We offer high throughput SNP Genotyping using the Illumina iScan platform and any available Illumina Infinium or GoldenGate® genotyping arrays. Infinium genotyping arrays can be used to genotype between 300,000 and 5 million SNPs based on chip format, while custom selected SNPs can be multiplexed between 96 to 1 million and used to interrogate from a few dozen to thousands of samples. Accuracy and reliability for the assays are usually above 99.5%. Some Illumina genotyping arrays also offer built-in copy number variation (CNV) analysis. The customer needs to choose which chips to run, order the chips through the Core Facility, and provide us with genomic DNA samples. Our facility will perform the array processing, array scanning, and data export from Illumina’s GenomeStudio software.

Platform: Illumina iScan instrument with Illumina genotyping arrays

Sample Requirement: 4 uL of sample at 50 ng/uL concentration will be used for all arrays except the Omni5 and Omni5Exome, which require 8 uL at 50 ng/uL. Please contact the Genomics Core Facility for instructions on sample submission volume, submission plate layout, and off-campus shipping as this will vary from project to project. Our facility offers Qubit concentration measurement for Illumina iScan projects. Nanodrop or UV spec concentration readings are not acceptable for this platform. Samples should be high quality genomic DNA with minimal fragmentation for best results. A 260/280 OD ratio near 1.8 is recommended. The DNA can be suspended in Tris buffer.

Genotyping Arrays: Illumina offers a variety of arrays to genotype between 300,000 and 5 million SNPs per sample. The least expensive array with 300,000 SNPs can be used to quickly and easily obtain baseline sample datasets for a variety of downstream applications, including common variant, mtDNA, ancestry, sex confirmation, loss-of-variant, indel, and CNV detection studies. The Omni5Exome array with nearly 5 million SNPs delivers the most comprehensive coverage of the genome, providing functional exonic content for whole-genome genotyping and copy number variation (CNV) analysis, along with optimized tag SNPs targeting genetic variation down to 1% minor allele frequency (MAF).

The following table lists some of the more common Illumina BeadChip arrays that our facility processes on the iScan platform. Please note that the number of samples processed on each array varies by array type. For example, the HumanOmniExpress chip processes 24 samples per array while the HumanOmni5 chip processes 4 samples per array. Illumina sells the arrays in kits for specific numbers of samples so be sure to check with the Genomics Core Facility or the Illumina web site to determine the number of kits required to process your sample set. On-campus users should contact the Genomics Core Facility for assistance with ordering the Illumina genotyping array kits. Off campus users will want to contact Illumina and their local Illumina sales specialist to order the array kits and have them shipped to our facility for processing.



Pricing – for 96 or more samples

Samples per chip Final Rate (Internal) Final Rate (External Academic) Final Rate (External commercial)
Core Run Core Run Core Run
4 $127 per sample $194.95 per sample $254.00 per sample
8 $64 per sample $98.24 per sample $128.00 per sample
12 $47 per sample $72.15 per sample $94.00 per sample
24 $26 per sample $39.91 per sample $52.00 per sample

Delivered Product: The Genomics Core Facility will provide you with text files containing genotype calls for your samples. We use Illumina’s GenomeStudio software to analyze the raw data from the instrument and generate the calls. This software can be purchased directly from Illumina if you wish to do additional analysis of the run data. Raw data files can be provided upon request when we are running your project. A variety of third-party analysis software plugins are available for GenomeStudio to export data in file formats compatible these software packages. Please be advised, due to the large sizes of files the iScan generates, we cannot store your data long term. Therefore, please plan on archiving your own data once we release it to you.