Array Products

CIDR offers a variety of Array Products. Specifics are listed below.

GWAS and Custom Products

GWAS chips

Genomic coverage of many of the arrays we offer has been assessed using imputation to Phase3 of the 1000 Genomes Project and detailed in a recent publication. In general, coverage increases with increasing array density.



Array SNPs per Sample Comments
Genotyping by Sequencing – low pass whole genome Low-input The NovaSeqXPlus is used to achieve 0.5X-4X coverage depending on the study aims and population structure.
Illumina Global Diversity Array ~1,900,000 The GDA is built on a high-density single nucleotide polymorphism (SNP) global backbone optimized for cross-population imputation coverage of the genome. The GDA enables polygenic risk score development and characterization of genetic architecture in diverse populations.
Illumina Global Diversity Array with Enhanced PGx ~1,900,000 The Infinium Global Diversity Array with Enhanced PGx supports pharmacogenomics (PGx) research in diverse populations. It is a powerful tool for polygenic risk score development, ancestry determination, and genetic disease research.
Illumina Global Diversity Array with Polygenic Risk Score Content-8 v1.0 ~1,900,000 The Infinium Global Diversity Array with Polygenic Risk Score Content-8 v1.0 is a high-performance microarray featuring ~2.0M markers on the genome-wide backbone of the Infinium Global Diversity Array-8 v1.0, enabling highly accurate, pan-ethnic PRS determination.
Illumina Global Screening Array >650,000 The Global Screening Array combines a highly optimized, genome-wide backbone and hand curated clinical research variants. Coverage information
Illumina Asian Screening Array >650,000 The Asian Screening Array contains a genome-wide backbone developed from 9000 Asian Whole Genomes and clinical research variants.
Illumina H3 Africa Array >2,000,000 The H3 Africa Array is a powerful array for research studies that enables identification of genetic associations with common and rare traits among African populations.

Genotyping by Sequencing

Two recent developments allow the utilization of low pass human whole genome sequencing (lpWGS) data for “genotyping by sequencing”. Imputation methods have been developed which optimize the speed and accuracy of genotype estimation using low-pass whole genome sequencing (lpWGS) and library preparation assays are available at much higher throughput and lower cost. Compared to SNP arrays with pre-selected variant sites which often target specific populations, lpWGS is unbiased in terms of variant sites, limited only by the sites observed in increasingly comprehensive population reference panels. Indeed, studies have shown that lpWGS can increase the power of GWAS1 and has more advantages than arrays in non-European populations2. The emergence of both new reference panels derived from large-scale diverse deep whole genome sequencing (WGS) data and more computationally efficient algorithms designed for imputation and phasing of lpWGS is now making lpWGS possible as a better alternative for SNP arrays1, 3, 4

CIDR has completed a pilot study to validate the practical implementation of this “Genotyping by Sequencing” service, presented at the Advances in Genome Biology and Technology General Meeting.

References:

1. Li, J.H., Mazur, C.A., Berisa, T., Pickrell, J.K. (2021). Low-pass sequencing increases the power of GWAS and decreases measurement error of polygenic risk scores compared to genotyping arrays. Genome Res. 31, 529-537.

2. Martin, A.R., Atkinson, E.G., Chapman, S.B., Stevenson, A., Stroud, R.E., Abebe, T., Akena, D., Alemayehu, M., Ashaba, F.K., Atwoli, L. (2021). Low-coverage sequencing cost-effectively detects known and novel variation in underrepresented populations. The American Journal of Human Genetics 108, 656-668.

3. Rubinacci, S., Ribeiro, D.M., Hofmeister, R.J., Delaneau, O. (2021). Efficient phasing and imputation of low-coverage sequencing data using large reference panels. Nat. Genet. 53, 120-126.

4. Davies, R.W., Kucka, M., Su, D., Shi, S., Flanagan, M., Cunniff, C.M., Chan, Y.F., Myers, S. (2021). Rapid genotype imputation from sequence with reference panels. Nat. Genet. 53, 1104-1111.

Consortium Boosters

Neuro, Psych, Multi-Disease and Confluence Oncology products are available additions to arrays. If you have a project that requires one of them or another array provided by Illumina, please inquire for pricing. Specifics for content can be found on Illumina's website. Consortium Boosters.

Custom

Custom panels can be created using between 3,000 and 1,000,000 SNPs, for any species with sequence information. The minimum number of samples for this to be cost-effective is 1,100.  Custom content can also be added to any of Illumina’s GWAS chips, often at a lower cost than a completely custom chip. Pricing on this product is based on increments of both SNP numbers and sample numbers. Please inquire for pricing.

Note: When selecting SNPs for this platform, one should select as many SNPs as possible within the appropriate increment, as Illumina estimates up to 20% of the selected SNPs will fail the manufacturing process and will not be placed on the custom chip. The SNP number calculations are further complicated by the fact that there are two different forms of the Infinium chemistry, one of which requires two bead types, the other of which requires only one. Bead types need to be counted when the final number of SNPs in selected. This information is provided by Illumina when the SNP selection files are returned.

Methylation

CIDR offers the Infinium MethylationEPIC v2.0 Kit array for methylation profiling studies. The bisulfite conversion necessary for the assay is included for CIDR Program studies.

FFPE samples are supported for MethylationEPIC v2.0 BeadChip.

The Infinium MethylationEPIC v2.0 BeadChip Kit is a genome-wide methylation screening tool that targets over 935,000 CpG sites in the most biologically significant regions of the human methylome, while maximizing backwards compatibility with it's predecessor, MethylationEPIC v1.0. The array maintains the ability to quantitatively interrogate CpGs across the genome at single-nucleotide resolution, while providing highly accurate and precise methylation measurements independently of read depth. Multiple DNA sample types, including those isolated from FFPE, can be analyzed using the streamlined, user-friendly Infinium Methylation assay. Due to the scalability and low total cost per sample compared with alternative methods, large cohorts can be screened using MethylationEPIC v2.0 to discover powerful biological insights into disease mechanisms.

Mouse Linkage Scans

Mouse linkage scans are performed using the Illumina GigaMUGA array, developed at the University of North Carolina at Chapel Hill under the supervision of Fernando Pardo-Manuel de Villena and Leonard McMillan. The GigaMUGA array consists of >140,000 probes with average spacing of 22.5kb. Selection of probes for this array was based on 159 inbred lines.

A complete description of GigaMUGA can be found at: The Mouse Universal Genotyping Array: from substrains to subspecies. Andrew P Morgan, et al G3, Genes, Genomes, Genetics (2015).

Mouse Methylation

CIDR offers the Illumina Infinium Mouse Methylation array for methylation profiling studies. The bisulfite conversion necessary for the assay is included for CIDR Program studies.The Illumina Infinium Mouse Methylation Beadarray features more than 275,000 markers across the methylome. This allows high-resolution epigenetic analyses of diverse murine strains, which is useful for epigenome-wide association studies, xenograft experiments, preclinical research, toxicology, embryology and other applications.

  • High-value content includes:
    • 28,847 transcription start sites
    • miRNA Promotor transcription start sites
    • Noncoding RNA transcription start sites
    • Enhancers
    • Imprinted loci
    • 16,000 CpG islands
    • Hypermethylated regions in cancer
    • 25,000 highly conserved human EPIC array probes
    • Strain-specific SNP probes from 18 mouse strains