title: Whole-genome genotyping.
abstract: We have developed an array-based whole-genome genotyping (WGG) assay (Infinium) using our BeadChip platform that effectively enables unlimited multiplexing and unconstrained single nucleotide polymorphism (SNP) selection. A single tube whole-genome amplification reaction is used to amplify the genome, and loci of interest are captured by specific hybridization of amplified gDNA to 50-mer probe arrays. After target capture, SNPs are genotyped on the array by a primer extension reaction in the presence of hapten-labeled nucleotides. The resultant signal is amplified during staining and the array is read out on a high-resolution confocal scanner. We have employed our high-density BeadChips supporting up to 288,000 bead types to create an array that can query over 100,000 SNPs using the Infinium assay. In addition, we have developed an automated BeadChip processing platform using Tecan's GenePaint slide processing system. Hybridization, washing, array-based primer extension, and staining are performed directly in Tecan's capillary gap Te-Flow chambers. This automation process increases assay robustness and throughput greatly while enabling laboratory information management system control of sample tracking.
authors.affiliation: Illumina Inc., San Diego, California, USA.
authors.forename: Kevin L
authors.initials: KL
authors.lastname: Gunderson
authors.forename: Frank J
authors.initials: FJ
authors.lastname: Steemers
authors.forename: Hongi
authors.initials: H
authors.lastname: Ren
authors.forename: Pauline
authors.initials: P
authors.lastname: Ng
authors.forename: Lixin
authors.initials: L
authors.lastname: Zhou
authors.forename: Chan
authors.initials: C
authors.lastname: Tsan
authors.forename: Weihua
authors.initials: W
authors.lastname: Chang
authors.forename: Dave
authors.initials: D
authors.lastname: Bullis
authors.forename: Joe
authors.initials: J
authors.lastname: Musmacker
authors.forename: Christine
authors.initials: C
authors.lastname: King
authors.forename: Lori L
authors.initials: LL
authors.lastname: Lebruska
authors.forename: David
authors.initials: D
authors.lastname: Barker
authors.forename: Arnold
authors.initials: A
authors.lastname: Oliphant
authors.forename: Kenneth M
authors.initials: KM
authors.lastname: Kuhn
authors.forename: Richard
authors.initials: R
authors.lastname: Shen
mesh_terms: D000818:Animals; D016678:Genome; D005838:Genotype; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*