Overview
The Infinium CytoSNP-850K BeadChip is the first SNP-based human microarray to leverage the latest input from the international community for cytogenomics studies.
Key features
Thorough coverage containing ~ 850K SNPs with 15× redundancy and enriched coverage for 3262 dosage-sensitive genes
Reproducible data with a broad range of sample types, including FFPE
Powerful analysis software provides an integrated framework for analyzing data
Expert-informed comprehensive coverage
The gene list was defined based on content from the International Collaboration for Clinical Genomics (ICCG)1 and the Cancer Genomics Consortium (CGC)2, providing a thorough view of cytogenomic activity.
High detection sensitivity for low-level mosaics
The use of long 50-mer probes with high specificity to the SNP target increases sensitivity for low-level mosaics3 and offers high resolution for copy-neutral loss of heterozygosity (LOH). High 15× bead redundancy increases the signal-to-noise ratio for making accurate CNV and absence of heterozygosity (AOH) calls across the genome.
Applications
The Infinium CytoSNP-850K BeadChip microarray includes ~850K SNPs spanning the genome and provides enriched coverage for 3262 genes of known relevance to enable researchers to study the impact of chromosomal aberrations for constitutional and cancer applications.
Example workflow
Infinium CytoSNP-850K BeadChip
iScan System
NextSeq 550 System
Related applications and methods
Cytogenomics
Together, next-generation sequencing and arrays enable cytogenomic analysis of chromosome aberrations for constitutional and cancer research.
Chromosomal microarray analysis for constitutional cytogenetics
Chromosomal microarrays reliably detect copy number and allelic contribution imbalances associated with constitutional disorders.
Cancer research
Illumina NGS and microarray technologies for cancer research are helping drive the revolution in cancer genomics.
Infinium CytoSNP-850K BeadChip coverage
The Infinium CytoSNP-850K BeadChip contains ~ 850K empirically selected single nucleotide polymorphisms (SNPs) spanning the genome. This high density of SNPs enables high-resolution analysis for discovery of meaningful chromosomal aberrations.
Probe spacing: Average distance
Targeted region probe spacing: ~1 kb
Targeted region resolution: ~10 kb
Genomic backbone probe spacing: ~5 kb
Overall probe spacing: ~1.8 kb
Overall effective resolution: ~18 kb
Infinium CytoSNP-850K BeadChip marker informationª
Marker categories b: iScan System
Total no. of markers: 848,902
RefSeq genes: 467,422
RefSeq +/- 10 kb: 541,515
ADME genes: 15,153
ADME +/- 10 kb: 18,590
COSMIC genes: 418,131
HLA markers: 5145
HLA genes: 276
GO genes: 137,873
Exonic regions: 68,801
Promoter regions: 26,814
X chromosome markers: 29,894
Y chormosome markers: 1197
PAR/homologous markers: 728
a. Values are obtained from the assay manifest file. Variations are due to different manifests/product files required to process the BeadChip for each instrument.
b. Compared against the human genome issue hg19 reference genome. Abbreviations: ADME, adsorption, distribution, metabolism, excretion; COSMIC, catalog of somatic mutations in cancer; MHC, major histocompatibility complex; HLA, human leukocyte antigen; PAR, pseudoautosomal region
Celebrating Infinium Array-powered progress
Learn about the comprehensive suite of Infinium microarray products designed to deliver exceptional data quality and high-density genomic coverage for targeted and whole genome studies.
Infinium CytoSNP-850K v1.4 Beadchip Kit (8 Samples)
20103480
Optimized for constitutional and cancer cytogenetics applications. The BeadChip can process 8 samples and analyze 850,000 single nucleotide polymorphisms (SNPs) for both copy number variants (CNVS) and absence of heterozygosity (AOH). Each package contains 1 BeadChip, along with reagents for amplifying, fragmenting, hybridizing, labeling, and detecting CNVs and AOH for 8 DNA samples. View less
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Infinium CytoSNP-850K v1.4 Beadchip Kit (16 Samples)
20103481
Optimized for constitutional and cancer cytogenetics applications. The BeadChip can process 8 samples and analyze 850,000 single nucleotide polymorphisms (SNPs) for both copy number variants (CNVS) and absence of heterozygosity (AOH). Each package contains 2 BeadChips, along with reagents for amplifying, fragmenting, hybridizing, labeling, and detecting CNVs and AOH for 16 DNA samples. View less
Infinium CytoSNP-850K v1.4 Beadchip Kit (48 Samples)
20103482
Optimized for constitutional and cancer cytogenetics applications. The BeadChip can process 8 samples and analyze 850,000 single nucleotide polymorphisms (SNPs) for both copy number variants (CNVS) and absence of heterozygosity (AOH). Each package contains 6 BeadChips, along with reagents for amplifying, fragmenting, hybridizing, labeling, and detecting CNVs and AOH for 48 DNA samples. View less
Infinium CytoSNP-850K v1.4 Beadchip Kit (96 Samples)
20103483
Optimized for constitutional and cancer cytogenetics applications. The BeadChip can process 8 samples and analyze 850,000 single nucleotide polymorphisms (SNPs) for both copy number variants (CNVS) and absence of heterozygosity (AOH). Each package contains 12 BeadChips, along with reagents for amplifying, fragmenting, hybridizing, labeling, and detecting CNVs and AOH for 96 DNA samples. View less
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Can FFPE samples be analyzed with the Infinium CytoSNP-850K Array?
FFPE samples can be run on CytoSNP-850K with the Infinium FFPE QC Kit and the Infinium FFPE Restore Kit .
FFPE-specific manifest and cluster files can be downloaded on the CytoSNP-850K support page .
How do I batch import Infinium CytoSNP-850K data?
A batch Import file can be created using the CytoSNP-850K Lab Planner tool . Once the batch import .txt file has been generated, go to File|Batch|Batch Import, locate the batch import file, then click Open.
More information can be found in the Import 24sure and BeadArray Experiments section of the BlueFuse Multi Software Guide .
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References :
1. Clinical Genome Resource. www.clinicalgenome.org . Accessed December 12, 2022.
2. Cancer Genomics Consortium. www.cancergenomics.org . Accessed December 12, 2022.
3. Conlin LK, Thiel BD, Bonnemann CG, et al. Mechanisms of mosaicism, chimerism and uniparental disomy identified by single nucleotide polymorphism array analysis . Hum Mol Genet. 2010;19(7):1263-75. doi: 10.1093/hmg/ddq003.
