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.
Expression Microarray
mRNA Expression 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 |
|
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
miRNA Expression Microarray Platforms
| Manufacturer | Specimen | Platform |
| Agilent |
|
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 |
|
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 |
|
– | 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
| 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.) |
