Illumina Sequences the First African Human Genome

Illumina, Inc. today announced that scientists at the Company have sequenced the genome of an anonymous African male (Yoruba from Ibadan, Nigeria), using the Genome Analyzer. Sequencing of this HapMap sample was conducted internally and marks the first human genome sequence generated exclusively with paired reads of 35 to 50 bases in length. Leveraging recent system improvements that increase the throughput and improve the accuracy of the Genome Analyzer, Illumina scientists were able to complete this project in a matter of weeks. More than 95 percent of production runs generated high-quality data with an average of over three billion bases (three Gb) per run. This achievement establishes the direct utility of Illumina’s sequencing technology for accurately sequencing large and complex genomes.

“This landmark project demonstrates that scientists can use the Genome Analyzer today to economically and rapidly complete large-scale sequencing projects including human genome sequencing,” said Jay Flatley, President and Chief Executive Officer of Illumina. “With this project we have established both the efficacy of our technology to consistently produce large volumes of high-quality data, and the utility of our unique short-insert paired read approach for large-scale sequencing.”

Using paired reads primarily from 200 base pair (bp) insert size libraries, supplemented with reads from 2000 bp insert size libraries, Illumina scientists initially conducted 27 runs to generate over 75 Gb of DNA sequence and achieve more than 90 percent coverage of the genome. An initial analysis yielded over 3.7 million single nucleotide polymorphisms (SNPs), including more than one million novel SNPs. As expected, the remaining SNPs correspond to those found in public databases. The data generated by the Genome Analyzer shows excellent concordance with those generated using other technologies: of previously known SNPs, Illumina’s Genome Analyzer shows both 98 percent concordance with data generated using Illumina’s HumanHap550 genotyping BeadChip, as well as with data generated by the HapMap project. The high concordance rate of SNPs detected by the Genome Analyzer with SNPs detected by independent technologies affirms the accuracy of Illumina’s sequencing technology for discovery and validation of polymorphisms. Additional analysis work is under way using both long- and short-insert read pairs to characterize known and novel structural variation in this genome.

“This study is a testament to the robustness of the system and the speed and economic benefits of Illumina’s sequencing technology,” said David Bentley, DPhil, Vice President and Chief Scientist at Illumina. “Making whole human genome sequencing routine will enable the study of natural human variation all over the world, and enable the use of medical sequencing at the whole genome level to unravel the full spectrum of mutations, which give rise to cancer.”

Data and analyses from this project will be presented by Dr. Bentley on February 8th at the 2008 Advances in Genome Biology and Technology (AGBT) conference in Marco Island, Florida.