Next Generation Sequencing

Applied Biosystems have released data to the public from the genome sequencing of a Yoruba Nigerian HapMap sample. In their press release, AB claim that the data were generated using only 7 runs of the SOLiD system and at a total sequencing costs of less than 60.000$.

The data covered the genome 12 fold and paired end information provided a physical coverage of a 100 fold, i.e. the coverage stemming from the inserted but not sequenced part of paired end reads. Millions of SNP’s and a large number of structural variations were identified from the data.

As an amusing aside, AB gave these funny facts about the dataset:

• If all 36 billion bases were spread out at 1 millimeter apart, they would extend 36,000 kilometers, or more than 4,000 times the height of Mt. Everest, which at 8,848 meters above sea level, is the highest mountain on Earth.
• If all 36 billion bases were spread along the Great Wall of China at 1 millimeter apart, this would equate to spanning the 5,000 kilometer wall more than 7 times.
• If a person were to proofread the 36 billion bases in this dataset at one letter per second for 24 hours-per-day, it would take 1,200 years to read the entire data set.
• If each base represented one individual in the world population, the dataset would account for more than 5 times the entire world population of 6.8 billion people.
• This dataset, at 36 billion bases of DNA sequence, is equivalent to 360 times all of the 100 million visible stars in the Earth’s galaxy.