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Genomics & Transcriptomics

Overview

Genomics is the systematic study of the relationship between the structure and biological function of an organism’s genome. More specifically, it concerns the genetic information contained in a single cell, organ, tissue or whole organism on a system-wide scale. Today, the term is also used to describe the analysis of the full complement of coding and non-coding RNA in a given biological system (also referred to as Transcriptomics).

The Genomics field includes efforts to determine an organism’s entire genetic code. It also extends to the study of phenomena such as heterosis, epistasis, pleiotropy and other similar interactions between loci and alleles within a genome.

A Brief History

Development in the field of Genomics was spurred by the invention of the Polymerase Chain Reaction (PCR) in 1983, and by the optimisation of DNA sequencing in the 1990s. These innovations led to the complete decoding of the human genome in 2001.

The data garnered from high-throughput sequencing, and other information-rich genomic applications, provides the raw data for the exploding field of bioinformatics. This field combines computer science with biology to explore the unchartered realms of biotech innovation.

The Importance of Genomics and Transcriptomics

The impact of Genomics on the fields of life sciences and biotechnology is manifold. It has been shown to:

  • Accelerate the identification of novel drug targets in genome-wide association studies (drug target discovery and validation)
  • Facilitate the identification of drug-risk profiles in early preclinical development by way of creating molecular go/no-go decision gates (Toxicogenomics)
  • Enhance the stratification of patients enrolled in late-stage drug development, therefore reducing the costs of clinical trials (Pharmacogenomics)
  • Stimulate the development of novel multivariate signature assays, thereby paving the way for improved Molecular Diagnostics tests and Personalised Medicine
  • Support the identification of quantitative traits underlying the more efficient molecular development of higher-yield crops (Molecular Crop Breeding)

Low-Density Genotyping

  • TaqMan Assay
    SNP genotyping using validated and inventoried genotyping assays

High-Density Genotyping Microarrays

Next Generation Sequencing

Digital PCR

  • Digital PCR
    SNP identification, gene expression analysis, miRNA profiling, and CNV determination using Fluidigm BioMark

Designed for the detection and analysis of relevant chromosomal aberrations.

Platform
Affymetrix
Deliverables
  • Analytical report
  • QC results
  • Raw .CEL files
Research Objectives Detection of known and novel chromosome aberrations across the entire human genome.
Related Services
  • Genome-wide Human 6 SNP Array
  • DNA-Seq

Overview

The CytoScan High Density array is based on the Genome-Wide Human SNP Array 6.0 and contains more than 2.6 million markers for copy number analysis and approximately 750,000 SNPs that fully genotype with greater than 99% accuracy. This array has the capability of detecting known and novel chromosomal aberrations across the entire human genome. A smaller targeted version of this array, the CytoScan 750K Cytogenetics Solution, provides high-resolution coverage of cancer and constitutional genes of interest along with high density SNP coverage for loss of heterozygosity (LOH) detection.

Service Details

The minimum batch size is 24 samples, however, samples belonging to the same project can be analysed in batches of 8-16. Isolated genomic DNA is interrogated by way of a series of processes that includes digestion with a restriction enzyme and ligation to common adaptors. This is followed by a complexity reduction PCR step.  The PCR product is purified, quantified, fragmented and labelled. QC steps are performed at each critical stage before proceeding to the next stage.  Following hybridization (GeneChip® Hyb Oven 645), the arrays are washed and stained using the GeneChip Fluidics Station 450 and scanned using the GeneChip® Scanner 3000 7G. Initial data analysis is carried out to assess the quality of the date using Affymetrix Chromosome Analysis Suite (ChAS).

Service Deliverables

Following initial analysis using Chromosome Analysis Suite software, an analytical report is provided which includes the QC results for critical stages of the assay.  The analytical report also includes a sample summary for each of the segments of interest generated by the software and the data QC report.  Raw data is also made available to the client.

Starting Material

DNA Quantity:  400ng
DNA Concentration: 50 ng/µl

RNA EXTRACTION

  • RNA Extraction
    RNA extraction using silica-membrane, spin-column technology or Trizol

RNA QUALITY CONTROL

  • miRNA Array
    Exploration of the regulatory mechanisms mediated by miRNAs and their importance in cancer and other diseases
  • miRNA-Seq
    Examine tissue specific expression patterns, disease associations, isoforms of miRNAs, and discover novel miRNAs
  • Total RNA-seq
    Next geneartion sequencing of mature, small and no-coding RNA
  • mRNA-seq
    Next generation sequencing the full complement of mature mRNA
  • miRNA-seq
    Next generation sequencing of small, non-coding microRNAs

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