In 2005, two landmark papers describing novel cycle-array sequencing methods ushered in a new era in genetics. Known at the time as next-generation sequencing (NGS), these methods are now more commonly described as second-generation sequencing.
Although initially expected to supplant Sanger sequencing, NGS technologies have done an end run around Sanger and are instead encroaching on technologies like the DNA microarray, or staking a claim on new fields like metagenomics.
Compared to conventional Sanger sequencing, second-generation sequencing has several advantages. One is a streamlined workflow that eliminates transformation and colony picking—major bottlenecks in the process. Another is mind-bogglingly massive parallelism. Array-based sequencing can theoretically capture hundreds of millions of sequences in parallel. These changes have dramatically reduced the cost of sequencing from about $0.50 per kilobase to as little as $0.001 per kilobase. For read length and sheer accuracy, however, Sanger sequencing still rules.
With 30 years of technology development behind it, a Sanger system can produce read lengths of 1,000 bp, with nearly perfect accuracy, whereas second-generation challengers tend to achieve read lengths of less than 100 bp, with roughly ten times the number of inaccurate base calls.
Second-generation sequencing technologies are still very much on the steep portion of the development curve, so improvements in accuracy and read length can be expected on a regular basis for years to come. In the meantime, however, second-generation sequencing has been embraced for myriad applications in which expensive Sanger sequencing would be out of the question.
At CHI’s “Exploring Next Generation Sequencing” meeting to be held later this month, a number of speakers are slated to present real-world next-generation sequencing results—a blossoming of the technology pioneered just four years ago.