Illumina-PG0000021
Individual human genome sequencing using the Illumina Genome Analyzer IIx
The individual genome sequence was requested by a physician after an approved consenting process. Blood and saliva samples were sent to Illumina Inc.'s Clinical Services Laboratory, San Diego, in barcoded tubes. All experimental work at Illumina was carried out in a CLIA-certified and CAP-accredited laboratory, and experimental data and patient records are kept on separate network systems with restricted access. The process followed the guidelines provided by an independent Ethics Advisory Board. John West, the individual whose genome sequence was determined, has requested and consented to the identified public release of these data. Genomic DNA was prepared from blood using standard procedures. Genotyping of DNA from blood and saliva was carried out using the Illumina Infinium Human1M-Duo array to confirm agreement between the separate samples. We generated a sequencing library with a median insert size of ~300 bp following random fragmentation and gel fractionation of the blood genomic DNA. We sequenced 100 bases from both ends of these templates using the Illumina Genome Analyzer IIx. We carried out purity-filtering (PF) to remove mixed reads, where two or more different template molecules are close enough on the surface of the flow-cell to form a mixed or overlapping cluster. The remaining aligned reads contain a total of  91,979,393,847  bases and cover the NCBI36 reference sequence of the autosomes to an average read depth of 33-fold. A genome sequence build was produced using ELAND and was used for calling of single nucleotide polymorphisms (SNPs) with CASAVA. The sequence-based genotypes were compared to those from the Infinium Human1M-Duo genotyping array to ensure the consistency of the data throughout the experimental process.
We have produced an individual human genome sequence using the Illumina Genome Analyzer. We generated paired-end sequence data covering the genome of John West to a sequence depth of more than 30-fold using the Illumina Genome Analyzer IIx. All experimental work was carried out in a CLIA-certified and CAP-accredited laboratory.