:

There are several methods that can be used to perform DNA sequencing. One of the first sequencing methods developed in the 1970s, the Maxam-Gilbert method relies on chemical modification of DNA and its subsequent cleavage at specific bases1. The more popular early method, Sanger sequencing, involves the use of specific DNA chain terminators during DNA synthesis to generate labeled DNA fragments of varying lengths that are then separated by size2

A more recent shotgun sequencing approach involves the breakdown of DNA into smaller fragments that are cloned and sequenced individually. This method allows the sequencing of longer sections of DNA by alignment and reassembly of sequence fragments based on partial overlaps.

Current next-generation sequencing technologies, often referred to as parallel sequencing, involve fragmenting the entire genome into small pieces that are ligated to adapters for reading during DNA synthesis. Thus fragments along the entire genome can be read randomly and in parallel.

Identifying mutations:

With the completion of the Human Genome Project, which aimed to determine the sequence of the entire human genome, it became possible to have a reference sequence when comparing different genomes, for example that of an individual with a given disorder to that of a control individual3,4.

One of the main applications of this technology is the identification of genetic mutations in individuals affected with different disorders. In addition to single point mutations, DNA sequencing allows the detection of small insertions and deletions.

Relevance to autism:

DNA sequencing has led to the identification of genetic mutations in patients with syndromic autism, including mutations in MECP2, FMR1, PTEN, TSC1 and TSC2. In addition, mutations have been identified in genes that cause autism not associated with a known genetic disorder. These include two neuroligins NLGN3, NLGN4, and SHANK3.

A list of genes associated with autism spectrum disorders can be found in SFARI Gene, an online searchable database. With recent advances in DNA sequencing technology, it is now possible to sequence an entire human genome or exome at once.

Researchers are undertaking whole-genome and whole-exome sequencing studies on large numbers of DNA samples from individuals with autism spectrum disorders in order to identify novel autism genes.


References:
  1. Maxam A.M. and W. Gilbert Proc. Natl. Acad. Sci. USA 74, 560-564 (1977)
  2. Sanger F. and A.R. Coulson J. Mol. Bio. 94, 441-448 (1975)
  3. Nature 414 (entire issue) (2001)
  4. Science 294 (entire issue) (2001)
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