OHSU

Arrays & Services

Current Illumina Arrays

Whole Genome Expression Arrays

HumanHT-12         

MouseWG-6          MouseRef-8          RatRef-12

 

Whole Genome Expression Arrays

HumanHT-12 -  The HumanHT-12 Expression BeadChip is a higher throughput version of the well-proven HumanWG-6 BeadChip and is designed to support highly efficient whole-genome expression studies.  Each array on the HumanHT-12 BeadChip targets more than 25,000 annotated genes with more than 48,000 probes derived from the RefSeq (Build 36.2, Rel 22) and the UniGene (Build 99) databases. Illumina guarantees that > 99.99% of the bead types will be present on any given HumanHT-12 array.  Each two pack has two slides with 12 arrays per slide.

Mouse WG-6 - Illumina's whole genome 6 mouse array contains all of the content of the MouseRef-8 array, plus an almost equal number of probes based upon other sources.  In total, the Mouse WG-6 interrogates more than 45,200 transcripts and allows the investigator to profile six samples at one time.  Each two pack has two slides with six arrays per slide.

MouseRef-8 -  Illumina's MouseRef-8 arrays targets approximately 25,600 well-annotated RefSeq transcripts and enables the interrogation of eight samples in parallel.  Probe design is based on RefSeq Build 26, Release 22.  Each two pack contains two slides with eight arrays per slide.

RatRef-12 -  Each of Illumina's RatRef-12 arrays contains > 22,000 probes selected primarily from the NCBI RefSeq database (Release 16). Each address and probe sequence has been carefully selected using a multi-step algorithm scoring several parameters including: similarity to other genes, sequence complexity, self-complementarity, Tm, distance from 3' end, and absence of highly repeated sequences in the genome.  Each two pack contains two slides with twelve arrays per slide.

Whole Genome Genotyping Arrays

Human1M-Duo -  More than 1.1 million markers with an median spacing of 1.5 kb.   Each slide assays two samples with as little as 400 ng of starting genomic DNA.  Illumina HD arrays can achieve average call rates greater than 99%.  The Human1M-Duo also targets regions of notable interest - including exons, the MHC, and ADME genes.  It also contains CNV-targeted markers that target regions of likely variation. 

Human660W-Quad - More than 658,000 markers with an median spacing of 2.5 kb.  Each slide assays four samples with as little as 200 ng of starting genomic DNA.  Illumina HD arrays can achieve an average call rate of greater than 99%.  The Human660W-Quad content is based on HapMap release 23.  It offers high value coverage across many populations, captures the majority of known variation, and targets common CNV regions.  It contains about 100,000 markers that specifically target regions of common copy number varation that were recurrently identified in a high-density CNV discovery project across mutiple population.

Human510S-Duo - greater than 510,000 markers with a median marker spacing of 3.2 kb.  Illumina HD arrays can achieve an average call rate greater than 99%.  The Human510S-Duo can assay two samples per slide with a starting amount of 750 ng of genomic DNA per sample.  This array targets more than 99.9% of RefSeq genes.   It also targets the MHC, ADME genes, and known and novel CNV regions.

HumanCytoSNP-12 - approximately 300,000 markers with a median marker spacing of 10 kb.  Each slide can assay 12 samples with as little as 200 ng of genomic DNA per sample.  Illumina HD arrays can achieve an average call rate of 99%. 

 Semi-Custom Human1MDuo+ and HumanHap550-Quad+ - add content to two Illumina HD arrays. Up to 60,800 SNPs assays per sample to meet the specific needs of a given study. 

Custom Genotyping Assays - GoldenGate assay

Custom Genotyping Assays - Custom panels for specific SNP assay can be created in panels of 96 and 384-1536 assays per OPA (oligonucleotide) tube.  Larger panels can be accommodated by multiple OPA tubes.  Panels for 384-1636 loci are available in multiples of 96.  We can handle both slide based custom panels and Sentrix Array Matrix (96-well plate) format.

Methylation and Focused Content Arrays

Illumina offers a variety of arrays for genotyping for focused human studies, for non-human samples and for methylation analysis.  Please contact the core director or visit the Illumina website for more information.  Briefly, among the focused arrays available are:

African American admixture panel

Cancer SNP panel

HumanCVD panel

MHC panel

Bovine, canine, equine, ovine, and procine arrays

In addition, custom arrays can be designed.

 

Methylation arrays includes the infinium methylation array and the cancer methylation panel, plus the option of creating a custom methylation panel.

related resources

 

The Illumina Microarray Core is a unit of the Gene Microarray Shared Resource (GMSR).  

The GMSR also includes the Affymetrix Microarray Core.

The Oregon Clinical & Translational Resource Institute (OCTRI) is available to investigators for Biostatistics and Computational support services.