Overview

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.

Human Genotyping Arrays

Chip Name Approx. Number of Markers Samples per Chip Illumina Kit Minimum Sample Order Illumina Kit Cost-per-Sample Core Lab Processing Cost-per-Sample University of Utah Core Lab Processing Cost-per-Sample Off-campus Academic Core Lab Processing Cost-per-Sample Commercial Illumina Link
Human Omni5 Exome 4.5 million 4 16 $278 $109.00 $164.59 $218.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-exome.html
Human Omni5-Quad 4.3 million 4 16 $278 $109.00 $164.59 $218.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-omni5-quad.html
Human Omni2.5 Exome-8 2.6 million 8 16 $177 $55.00 $83.05 $110.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-omni25-exome-8.html
Human Omni2.5-8 2.3 million 8 16 $172 $55.00 $83.05 $110.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-omni25-8.html
Human Multi-Ethnic Global-8 1.7 million 8 16 $119 $55.00 $83.05 $110.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-multi-ethnic-global.html
Human Multi-Ethnic EUR/EAS/SAS-8 1.5 million 8 16 $109 $55.00 $83.05 $110.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-multi-ethnic-eur-eas-sas.html
Human Multi-Ethnic AMR/AFR-8 1.4 million 8 16 $109 $55.00 $83.05 $110.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-multi-ethnic-amr-afr.html
Human OmniExpress Exome 958,000 8 16 $109 $55.00 $83.05 $110.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-omni-express-exome.html
Human OmniZhongHua-8 878,000 8 16 $110 $55.00 $83.05 $110.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-omni-zhonghua.html
HumanCytoSNP-12 300,000 12 12 $155 $40.00 $60.40 $80.00 https://www.illumina.com/products/by-type/clinical-research-products/human-cytosnp-12.html
Human OmniExpress-24 710,000 24 48 $94 $22.00 $32.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-omni-express.html
Human PsychArray-24 590,000 24 48 $65 $22.00 $32.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-psycharray.html
Human Core Exome-24 551,000 24 48 $54 $22.00 $32.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-core-exome.html
Human OncoArray-500K 500,000 24 48 $65 $22.00 $32.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-oncoarray-500k.html
Human DrugDev Consortium Array 485,000 24 Contact Illumina Contact Illumina $22.00 $32.22 $44.00 https://www.illumina.com/science/consortia/human-consortia/drug-development-consortium.html
HumanCore-24 306,000 24 48 $49 $22.00 $32.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-core.html
Human ImmunoArray-24 254,000 24 48 $43 $22.00 $32.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-immunoarray.html
Human Exome-24 243,000 24 48 $47 $22.00 $32.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-exome.html

Human Methylation Arrays

Chip Name Approx. Number of Markers Samples per Chip Illumina Kit Minimum Sample Order Illumina Kit Cost-per-Sample Core Lab Processing Cost-per-Sample University of Utah Core Lab Processing Cost-per-Sample Off-campus Academic Core Lab Processing Cost-per-Sample Commercial Illumina Link
Human MethylationEPIC 850,000 8 16 $330 per sample ($363 per sample for 16 sample kit) $55.00 $83.05 $110.00 https://www.illumina.com/products/by-type/microarray-kits/infinium-methylation-epic.html

Agrigenomics Commercial Infinium Arrays

Chip Name Approx. Number of Markers Samples per Chip Illumina Kit Minimum Sample Order Illumina Kit Cost-per-Sample Core Lab Processing Cost-per-Sample University of Utah Core Lab Processing Cost-per-Sample Off-campus Academic Core Lab Processing Cost-per-Sample Commercial Illumina Link
Cow BovineLD 7,900 24 48 $32 $22.00 $33.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/bovineld.html
Cow Bovine SNP50 53,000 24 48 $90 $22.00 $33.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/bovine-snp50.html
Cow BovineHD 777,000 8 48 $150 $55.00 $83.05 $110.00 https://www.illumina.com/products/by-type/microarray-kits/bovinehd.html
Dog CanineHD 172,000 12 48 $125 $40.00 $60.40 $80.00 https://www.illumina.com/products/by-type/microarray-kits/caninehd.html
Corn Maize SNP50 50,000 24 48 $90 $22.00 $33.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/maize-snp50.html
Corn MaizeLD 3,000 24 48 $28 $22.00 $33.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/maize-ld.html
Pig Porcine SNP60 64,000 24 48 $90 $22.00 $33.22 $44.00 https://www.illumina.com/products/by-type/microarray-kits/porcine-snp60.html
Sheep Ovine SNP50 54,000 12 48 $90 $40.00 $60.40 $80.00 https://www.illumina.com/products/by-type/microarray-kits/ovine-snp50.html

GeneSeek Genomic Profiler (GGP) Genotyping Arrays

Chip Name Approx. Number of Markers Samples per Chip Illumina Kit Minimum Sample Order Illumina Kit Cost-per-Sample Core Lab Processing Cost-per-Sample University of Utah Core Lab Processing Cost-per-Sample Off-campus Academic Core Lab Processing Cost-per-Sample Commercial Illumina Link
GGP Bovine 150K Array 134,000 24 288 $60 $22.00 $33.22 $44.00 https://www.illumina.com/products/ggp-whole-genome-genotyping-arrays.html
GGP Bos Indicus HD Array 74,000 24 288 $59 $22.00 $33.22 $44.00 https://www.illumina.com/products/ggp-whole-genome-genotyping-arrays.html
GGP Bovine LD Array 26,000 24 288 $30 $22.00 $33.22 $44.00 https://www.illumina.com/products/ggp-whole-genome-genotyping-arrays.html
GGP Porcine HD Array 70,000 24 288 $35 $22.00 $33.22 $44.00 https://www.illumina.com/products/ggp-whole-genome-genotyping-arrays.html
GGP Porcine LD Array 10,000 24 288 $25 $22.00 $33.22 $44.00 https://www.illumina.com/products/ggp-whole-genome-genotyping-arrays.html
GGP Mouse GIGA_MUGA Array 140,000 24 288 $110 $22.00 $33.22 $44.00 https://www.illumina.com/products/ggp-whole-genome-genotyping-arrays.html
GGP Equine Array 65,000 24 288 $70 $22.00 $33.22 $44.00 https://www.illumina.com/products/ggp-whole-genome-genotyping-arrays.html
GGP Potato Array 8,000 24 288 $45 $22.00 $33.22 $44.00 https://www.illumina.com/products/ggp-whole-genome-genotyping-arrays.html

Open Consortia Infinium Arrays

Chip Name Approx. Number of Markers Samples per Chip Illumina Kit Minimum Sample Order Illumina Kit Cost-per-Sample Core Lab Processing Cost-per-Sample University of Utah Core Lab Processing Cost-per-Sample Off-campus Academic Core Lab Processing Cost-per-Sample Commercial Illumina Link
Alfalfa Forage Genetics Alfalfa 10,500 24 288 Contact Illumina $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Apple Fruitbreedomics Apple20k 20,000 24 96 $74 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Apple RosBREED Apple 20,000 24 96 $74 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Brassica International Brassica SNP Consortium 52,000 24 48 $68 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Cherry RosBREED Cherry 6,000 24 48 $77 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Cotton International Cotton SNP Consortium 70,000 24 288 $78 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Goat International Goat Genome Consortium 60,000 24 48 $109 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Grape GrapeReSeq Consortium 20,000 24 96 $74 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Peach RosBREED Peach 9,000 24 48 $72 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Pepper UCD TraitGenetics Pepper (Capsicum) Consortium 19,000 24 192 $78 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Potato SOLCAP Potato 2013 10,000 24 48 $60 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Sheep AgResearch OvineLD Imputation Tool 6,000 24 96 $72 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Soybean BARCSoySNP6k 6,000 24 192 $45 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Tomato SolCAP Tomato 2013 9,000 24 48 $60 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html
Wheat US/Australia 9k Wheat Consortium 9,000 24 48 $61 $22.00 $33.22 $44.00 https://www.illumina.com/areas-of-interest/agrigenomics/consortia.html

Closed Consortia Infinium Arrays

Chip Name Approx. Number of Markers Samples per Chip Illumina Kit Minimum Sample Order Illumina Kit Cost-per-Sample Core Lab Processing Cost-per-Sample University of Utah Core Lab Processing Cost-per-Sample Off-campus Academic Core Lab Processing Cost-per-Sample Commercial Illumina Link
Barley Barley Consortia 2013 7,864 24 48 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com
Bean USDA Common BeanCAP 5,398 24 288 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com
Chicken Cobb Vantress Chicken 50k 57,636 24 48 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com
Deer Uni Edinburgh-AgResearch Deer Consortium 60,000 24 288 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com
Cat MORRIS ANIMAL FOUNDATION Feline 62,897 24 192 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com
Bird Great Tit WUR_Sheffield Great Tit 9,913 24 48 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com
Oat Oat Consortium 4,975 24 48 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com
Sunflower KWS-TraitGenetics Private Sunflower 30,000 24 288 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com
Sunflower Private Sunflower Consortium 9,480 24 288 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com
Wheat Private Wheat90k KSU 81,587 24 48 Contact Illumina $22.00 $33.22 $44.00 consortiamanager@illumina.com

 

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.[/vc_column_text][/vc_column][/vc_row]