Microarray Business Division


Macrogen provides various gene analysis services using precise DNA microarray technology. Known by various terms such as DNA chip, biochip and gene-array, microarray is a technology that measures the expression pattern of genes and verifies whether there is a mutation by arranging invisible probes on a chip and reacting DNA, RNA, protein, etc. For microarray analysis, correct execution of tests and the capacity to correctly select significant genetic information from test results, as well as the technology to integrate probes in high density and produce them in a small chip form, are essential.

Macrogen is the only company in Korea that has all the products of Illumina, Affymetrix and Agilent, which are the main suppliers of microarray products. Based on such equipment and on our extensive test and analysis experience, we offer genetic-testing services for research purposes such as mRNA, miRNA, SNP, CGH and DNA methylation.

microarray

Expression Microarray

mRNA Expression Microarray


Microarray

mRNA (messenger RNA) is a type of RNA produced when DNA goes through transcription. mRNA includes the coding region that contains protein information. Analysis of mRNA’s expression pattern is crucial to finding the gene that carries out the main function in a certain environment and the gene’s pathway.

With an mRNA expression microarray, tests are performed for the mRNA analysis of various organisms and significant genes can be selected by conducting a statistical analysis of the data obtained from the tests.

Expression Microarray Platforms

Manufacturer Specimen Platform
Agilent
  • Human
  • Mouse
  • Rat
  • Model Org/non-Human
SurePrint G3 Gene Expression
SurePrint G3 Exon
Customisation
Others
Affymetrix Gene ST (Whole Transcript)
GenomeArray (3’IVT)
Clariom™
Others
Life Technologies Taqman mRNA Expression
Openarray Customisation

Analysis

Analysis Items Contents
Data analysis of DE Basic statistics (fold change, group mean, SD, etc.)
Identifying differentially expressed genes (T-test, LPE test, ANOVA, etc.)
Multiple testing correction (FDR, Bonferroni, etc.)
Clustering Analysis for DEG (hierarchical clustering, K-means, etc.)
Functional analysis KEGG pathway, GeneOntologyannotation (DAVID, goProfiles, GOstats, etc.)
GeneSet Enrichment Analysis
Customised analysis Integrative analysis (mRNA-miRNA, methylation~mRNA, mRNA-CNV, etc.)

microRNA Expression Microarray


microRNA is a single-sequence small RNA composed of 21–25 nucleotides. microRNA controls gene expression by interrupting mRNA’s function of forming protein via the translation process. The microRNA study can widen the understanding of RNA silencing.
microRNAs exist in many forms according to the generation process. We have many microarray products to analyse the expression patterns of mature miRNAs known by many studies. Macrogen provides analysis services including selection of microRNAs where differential expression is confirmed and target mRNA prediction, as well as test services using microarrays.

miRNA Expression Microarray Platforms

Manufacturer Specimen Platform
Agilent
  • Human
  • Mouse
  • Rat
  • Model Org/Non-Human
SurePrint G3 miRNA Expression
Customization
Affymetrix miRNA 4.0 (203 specimens)
Life Technologies Taqman miRNA Expression

Analysis

Analysis Items Contents
Data analysis of DE Basic statistics (fold change, group mean, SD, etc.)
Identifying differentially expressed genes (T-test, LPE test, ANOVA etc.)
Multiple testing correction (FDR, Bonferroni, etc.)
Clustering Analysis for DEG (hierarchical clustering, K-means, etc.)
Customized analysis Target gene prediction
Integrative analysis (mRNA-miRNA

Genome Microarray


For the human genome, composed of about 3 billion pairs of bases, most DNA sequences of individuals match, but about 0.1% is SNP (single nucleotide polymorphism), which is where the difference lies. Such SNP causes the genetic diversity of an individual and sensitivity to different diseases.

Research institutes and medical institutions around the world are conducting research to define the functional characteristics of SNP. With various kinds of microarrays, Macrogen can easily provide analysis for hundreds of thousands to millions of human SNP.

SNP Genotyping Microarray Platforms

Manufacturer Specimen Type Platform SNP contents
Illumina
  • Human
  • Model Org/Non-Human
Genome Wide SNP Array Infinium Omni5Exome-4 4.5M
Infinium Omni5-4 4.3M
Infinium Omni2.5Exome-8 2.7M
Infinium Omni2.5-8 2.5M
Infinium OmniExpressExome-8 950K
Infinium OmniExpress-24 715K
Infinium CoreExome-24 540K
Infinium Core-24 300K
Infinium GlobalScreeningArray 660K
Etc
Targeted Array Infinium QC Array-24 16K
Infinium Exome-24 250K
Infinium OncoArray-500K 500K
Infinium ImmunoArray-24 250K
Infinium ImmunoArray-24 590K
Etc
Life Technologies
  •  Any pre-designed probes
  •  Customised probes
Openarray Customisation up to 240 SNPs
Taqman genotyping

Analysis

Analysis Items Contents
SNP analysis SNP analysis
Single Based Association Study (PLINK, R)
Gene Based Association Study (SKAT, Score-Seqetc)
Family based Association Study (TDT, FBAT)
Linkage analysis (Merlin)
CNV analysis CNV segments Data (cnvPartition)
CNVR association study
DGV mapping
Customised analysis Additional plotting, annotation, etc..

CGH Microarray


CNV (copy number variation) means the DNA variation that a certain sequence section of more than 1 Kb is lost or amplified and repeated in the chromosome. Such copy number variation can cause various genetic diseases as well as the proliferation of cancer cells.

Macrogen analyses structure variation in chromosomes including CNV using CGH (comparative genome hybridization) microarray.

CGH Microarray Platforms
Agilent CGH
– High resolution (60mer) & sensitivity CGH/CNV chips are provided
– CGH/CNV chips related to organisms other than human are provided and can be customised
– CGH test using FFPE samples available

CGH Microarray
Products No. of probes Average marker spacing
CGH 1x1M 1M 3,118 base
CGH 2x400K 400K 7,304 base
CGH 4x180K 180K 17,627 base
CGH 8x60K 60K 54,455 base

Analysis

Analysis items Contents
CNV analysis CNV segments Data (cnvPartition)
CNVR association study
DGV mapping
Customised analysis Additional plotting, annotation, etc..

Epigenome Microarray 

DNA Methylation Microarray


DNA methylation is a chemical transformation that controls gene expression. This phenomenon of methyl generated in cytosine at the CpG site exists around the promoter region of a gene.

If methyl affects genes that play an important role in suppressing a tumour, such as tumour-suppressor genes, it can cause a fatal result—cancer. Macrogen can correctly identify whether there is genome methylation using Illumina microarray and give biological meaning with statistical analysis of the results.

DNA Methylation Microarray Platforms

Product Contents Feature
Infinium Methylation >860,000 CpG sites * 8 samples are tested per chip
EPIC Bead Chip (>26,000 genes)  Test on FFPE sample is available

Analysis

Analysis item Contents
Data analysis of DM CpG Basic statistics(delta_mean, group mean, SD, etc.)
Identifying differentially methylated CpGs(T-test, LPE test, ANOVA, etc.)
Multiple testing correction (FDR, Bonferroni, etc.)
Clustering Analysis for DM CpGs (hierarchical clustering, K-means, etc.)
Functional analysis KEGG pathway, Gene Ontology Annotation (DAVID, goProfiles, GOstats, etc.)
GeneSet Enrichment Analysis
Customized analysis Integrative analysis (methylation~mRNA, etc.)
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