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Microarray Genotyping and Gene Expression Profiling


Microarray was the first high-throughput genome technology developed in the mid-1990s. KMSR offers traditional microarray services to analyze gene expression pattern, DNA sequence polymorphism (SNPs genotyping) and methylation using the Affymetrix GeneChip and/or the Illumina BeadArray systems.

Our gene expression profiling service using the Affymetrix GeneChip system offers multiple array designs to interrogate genome-wide expression profiles of mRNA, lncRNA, and miRNA of human and widely used model species, as well as many agricultural species. Affymetrix’ whole-transcript analysis approach enables researchers to detect not only the level of expression (Clariom S Array), but also precisely what is being expressed, including alternative isoforms or genomic deletions (Clariom D Array).

Besides gene expression profiling, KMSR also offer in-depth copy number variant (CNV) analysis using Affymetrix OncoScan and CytoScan assay, which can start from as little as 80 nanograms of DNA per sample and is designed specifically for use with fixed-formalin paraffin-embedded (FFPE) samples.

The Infinium BeadChip from Illumina enables genotyping projects spanning from moderate scale (around 3,000 SNPs) to genome-wide applications (up to 5 million SNPs), encompassing both custom and predesigned content for human, mouse, and a variety of species. In addition to SNP genotyping, Illumina has developed a robust methylation BeadChip capable of delivering quantitative methylation measurements for both human and mouse samples. KMSR offer both whole genome DNA methylation and genotyping service using Illumina platform. Our services include full automation of BeadChip processing and scanning, enabling the efficient execution of high-throughput population-based studies involving tens of thousands of samples. This approach ensures quick, cost-effective, and reproducible results.

Free analysis software available for both Affymetrix and Illumina microarray services.

  • Transcriptome Analysis Console (TAC) for Affymetrix Gene Expression
  • Chromosome Analysis Suite (ChAS) for Affymetrix OncoScan and CytoScan Assay
  • Genome Studio for Illumina Genotyping Analysis.

Sample Submission

  • Before submitting samples to the KMSR core laboratory, please contact for project specifications. The KMSR team is available to share their experience on working with multiple sample types and provide guidance on the specifics of optimal sample preparation for your study.
    • Please do not deliver or ship samples without first contacting KMSR staff to set-up a delivery time.
  • Complete the service request form and submit request for KMSR services through KMSR online sample submission and tracking system: KMSR PPMS. After service order received and approved by the core staff, prepare samples and deliver/ship to the core lab as described below.
    • Nucleic Acid Isolation and Assessment Service Request Form
  • Samples can be dropped off at our campus locations:
    • Tuesday and Thursday: 300 George St., (Room 2127)
    • Monday, Wednesday, and Friday: 300 Cedar St. (TAC), (Room S352),
    • Samples are picked up at 8 AM.
    • Please complete the sample submission form and place a hard copy in a Ziploc bag along with your samples.
  • Shipping information
    • *Please send the tracking information to
    • Yale Center for Genome Analysis
      Keck Microarray Shared Resource
      ATTN: Guilin Wang/Evelyn Ng
      830 West Campus Dr.
      West Haven, CT 06516

Service Fees

Rates as of 7/1/2023

Illumina Microarrays Service Prices

Services Yale Fee Non-Yale* Fee
Ill Infinium Genotyping $34 $52
Ill Methylation EPIC (includes bisulfite conversion) $49 $71
Ill FFPE Restoration and QC $36 $50

When considering an Illumina Infinium project, pricing encompasses two main components: 1) the BeadChip kit, including stock or custom SNP microarrays and processing reagents, and 2) the cost of BeadChip processing, assessed on a per-sample basis. Our processing cost only covers the second part. User would need to purchase the BeadChip kit from Illumina and send it to us directly.

Affymetrix Service Prices

Services Yale Fee Non-Yale* Fee
Affy WT (Whole Transcript) Assay* $99 $170
Affy miRNA Assay $158 $356
Affy OncoScan/CytoScan Assay (min 8 samples) $242 $327
Misc: Sample QC $22 $36