The first decade of the new millennium has seen rapid development of high-throughput sequencing methods—fast, cheap ways to sequence and analyze large genomes. A variety of different approaches are being used. They generally involve the amplification of DNA templates by the polymerase chain reaction, and the physical binding of template DNA to a solid surface or to tiny beads called microbeads. These techniques are often referred to as massively parallel DNA sequencing, because thousands or millions of sequencing reactions are run at once to greatly speed up the process. This animation describes one such high-throughput method, in which a single 10-hour run can produce 400 million or more base pairs of DNA sequence information.
In the past few decades, researchers have sequenced the genomes of multitudes of species. The first whole genome of a free-living organism (the bacterium Haemophilus influenzae) was sequenced in 1995. The researchers used a method called shotgun sequencing, in which genomic DNA is cut into smaller, overlapping fragments that are cloned and sequenced, and then powerful computers align the fragments by finding sequence homologies in the overlapping regions.
Shotgun sequencing generated the Haemophilus sequence of 1.8 million base pairs in just a few months. The shotgun method later generated the 180 million-base-pair fruit fly genome sequence in little over a year, followed by the 3 billion-base-pair human genome sequence in about 9 months. Sequencing methods are being continually refined to increase speed and accuracy and decrease costs. In recent years, a variety of sequencing methods have been developed to yield tens or hundreds of millions of base pairs in just a few hours.
Textbook Reference: Concept 12.1 There Are Powerful Methods for Sequencing Genomes and Analyzing Gene Products