Agilent whole human genome oligonucleotide arrays were used for any transcriptomic analysis carried out at IOB. A 60-mer oligonucleotide probe represents each spot in an array. Each array contains 44k spots representing 41,000 genes. A high density array, 4X44K was used for simultaneous analysis of 4 samples.

High resolution whole human genome array from Agilent was used to analyze copy number variations. High throughput analyses were carried out using high density arrays 4X44K or 8X60K, where 4 or 8 samples could be analyzed simultaneously. Comprehensive probe coverage spans coding and non-coding regions with emphasis on known genes, promoters, miRNAs, disease, pseudoautosomal, and telomeric regions.

IOB has designed human X-chromosome tiling microarrays using Agilent’s e-array, a web portal for designing custom arrays.  The custom designed array has 244,000 probes covering human X-chromosome with an average spacing of 635 bp that provides high resolution.  The array encompasses unique probes that represent most exons of the X-chromosome genes. These arrays will be able to detect micro-duplications and micro-deletions of size less than 1 Kb.  These custom designed high resolution X-chromosome tiling arrays will be used to study the copy number variations in X-linked mental retardation.

Use of tissue microarrays and cell pellet arrays provides us another high throughput platform to validate and test numerous potential biomarkers which have been identified using high resolution genomic and proteomic technologies.  Advantage of using these microarrays is that we can validate a potential molecular signature in cancer or any other context against hundreds of tissue samples or cell lines belonging to different pTNM, age group, gender and population.  This will also provide confidence and statistical proof for the biomarkers identified from otherwise low number of samples used for DNA microarrays and mass spectrometry approaches in the biomarker discovery phase.