Custom Array Design

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Custom array designing and genotyping is the ideal solution for screening large sample sets against novel or targeted content. With custom designs, researchers can target regions of the genome relevant to their specific research interests. Illumina offers flexible options and simple online design tools to maximize success with our customized genotyping assays.


  • focus on improving working algorithms for their Processing Times, Accuracy
  • Sensitivity
  • Specificity through Genomics Bioinformatics

Custom array designing applications are:

  • Gene expression
  • MicroRNA
  • Pan Genome
  • Alternative Splicing
  • Chip-on-chip
  • DNA Methylation
  • SNP
  • Target Capture
  • metagenome profiling
  • fusion gene study
  • disease specific gene profiling
  • pathway specific gene profiling

Researchers can design custom assays to sequence only those genome regions relevant to their specific research interests. Custom targeted sequencing is ideal for examining genes in specific pathways, or for follow-up studies from GWAS or whole-genome sequencing.


After target amplification, the steps of the protocol are mostly straight-froward and generally work well when following the manufacturer’s protocol. 

Pooling and normalization of PCR products: when using short-range PCRs, normalization is not required on each run, but it should be estimated based upon gel intensity of the product after examining several optimized PCR results. 

PCR clean-up and concentration: QIAquick PCR purification columns are used. If more than one column is needed because of pooled PCR volume, then eluates are combined. The eluate is then concentrated to the appropriate volume through the use of a SpeedVac, and the concentration of DNA is assessed by absorbance spectrometry.

Fragmentation: This is one of the most finicky steps to the protocol and must be monitored carefully. Overfragmentation and under fragmentation can cause problems. For example, it has observed that under fragmentation leads to weak hybridization, which in turn leads to reduced call rates. After fragmentation is complete (smear of fragments from 20 to 200 bp), success is analyzed using either a high-resolution agarose gel or an Agilent Bioanalyzer 2100. If the sample is under fragmented, more enzymes can be added.

Labeling, hybridization, washing, staining, scanning: These steps are well represented by the manufacturer’s recommendations.


  • Enable studies of species or populations not supported by standard products
  • Allow researchers to focus on genes, variants, and/or genomic regions of interest relevant to certain diseases or traits of interest, but not covered in pre-designed products
  • Conserve resources by avoiding irrelevant regions of the genome

Keeping in trend with the growth and demands of the Bioinformatics services industry, Custom array analysis provides customizable, accurate, sensitive and specific solutions to the following areas of researchers’ interests:

  • Functional Gene Annotations / Genome Annotation
  • Gene / ORF Prediction
  • Gene Ontology and Pathway Enrichment Analysis
  • Genome alignment and Analysis
  • Motif Prediction
  • Multiple sequence alignment
  • BLAST / BLAT Data Analysis
  • Comparative Genomics
  • Phylogenetic Analysis
  • Custom array designing for any application, any organism, any sequence
  • Targeted resequencing baits for custom Disease gene panels
  • Microarray Data Analysis
  • NGS Data Analysis
  • Bioinformatics Databases and Data mining

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