A recent paper in Nature Biotechnology (Lam et. al, 18 Dec 2011) reports on the results of sequencing the same human genome at an average coverage depth of 76x using two different sequencing technologies. The authors, all from the Snyder lab at Stanford University, compared the accuracy and sensitivity of results obtained using an Illumina HiSeq 2000 instrument and Complete Genomics’ whole genome sequencing service.

To our knowledge, this is the only published direct comparison of the two platforms, and we applaud the authors for having undertaken this analysis. We eagerly dived into their comparison data to see what we could learn.

Updated to clarify information about commercial exome kits

Today, researchers use two approaches to identifying disease-associated variants in the human genome: exome sequencing, which targets the protein-coding regions that make up approximately 1% of the genome, and whole genome sequencing, which investigates the vast majority of the genome and includes both coding and non-coding regions.

The dramatic decline in the cost of sequencing whole human genomes over the past five years surprised even the most optimistic scientists (except possibly George Church). Starting from Roche 454’s $1 million Watson genome in 2006, we are now sequencing genomes for a few thousands of dollars each.

Back in college, my classmates were enthusiastically enrolling in classes with Professor Walter Gilbert, Nobel Prize winner in chemistry and a father of modern genetic sequencing. Not me. In those days I was either buried in the library stacks researching my undergraduate thesis or throwing myself into the maelstrom of student politics. But now as Chief Commercial Officer at Complete Genomics, I’ve been given something rare in life – a second chance.

Deep sequencing of a human genome produces large datasets sized in the hundreds of gigabytes, while the associated genome variant file measures about half a gigabyte. Now that we are sequencing thousands of human genomes has the time come to store and use only this variant file?