The Next generation: Our final frontier?

It’s hard enough to keep up with the lastest Indie band or the newest Hollywood star or the sports star who cheated, but apologized, reformed and now it’s all okay.  Most of the time when I ask a question about something of apparent cultural relevance, I sound like I’ve had my head amputated.

These days, the scientific literature is starting to sound a little like the entertainment news.  Terms like epigenome, interactome, proteome, transcriptome and acronymns like NGS, E-MAPs, DHS-seq, RNA-seq, ChIPseq, SNP-CHiP, CHiP-chip are commonplace in the literature.   I hear terms like mate-pair templates, pair-ended sequencing and 2x 100, 30X coverage in daily use and I wonder if my genetics degree is at all useful.  Papers published in January of this year are already outdated in terms of the output of the technology.  As an evolutionary biologist, whose PhD used old-fashioned tools like microsatellites and Sanger sequencing, I feel like this technological wave is far outpacing our ability, as molecular ecologists, to surf it, effectively.

What I’m referring to, of course, is the “revolution” that is currently happening in genome sequencing.  I chose the word revolution because if you read most papers written on the subject (Nature seems to have captured the market on this), the authors use descriptors like “revolutionary”, “fundamental shift”, and “unprecedented”.  And at meetings, you hear scientists talking in frenzied and slightly competitive tones about the 280 million reads while another proudly states that he was able to get 822 billion reads at 100X coverage of the genome.  Claims in the literature suggest that massive parallel sequencing will enable us to resolve a large number of outstanding questions that previously, we couldn’t dream of tackling.

And I wonder are we really there yet?

The potential of NGS to produce unimaginable data was clearly outlined by Bentley (2006) when he described that it would take $10 million and 30 instruments sequencing on a continuous basis for 1 year to complete the human genome using Sanger sequencing.  Using NGS technology, the idea of personal genome sequencing at a reduced cost ($1000) is definitely becoming a reality.  Although I recognize the potential of NGS, I’m skeptical about the exaggerated claims that NGS will solve our deepest and most difficult questions.

Over the next few weeks, I will be writing a series of posts that will describe in the most basic of ways what each of these different sequencing technologies are and how they are used in the field of ecology and evolution.  Instead of covering territory already presented in many papers, I will try and present at least one relevant example how this technology was used to answer a question from the field of ecology and evolution.   During the discussion of the question tackled by the researchers, I will explain the underlying concept of the sequencing technologies used.  Because as a evolutionary geneticist, I am most interested in the possible pitfalls of this technology, I will attempt to address some possible issues.

Next post:  Hybrid sequencing using Roche 454 and Illumina

WORKS CITED

Bentley DR  2006.  Whole genome re-sequencing.  Current Opinion in Genetics and Development 16:545-552.

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About Dilara Ally

Dilara Ally works as a Bioinformatics Scientist for one of the hottest biofuel companies in San Diego, CA called SG Biofuels.
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