Infinium CytoSNP-850K BeadChip

A consortium-built SNP-based microarray providing thorough coverage of 3262 cytogenetically relevant genes for constitutional and cancer research.

960 samples/week on an iScan System (with automation, 24 BeadChips/batch, and 2 batches/FTE/Tecan per week). 128 samples/week on a NextSeq 550 System (with 8 BeadChips/batch and 2 batches/FTE/Tecan per week).

Sample throughput

8 samples per array

Number of samples

Fixed markers: ~848,000 Custom marker add-on capacity: none

Number of markers

See full details in the specifications table

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.


Specifications


Required products

Match your chosen kit size to the number of samples you run at a time. Each kit is processed as a single batch and is not designed to be divided across multiple experiments. If you are processing several low-throughput batches, order multiple small kits.

/ Results

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

1
Select array

Infinium CytoSNP-850K BeadChip

2
Process and scan arrays
3
Analyze


Related applications and methods

Compare

Infinium CytoSNP-850K BeadChip Infinium Global Diversity Array with Cytogenetics-8 Infinium Global Screening Array with Cytogenetics-24
Assay time 3 days 3 days 3 days
Assay type Infinium HD Super
Automation capability Liquid handling robots, Automated array loader Liquid handling robots, Automated array loader Liquid handling robots, Automated array loader
Cancer type Hematologic, Solid Tumor Hematologic, Solid Tumor Hematologic, Solid Tumor
Description The Infinium CytoSNP-850K BeadChip enables high-resolution analysis for discovery of meaningful chromosomal aberrations through disease-focused coverage of 3262 genes of known cytogenetics relevance. The 8-sample Infinium Global Diversity Array with Cytogenetics-8 provides extensive targeted coverage of more than 4800 key genes across the genome. Approximately 1.8M markers are included on the BeadChip for high exonic coverage in regions of disease relevance, providing highly accurate copy number variation calls, and an average resolution of 1.5Mb. The 24-sample Infinium Global Screening Array with Cytogenetics-24 provides targeted coverage of more than 4800 key genes across the genome. Approximately 700K markers are included on the BeadChip for high exonic coverage in regions of disease relevance, providing highly accurate copy number variation calls, and an average resolution of 2.5Mb.
Hands-on time

1 hr 5 min for automated 8-beadchip workflow, 6 hr 15 min for manual 8-beadchip workflow

1 hour and 5 minutes for automated 8-beadchip workflow 1 hour and 5 minutes for automated 8-beadchip workflow
Input quantity 200 ng DNA 200 ng DNA 200 ng DNA
Instruments NextSeq 550 System, iScan System iScan System iScan System
Method Cytogenomic array, Genome-wide genotyping array Cytogenomic array, Genome-wide genotyping array High-throughput genotyping array, Cytogenomic array
Nucleic acid type DNA DNA DNA
Number of markers Fixed markers: ~848,000
Custom marker add-on capacity: none
Number of samples 8 samples per array 8 samples per array 24 samples per array
Sample throughput

960 samples/week on an iScan System (with automation, 24 BeadChips/batch, and 2 batches/FTE/Tecan per week).

128 samples/week on a NextSeq 550 System (with 8 BeadChips/batch and 2 batches/FTE/Tecan per week).

Specialized sample types FFPE Tissue, Blood, Saliva Blood, FFPE Tissue, Buccal Swabs, Saliva Blood, FFPE Tissue, Buccal Swabs, Saliva
Species category Human Human Human
Technology Microarray Microarray Microarray
Variant class Single nucleotide polymorphisms (SNPs), Loss of heterozygosity (LOH), Chromosomal abnormalities, Copy number variants (CNVs) Single nucleotide polymorphisms (SNPs), Loss of heterozygosity (LOH), Chromosomal abnormalities, Copy number variants (CNVs) Single nucleotide polymorphisms (SNPs), Loss of heterozygosity (LOH), Chromosomal abnormalities, Copy number variants (CNVs)

Selection tools:

Figures

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 categoriesb 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

Resources

Thumbnail

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

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.

Sign in to add to cart or see pricing.

List Price:

Discounts:

Showing of

Selection summary

Product

Qty

Unit Price

FAQs

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.

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

/ Results

Order the NovaSeq X Series

Advanced chemistry, optics, and informatics combine to deliver exceptional speed and data quality, outstanding throughput and scalability.

MiSeq Reagent Kit v3

Optimized reagent kit that provides increased cluster density and read length, improving sequencing quality scores compared to earlier versions.

TruSight Oncology 500

Enable CGP with a large pan-cancer panel covering all major variant classes plus gene signatures (TMB, MSI, and HRD) from FFPE tissue.

Illumina DNA Prep

A fast, integrated workflow for preparing libraries for use in a wide range of sequencing applications.

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.

Speak with a specialist

Reach out for information about our products and services, or get answers to questions about our technology.