Infinium Methylation Screening Array-48 Kit

Ultra-scalable methylation array optimized for population health research. Ideal for studies >1,000 samples, up to millions of samples.

16,128

Sample throughput

48

Number of samples

See full details in the specifications table

Overview

The Infinium Methylation Screening Array is an affordable and highly scalable epigenomics tool for population health research. 

Key features

Highly informative content for common disease in human populations

  • ~270K unique methylation sites selected from mining over a decade of research from methylation arrays and sequencing studies and databases

  • Comprehensive coverage of DNA methylation sites implicated in genetic diseases, environmental exposures, aging, and development

  • Coverage of emerging functional genomics markers, including cell-type specific methylation, intermediate methylation, correlated regions of systemic interindividual variation (CoRSIVs), and more

Exceptional sample processing efficiency

  • Process up to 600,000 samples/year on a single iScan System with automation

  • Lower sample processing costs with 48-sample BeadChip and automation

Reliable methylation data and simple informatics

  • Precise, read-depth independent DNA methylation measurements results in > 98% beta value reproducibility between replicate samples

  • Straightforward data analysis with free, easy-to-use third-party packages


Specifications


Required products

The Infinium Automated Pipetting System with ILASS and iScan are required for the EX Methylation workflow. The Infinium EX/ XT starter kit is required for customers who are new to Infinium and do not already have a XT starter kit. The AutoLoader 2.x is an optional device for automatic loading of beadchips onto the iScan.

/ Results

Applications

The Methylation Screening Array enables affordable, large-scale epigenetic analysis for population health studies.

Example workflow


Related applications and methods

Compare

Infinium Methylation Screening Array-48 Kit Infinium MethylationEPIC v2.0 Kit
Automation capability Liquid handling robots, Automated array loader Automated array loader
Description Highly scalable and affordable methylation analysis of known common disease associations for population health applications. Ideal for studies >1,000 samples and up to millions of samples. The Infinium MethylationEPIC v2.0 BeadChip is a genome-wide methylation analysis tool with enhanced, expert-selected functional content. The kit is processed on the iScan or NextSeq 550 Systems and follows a straightforward, user-friendly workflow that does not require sample pooling and indexing.
Input quantity 50 ng DNA 250 ng DNA
Instruments iScan System NextSeq 550 System, NextSeq 550Dx in Research Mode, iScan System
Method Methylation array Methylation array
Nucleic acid type DNA DNA
Number of samples 48 samples per array 8 samples per array
Sample throughput 16,128 samples per week 3024 samples per week on a single iSCAN
Specialized sample types Low-input samples Blood, FFPE tissue
Species category Human Human
Technology Microarray Microarray
Variant class Differentially methylated cytosines Differentially methylated cytosines

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Figures

Highly reproducible methylation results—(A) Methylation results are highly correlated between Infinium Methylation Screening Array and Infinium MethylationEPICv2.0 BeadChips. (B) Methylation results demonstrate excellent reproducibility between replicate samples analyzed on the Infinium Methylation Screening Array.

Markers on the Infinium Methylation Screening Array are highly enriched in known trait-associated CpGs across diverse trait types—Markers on the Methylation Screening Array (MSA) are selected based on evidence for trait association, shown in comparison with trait enrichment on Infinium MethylationEPICv2.0 (EPICV2).

Infinium Methylation Screening Array-48
Targeted methylation screening for population health research
Recommended applications Common disease research (noncancer)
Environmental epidemiology
Population genomics
Consumer genomics
Content focus Known common disease trait associations
Known environmental exposure associations
Cell-type specific methylation
Intermediate methylation
Multiomic capabilities to measure high MAF SNPs
Total methylation sites 270K
Number of samples per BeadChip 48
DNA input requirement 50 ng
Assay chemistry Infinium EX Methylation
Instrument support iScan
iScan System maximum sample throughputa 16,128 samples/week
Liquid Handling Automation Infinium Automated Pipetting System with
ILASS (required)

a Approximate values, scan times, and maximum throughput will vary depending on laboratory and system configurations. Sample throughput listed here is achieved with integration of AutoLoader 2.x automated array loading.

High-level comparison of Infinium Methylation Screening Array and Infinium MethylationEPICv2.0 BeadChip content

  Infinium Methylation Screening Array Infinium MethylationEPIC v2.0
Total unique sites 269,094 930,301
CpG 262,470 926,849
From Infinium methylation arrays 161,569 -
From sequencing studies and databases 101,901 -
CpH 2776 2914
From Infinium methylation arrays 308 -
From sequencing studies and databases 2468 -
SNP rsID 3848 538
From Infinium methylation arrays 64  
From sequencing studies and databases 3784  

Previously validated trait-associated content on Infinium Methylation Screening Array

Trait category No. of probes targeting trait association
Development/aging 102,533
Environmental exposures 44,043
Inflammation/autoimmune diseases 41,894
Ancestry 31,843
Sex 23,806
Infectious diseases 14,844
Metabolic diseases 13,739
Rare genetic disorders 13,429
Neurological/neurodevelopmental diseases 8874
Body features (body morphology) 8109
Psychiatric disorders 7280
Cardiovascular disease 7007
Reproductive biology/health 6999
Neurodegenerative diseases 4733
Lung/respiratory diseases 1748
Renal disease 982

Infinium Methylation Screening Array-48 Kit (48 samples)

20112611

Optimized methylation array with 270K markers for high-throughput common disease research & screening. Kit contains 1 48-sample BeadChip and all required reagents for processing 48 samples after bisulfite conversion. Requires iScan System and Infini

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Infinium Methylation Screening Array-48 Kit (96 samples)

20112612

Optimized methylation array with 270K markers for high-throughput common disease research & screening. Kit contains 2 48-sample BeadChips and all required reagents for processing 96 samples after bisulfite conversion. Requires iScan System and Infin

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Infinium Methylation Screening Array-48 Kit (1,152 samples)

20112613

Optimized methylation array with 270K markers for high-throughput common disease research & screening. Kit contains 24 48-sample BeadChips and all required reagents for processing 1,152 samples after bisulfite conversion. Requires iScan System and I

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Methylation Screening Array semi-custom kits (3)

Inf Methyl Screening Array+ Kit (48 Spl)

20119540

Reagent kit for 48 samples. Contains 1 48-sample BeadChip and all required reagents for EX Methylation Assay after bisulfite conversion. Sample processing requires the iScan System and Infinium Automated Pipetting System with ILASS.

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Inf Methyl Screening Array+ Kit (96 Spl)

20119541

Reagent kit for 96 samples. Contains 2 48-sample BeadChips and all required reagents for EX Methylation Assay after bisulfite conversion. Sample processing requires the iScan System and Infinium Automated Pipetting System with ILASS.

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Inf Methyl Screening Array+ Kit (1152 Spl)

20119542

Reagent kit for 1,152 samples. Contains 24 48-sample BeadChips and all required reagents for EX Methylation Assay after bisulfite conversion. Sample processing requires the iScan System and Infinium Automated Pipetting System with ILASS.

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FAQs

The Infinium MethylationEPIC v2.0 BeadChip offers a comprehensive genome-wide discovery tool with ~930K CpG sites covering >99% RefSeq genes with promoter and enhancer-focused content. The Infinium MethylationEPIC v2.0 BeadChip is ideal for projects in which methylation profiling across all genes and promoter regions is desired for maximum discovery power. It is also ideal for all oncology applications due to its coverage of critical oncogenes, compatibility with FFPE tissue, and copy number variation profiling capabilities.

The Infinium Methylation Screening Array offers a more cost-effective methylation screening tool for the study of common disease for population health projects. The ~270K methylation sites are focused on known trait associations from epigenome-wide association studies over the past decade, as well as novel content covering cell-type specific methylation, intermediate methylation, CoRSIVs, SNPs, and more. The Infinium Methylation Screening Array is ideal for large-scale epigenome-wide association studies (EWAS) and biobank screening projects.

A comprehensive product comparison table can be found on the Infinium Methylation Screening Array datasheet.

Yes, the Methylation Screening Array requires the EX Methylation workflow while the EPICv2.0 uses HD Methylation workflow. EX Methylation delivers new sample processing efficiencies enabled by the 48 sample EX BeadChip and automation., and has a lower DNA input of 50ng. The EX Methylation workflow requires the Infinium Automated Pipetting System with ILASS for automated liquid handling.

While the Illumina product manifest file provides basic genomic mapping annotations, the Zhou Lab Infinium Annotations GitHub page provides detailed annotations including trait associations covered on the Infinium Methylation Screening Array.

The Infinium Methylation Screening Array is not recommended for oncology applications due to the following reasons:

· FFPE compatibility unvalidated

· Does not have sufficient coverage of probes for widely-used cancer classifiers

· Does not cover MGMT promoter methylation

· Limited ability to profile copy number variations

· Larger minimum batch size of 48 samples per BeadChip may result in longer turnaround times for results

Illumina offers user friendly tools to analyze Infinium controls built into the Methylation Screening Array. For more information visit the Methylation Array Data Analysis Tips page.

Yes, service labs can use the GenomeStudio Methylation Module Controls Dashboard for assessing assay performance. For downstream methylation analysis, Bioconductor packages such as SeSAMe are recommended.

The scan takes ~20 minutes per BeadChip.

/ Results

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