Global Diversity Array Global Screening Array Multi-Ethnic Global Array (MEGA)
CIDR and the University of Washington have published a paper discussing the usefulness of these arrays for imputation in various populations, which may help you with your selection of an array.
See pricing details for a description of what is included in the prices listed below.
Human CytoSNP12 Chip: The HumanCytoSNP-12 BeadChip is designed to scan the whole genome in an efficient, high-throughput analysis of genetic and structural variations that are most relevant to human disease. Resolution is better than with FISH or CGH. The chip can be used to detect duplications, deletions, amplifications, copy-neutral LOH and mosaicism. The panel contains 200,000 “best of the best” SNPs with high tagging power, and includes dense coverage around the 250 genomic regions commonly screened in cytogenetics laboratories.
Human CytoSNP850 Chip: The HumanCytoSNP-850 BeadChip features nearly 850,000 SNPs that have been chosen with input from the international cytogenetics community and peer-reviewed literature to optimize used for constitutional and cancer studies. Coverage is enriched for dosage sensitive genes and designed to pick up challenging mosaics.
|Number of Samples||Cyto12||Cyto850|
|49 or 94||$225/sample||$345/sample|
|5001 or more||Please inquire||Please inquire|
|FFPE restore||Add $100/sample||Add $100/sample|
Global Diversity Array
The Infinium Global Diversity Array is the commercial version of the array chosen by the All of Us Research program. This array was designed to meet the needs of the program’s goals of genotyping the rich diversity of the United States. As such, the markers chosen for the array combine highly optimized multi-ethnic, genome-wide content with curated clinical research variants. The array is highly informative, with a backbone optimized for cross-population imputation coverage of the genome. It also enables polygenic risk score development and characterization of genetic architecture in diverse populations.
|Pricing Without Pretesting||Full Service Pricing|
|94 - 5000 samples||$130/sample||$145/sample|
Global Screening Array
The Infinium Global Screening Array combines multi-ethnic genome-wide content, curated clinical research variants, and quality control (QC) markers for precision medicine research.
The 640,000 genome-wide markers were selected for high imputation accuracy at minor allele frequencies of >1% across all 26 1000 Genomes Project populations. The clinical research content includes variants with established disease associations, relevant pharmacogenomics markers, and curated exonic content based on ClinVar, NHGRI, PharmGKB, and ExAC databases. Quality control content enables sample identification and tracking for large-scale genomics and screening applications.
The array provides a genomic tool for clinical research applications including disease risk profiling studies, pharmacogenomics research, wellness characterization, and complex disease discovery.
|Number of Samples||Standard content|
|94 - 5000||$110/sample|
|5001 or more||Please inquire|
Human Core Product Line
Human Core BeadChip: The HumanCore BeadChip contains about 240,000 highly informative genome-wide tag SNPs found across diverse world populations and an additional 20,000 high-value markers. It is ideal for obtaining baseline sample datasets for downstream applications: common variant, mtDNA, ancestry, sex confirmation, loss of variant, indel, linkage and CNV detection. It can be ordered with Exome content or customized with up to 200,000 SNPs for an additional charge.
|Number of Samples||Standard content, without pretesting||Standard content, full service||Standard + Exome Content, without pretesting||Standard + Exome Content, full service|
|94 - 5000||$100/sample||$135/sample||$105/sample||$140/sample|
|5001 or more||Please inquire||Please inquire||Please inquire||Please inquire|
Human Multi-Ethnic Global Array (MEGA) Product Line
Human Multi-Ethnic Global Array: Consortium partners developed content for this multi-ethnic global genotyping array using tagging strategies with the power to perform more effective association studies in diverse populations. The novel algorithm selects population-specific and transethnic tag SNPs that maximize imputation accuracy, as imputation has become a standard practice in the interpretation of genotyping data and allows for more accurate statistical inference of genotypes not directly genotyped.
Human Multi-Ethnic EUR/EAS/SAS BeadChip: The Infinium Multi-Ethnic EUR/EAS/SAS chip provides a multi-purpose, multi-ethnic genotyping array focused on European, East Asian, and South Asian populations.
Human Multi-Ethnic AMR/AFR BeadChip: The Infinium Multi-Ethnic AMR/AFR chip provides a multi-purpose, multi-ethnic genotyping array focused on Hispanic and African American populations.
With > 1.4 million expertly selected markers, either of these arrays enable identification of genetic associations with common and rare traits, providing insight to epidemiologists, health care researchers, population geneticists, and genomic researchers.
|Number of Samples||Standard Content||Regional only content (either chip)|
|5001 or more||Please inquire||Please inquire|
Human Omni Product Line
HumanOmni Express, 2.5 and 5M chips are still available as products, but are used less frequently in the current genotyping environment, due to the informatic improvements made in the SNPs selected for the newer arrays. If you have a project that requires one of them, please inquire for pricing.
For GWAS projects with more than 94 samples, our full service pricing includes:
- Pretesting with the Illumina QC array (15,000 snps used to barcode the sample and verify the GWAS dataset released matches the sample submitted, as well as used to verify gender, family relationships, sample performance).
- Identification of problems and replacement of problem samples before running the sample on the GWAS arrays.
- Two HapMap controls per 96 well plate and 1 blind duplicate every other plate.
- Repetition of any sample which has less than a 96.5% call rate for an Illumina array. We attempt the GWAS assay only twice.
- Full data release, which includes hapmap concordance, reproducibility of genotype calculations broken down by MAF bin for each sample pair, GenomeStudio project, SNP and samples tables, full SNP technical filter applied, samples reclustered on own data, final reports, PLINK file and README docs explaining the data in each directory
Other pricing options exist, including ones with no controls or redos, no pretesting, raw data only and combinations of each of these. Please inquire for pricing for these other options.
Assistance with plate map design, data cleaning, imputation and assistance with upload into dbGAP and other databases are available. Please inquire for pricing.