We Offer the Full Line of Illumina Genotyping Arrays
Not sure which one to choose? CIDR and the University of Washington have published a paper discussing the usefulness of these arrays for imputation in various populations, which may help with array selection. Please note that the Global Diversity Array (GDA) is an updated version of MEGA, so the information in the paper about MEGA will also be true for GDA.
Global Screening Array
The Infinium Global Screening Array (GSA) 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 array provides a genomic tool for clinical research applications including disease risk profiling studies, pharmacogenomics research, wellness characterization, and complex disease discovery.
Global Diversity Array
The Infinium Global Diversity Array (GDA) 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.
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.
94 – 4,999 samples
94 – 4,999 samples
140 samples or more
Our full service pricing includes:
- Two HapMap controls per 96 well plate
- 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
- Pretesting on the Illumina QC array (15,000 snps used to barcode the sample)
- Prediction of sample performance
- Verification of gender & family relationships
- Problems report provided prior to run on GWAS array
- Opportunity to replace problem samples prior to running the sample on the GWAS array.
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 upload into dbGAP and other databases are available. Please inquire for pricing.