Illumina-PG0000001
Individual human genome sequencing using the Illumina Genome Analyzer II
              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.              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       ~200 bp following random fragmentation and gel fractionation of the blood genomic DNA. We      sequenced 75 bases from both ends of these templates using the Illumina Genome Analyzer II.      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 reads contain a total of 92,254,659,274 bases and cover the reference genome to an       average read depth of 32-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 Jay Flatley to a sequence       depth of more than 30-fold using the Illumina Genome Analyzer II. All experimental work      was carried out in a CLIA-certified and CAP-accredited laboratory.         