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Precision Medicine

Precision Medicine refers to the tailoring of disease interventions to a patient’s individual ‘data fingerprint’, based on the systematic collection and interpretation of molecular and clinical information.

Genomics is playing a strong role in advancing the Precision Medicine paradigm, notably due to the known contribution of genetic traits to disease development as well as the widespread availability of molecular genetic applications.

Microarrays have been in use since the early 1990s and have recently emerged as a tool of choice to study the contribution 100s of 1000s of genetic variants towards disease development and progression in large-scale Genome Wide Association Studies (GWAS).

Here, we introduce the Axiom® Precision Medicine Research (PMR) array, a high-density genotyping application that allows researchers to reliably study over 900,000 SNPs, CNVs, and in/del markers in a high-throughput and affordable fashion[1].

PMR array

  • Designed to power cohort studies seeking lot-to-lot reliability backed by the industries greatest number of GWAS and clinically actionable markers
  • GWAS imputation module of 800,000 markers with the most powered pan-ethnic genomic coverage in 5 ethnic and admixed populations around the world
  • Coverage of 100,000 common and rare variants including markers of clinical relevance, pharmacogenomics, cancer variants, immune function, functional variants, and blood phenotype, as well as fingerprint markers for sample tracking and quality control
  • Up to 50K SNP’s custom content with projects of 100,000 samples or more
  • Available at R 999,- through the CPGR at minimum sample orders of 96 and above, until 31st December 2016, thereafter dependent on study scope and scale[2]

 

PMR array variants by disease

In addition to 800,000 GWAS SNPs, the PMR array contains probes to interrogate 100,000 variants with known clinical relevance:

CPGR genotyping platform

CPGR provides a comprehensive, end-to-end genotyping solution, allowing for

  • Automated sample preparation and DNA extraction in accordance with study needs
  • Effective sample quality control, including DNA barcoding in large-scale studies
  • High throughput processing of PMR arrays in 96-well plates
  • Result validation on custom Axiom®, digital or PCR arrays
  • Study execution in an ISO 9001:2008 certified environment

CPGR genotyping platform - Sep 2016

About CPGR

The CPGR is a non-profit company located in Cape Town, South Africa, based on an initiative by the Department of Science and Technology (DST), and financially supported by the Technology Innovation Agency (TIA). The CPGR combines state-of-the-art information rich genomic and proteomic (‘omics’) technologies with bio-computational pipelines in an ISO 9001:2008 certified environment. It has recently launched an accelerator program, together with its first start-up, Tokeid Biotech, and founded Artisan Biomed, a commercial venture to implement Precision Medicine solutions in (South) Africa.

The CPGR is an integrated ‘omics’ service provider, built to leapfrog South Africa’s ability to conduct information-rich biomedical research onto a globally competitive level. Amongst others, the organization offers the following ‘omics’ capacity: Next-Generation Sequencing: NextSeq500 (1x), MiSeq (1x), MiniSeq (1x), IonTorrent PGM (2x), IonProton (1x), for sequencing projects; Microarrays: Affymetrix GS 3000 and Affymetrix GeneTitan™ for genoytping and gene-expression analysis; Mass spectrometry: ABI 4800 MALDI TOF/TOF, Thermo Q-Exactive Orbitrap, Waters Xevo TQ-S and Sciex API 4000 Triple Quadrupoles; High-throughput PCR: ABI 7900, Quantstudio™ 12KFlex for qRT-PCR and digital PCR applications; Automated DNA/RNA QC, library handling and sample processing; dedicated IT infrastructure and bioinformatic applications for data analysis and interpretation.

Information about the CPGR can be obtained at www.cpgr.org.za and www.cpgr.org.za/blogspot.

For information, contact jo.mcbride@cpgr.org.za or lindsay.petersen@cpgr.org.za.

Footnotes

[1] SNP, Single Nucleotide Polymorphism; CNV; Copy Number Variant; in/del, insertion/deletion.

[2] Price is excluding VAT and subject to exchange rate fluctuations. For grant applications, please contact the CPGR for budgeting purposes.