Illumina Array-Based Services on the iScan

Array Services

The Illumina iScan instrument utilizes Illumina’s BeadArray Technology which is based on 3-micron silica beads that self assemble in microwells on either of two substrates: fiber optic bundles or planar silica slides. When randomly assembled on one of these two substrates, the beads have a uniform spacing of ~5.7 microns. Each bead is covered with hundreds of thousands of copies of a specific oligonucleotide that act as the capture sequences in one of Illumina’s assays.

The iScan System provides the fastest scan times for Illumina’s high-multiplex BeadChips. The iScan grants users access to a range of applications, including whole-genome genotyping, gene expression analysis, methylation analysis, and more. The following are currently provided at the Biospecimen Processing Facility.

The Biospecimen Processing Facility provides the following arrays (among others) on the iScan listed below:

Human OmniExpressExome
Illumina’s Infinium HD BeadChips profile the human genome with 300,000 to approx. 1.2 million markers. With Illumina’s Omni family of microarrays, there’s a wide selection of flexible arrays featuring markers selected from the International HapMap and 1000 Genomes Projects.

Other Examples of Infinium BeadChips that we process: HumanOmniExpress, HumanExome, Human Immuno DNA Analysis BeadChip, Human Omni1-quad, and Human Omni1S

Methylation EPIC BeadChip

Illumina’s Infinium MethylationEPIC BeadChip allows the interrogation of 850,000 methylation sites per sample. The Infinium MethylationEPIC BeadChip provides exceptional coverage of CpG islands, RefSeq genes, ENCODE open chromatin, ENCODE transcription factor binding sites, and FANTOM5 enhancers. Infinium HD technology enables content selection independent of bias-associated limitations often associated with methylated DNA capture methods.

Importantly, the Infinium MethylationEPIC BeadChip contains > 90% of the original Infinium Methylation450 BeadChip content, chosen to provide a broad, comprehensive view of the methylome

Global Screening Array (GSAv2) add-on/ included

With over 750K variants for whole-genome coverage and representing all 26 major and sub-continental populations, GSA will serve as a complimentary add-on to your WES data. GSA boosts your ability to detect ancestry from WES but also serves as a fingerprinting and QC of all samples. GSA includes more than 10,000 highly penetrant variants across 20 different common disease categories from ClivVar making it a great research tool to identify risk alleles and validate or even augment findings from WES.

Designed to extend beyond academic research, GSA also includes priority translational and clinical research applications. This content includes more than 15,000 variants across all ACMG-59 genes for disease risk and prevention, more than 17,000 variants spanning PharmGKB, CPIC-17 and ADME genes for broad coverage and utility in Pharmacogenomics (PGx) and areas supporting development toward Precision Health. PGx also includes copy number capabilities and couples well with the Ancestry information, particularly relevant in research concerning a precision medicine approach (content currently relevant to 145 drug associations). Approximately 10,000 variants cover HLA-MHC regions as well.

Multi-Ethnic Global (MEG) Array

The Infinium Multi-Ethnic Global BeadChip harnesses content from Phase 3 of the 1000 Genomes Project (1kGP)1, Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA), Population Architecture using Genomics and Epidemiology (PAGE), T2D-Genes Consortium, OMIM, ClinVar, ACMG, carrier screening panels, and other resources to create a multipurpose, multiethnic array. With > 1.7 million expertly selected markers, the Infinium Multi- Ethnic Global BeadChip enables identification of genetic associations with common and rare traits, providing insight across diverse populations to epidemiologists, health care researchers, population geneticists, and genomic researchers

The Infinium Multi-Ethnic Global BeadChip combines expertly selected markers and content from the most popular Illumina commercial arrays with the most current genomic information. Researchers can detect both common and rare variants across the most commonly studied 5 superpopulations and impute variants in a vast number of subpopulations.

The Infinium Multi-Ethnic Global BeadChip contains the following content:

• Infinium HumanCore-24 BeadChip content with highly informative genome-wide tag SNPs
• African Diaspora Consortium Power Chip content identified through sequencing of 692 individuals by CAAPA
• Genome-wide coverage for diverse populations selected by PAGE using a new cross-population tagging strategy
• Total exonic content of > 420,000 markers including the Infinium Exome-24 BeadChip content and Multiethnic exome content designed by PAGE
• Over 17,000 variants chosen to be relevant to clinical and pharmacogenetic studies and 23,000 hand-curated variants picked for functional, immunological, oncological, ancestry, and forensic applications

Infinium Omni2.5

The Infinium Omni2.5Exome-8 BeadChip array delivers comprehensive coverage of common, rare, and exonic SNP content from the 1000 Genomes Project (1kGP)1, providing maximum genomic information of diverse world populations. With combined markers from the Infinium Omni2.5-8 Kit and Infinium Exome-24 Kit, the Infinium Omni2.5Exome-8 BeadChip is a powerful tool for next-generation genotyping and genome-wide association studies (GWAS) with as low as 1%MAF. 2.5M markers.

Due to the customizable nature and larger scope of these projects, pricing is charged on a per project basis using our current custom rates. Please contact us with your project needs and we will provide you with a quote inclusive of all QC, sample handling, assay consumables, preliminary data analysis and data delivery

Array Submissions

We require the following:

1. Contact Hong Quach to initiate a sample submission.
2. Generally, samples should be submitted in Thermo Scientific 96-well PCR Plates catalog # AB-1400L. Please contact us if you require us to send plates to you for an additional charge. If you are submitting 5 or more plates and prefer to use your own plates, please contact us for the possibility of programming your plates into our robot (additional charge applies).
3. Plates being delivered at drop off locations should be sealed with Thermo Scientific Plate Seals Catalog # AB0558 or equivalent. Plates being shipped should be heat sealed if possible. Please ensure that your plates are sealed completely to prevent evaporation or possible cross contamination during shipping.
4. We require 1 ug of DNA for all arrays except the HumanMethylation450 BeadChip which requires 2 ug of DNA (we will return any unused DNA).
5. The front edge and top of the plate should contain the plate name and PI name. The right side edge of the plate should contain your name. Plate name should match the name provided on the Sample Submission Form exactly.

Sample Drop off Location:

Hong  Quach
431 Stanley Hall
M-F 10am-5pm

Shipping Samples to the Biospecimen Processing Facility

Please ship your samples on dry ice overnight to the following address:

Hong Quach
University of California Berkeley
431 Stanley Hall
Berkeley, CA 94720-3220
(510) 643-0829