This holiday season, while sipping eggnog and eating some delicious holiday treats, we invited Dr Sandeep Pingle, editor of Roundtable Review[1] to muse about next generation sequencing – a technology that has transformed the field of science. In a four-article series, he will discuss in brief, the advances that encompass this genomic revolution.

 

A question people commonly ask today: is it really possible to sequence the entire genome for a mere $1000? Well, something like this did seem unthinkable only a few years ago. Then the human genome project and advances in the “omics” field drove the development of new technologies that rapidly decreased sequencing costs. Of course, $1000 genome was and still remains an exaggeration. But we have reduced expenses significantly, from a decade ago when whole genome sequencing cost millions of dollars to only thousands of dollars today [2]. However, apart from reduced expenses, has this really made a difference in terms of how it affects the layperson? Well, try digesting this – now there is an app for receiving and securely storing next generation sequencing data on smartphones and tablets [3]. So, along with Twitter and LinkedIn apps, all you mobile Health (mHealth) [4] fans can now check out your genome while waiting in line at the grocery store or the bus stop!

 

Next generation sequencing

Genome Sequencing Image: Courtesy Jane Ades, National Human Genome Research Institute (genome.gov)

It is clear that more and more people will choose to have their genomes sequenced when inexpensive tools are available. In fact, in response to an online survey by the National Public Radio, more than 80% individuals responded by saying that they would like their genomes sequenced [5]. But the big question is: why get one’s genome sequenced and what is the potential use of data thus obtained? In today’s clinical practice, sequencing is limited to a few cancer patients to determine what specific targeted agents will be most effective in a particular individual. In addition, genomic analyses can help in diagnosing rare diseases; the United Kingdom recently pledged £100 million for 100,000 patients with cancers or rare diseases [6]. However, with advances in the field, the rationale for genome sequencing will be to identify genetic variants that may have long-term implications for health and disease of every individual. As an illustration, Norway has recently pledged to incorporate genome sequencing into its national health-care system [7].

 

All these factors have led to an increased demand for sequencing. Coupled with observations from genomics projects over the last few years, it was obvious that Sanger sequencing, the “first-generation” technology had limitations. Hence the need to develop novel, improved and more efficient methods of sequencing. Enter: Next Generation Sequencing that is revolutionizing the field of genomics! This includes technologies that, in contrast to the Sanger method, sequence large numbers of DNA fragments in parallel, with runs that produce up to billions of short reads (hence the other name: massively parallel sequencing). So, what is the technology behind next generation sequencing, what are its applications and what clinical translation, if any, does it have? Please stay tuned and find out all you wanted to know about next generation sequencing but were afraid to ask!

 

References:

  1. Sandeep Pingle is the San Diego Editor for the blog “Roundtable Review” by Oxbridge Biotech Roundtable
  2. Illumina launches personal genomic sequencing: by Daniel MacArthur (2009)
  3. MyGenome iPhone and iPad app: by Brian Dolan (2009, 2012)
  4. Mobile Health (mHealth): Wikipedia
  5. Will Low-Cost Genome Sequencing Open ‘Pandora’s Box’? by Rob Stein (2012)
  6. UK pushes whole genome sequencing into clinical practice: by Daniel Cressey (2012)
  7. Norway to bring cancer-gene tests to the clinic: by Ewen Callaway (2012)