BMC Bioinformatics. 2010 Oct 13;11(1):509. [Epub ahead of print]

Yang CH, Cheng YH, Chuang LY, Chang HW.

Abstract

ABSTRACT:

BACKGROUND: Polymerase chain reaction with confronting two-pair primers (PCR-CTPP) method produces allele-specific DNA bands of different lengths by adding four designed primers and it achieves the single nucleotide polymorphism (SNP) genotyping by electrophoresis without further steps. It is a time- and cost-effective SNP genotyping method that has the advantage of simplicity. However, computation of feasible CTPP primers is still challenging.

RESULTS: In this study, we propose a GA (genetic algorithm)-based method to design a feasible CTPP primer set to perform a reliable PCR experiment. The SLC6A4 gene were tested with 288 SNPs for dry dock experiments which indicated that the proposed algorithm provides CTPP primers satisfied most primer constraints. One SNP rs12449783 in the SLC6A4 gene was taken as an example for the genotyping experiments using electrophoresis which validated the GA-based design method as providing reliable CTPP primer sets for SNP genotyping.

CONCLUSIONS: The GA-based CTPP primer design method provides all forms of estimation for the common primer constraints of PCR-CTPP. The GA-CTPP program is implemented in JAVA and a user-friendly input interface is freely available at http://bio.kuas.edu.tw/ga-ctpp/.

PMID: 20942913 [PubMed - as supplied by publisher]

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Public release date: 22-Sep-2010

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Contact: Karin Heuss
KarinHeuss@eurofins.com
Eurofins Medigenomix GmbH

Cooperation in the areas of DNA banking and pharmacogenetics, pharmacogenomics

This release is available in German.

Ebersberg/Biberach an der Riss, September 16, 2010. Boehringer Ingelheim Pharma GmbH Co. KG, an international research-driven pharma company, and
Eurofins Medigenomix GmbH, a competence center for genetic analyses of the Eurofins Scientific Group, concluded a long-term service agreement in the area of
DNA banking, as well as a master service agreement for pharmacogenetic and
pharmacogenomic services. For DNA banking Eurofins Medigenomix is supporting operations of Boehringer Ingelheim’s central DNA bank at Biberach an der Riss.

Within the scope of clinical phase I-IV studies, which Boehringer Ingelheim is conducting worldwide in its different therapy areas, blood samples are collected for
DNA banking purposes. On behalf of Boehringer Ingelheim many thousands of blood samples per year will be processed at Eurofins Medigenomix using a fully automated
robot-based system: In this automated process genomic DNA is extracted from blood samples. DNA samples then are normalized and aliquoted into plates. Subsequently,
plates with DNA samples are shipped back from Eurofins Medigenomix to Boehringer Ingelheim. Upon receipt at Biberach DNA samples will be stored frozen in the fully automated DNA bank with a storage capacity of several millions of samples. In the
area of pharmacogenetics / pharmacogenomics Eurofins Medigenomix will support

Boehringer Ingelheim’s Pharmacogenomics Unit in analyses of stored samples from the central DNA bank, e.g. in genotyping, as well as in analyses which shall be
performed in the scope of clinical studies. Both services, later analyses of stored DNA samples and parallel analyses of samples coming from global clinical trials, support
Boehringer Ingelheim’s research and development activities and make a contribution to the development of effective and safe drugs.

Company profile of Eurofins Medigenomix GmbH (www.medigenomix.de):

Eurofins Medigenomix is a competence center for genetic analyses of the Eurofins Scientific Group.
The company expanded successfully their service portfolio by the addition of services in the areas of
pharmacogenetics and pharmacogenomics. Eurofins Medigenomix offers a comprehensive Pharma services portfolio for the entire drug development process, from preclinical research to clinical phase III trials e.g. DNA/RNA preparation, genotyping, polymorphism screening, mutation and biomarker analysis, expression analysis, assay development validation, transcriptome analysis, metagenomic approaches and exclusive marker set for the general identification of responder/non-responder in the scope of clinical studies. Eurofins Medigenomix is certified according to DIN EN ISO 9001:2008. For the areas of Forensic Genetics, Veterinary Diagnostics and Food authenticity analysis, the company is accredited according to ISO 17025:2005.

Company profile of Boehringer Ingelheim:

The Boehringer Ingelheim group is one of the world’s 15 leading pharmaceutical companies.
Headquartered in Ingelheim, Germany, it operates globally with 142 affiliates in 50 countries and more than 41,500 employees. Since it was founded in 1885, the family-owned company has been committed
for 125 Years to researching, developing, manufacturing and marketing novel products of high
therapeutic value for human and veterinary medicine. In 2009, Boehringer Ingelheim posted net sales of 12.7 billion euro while spending 21% of net sales in
its largest business segment Prescription Medicines on research and development.

For more information please visit www.boehringer-ingelheim.com.

For further information please contact:

Eurofins Medigenomix GmbH:

Dr. Brigitte Obermaier

phone: +49 (8092) 8289-217

brigitteobermaier@eurofins.com

Boehringer Ingelheim Pharma GmbH Co. KG:

Dr. Andreas Khler

phone: +49 (7351) 54-5355

andreas.koehler@boehringer-ingelheim.com

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