Low-density SNP chip for pharmacogenetic applications

S. Haucha, M. Lustiga, M. Heisingera, S. Waschützaa and E. Schnakenberg a

AdnaGen AG, Hannover-Langenhagen, Lower Saxony Germany

Aim: DNA microarrays represent a technological platform that enables SNP detection in the area of pharmacogenetic diagnosis. Furthermore, this application can be expected to prove extremely valuable for the study of the genetic basis of complex diseases. To our knowledge, no commercial microarray system is available that allows SNP-based pharmacogenetic in routine laboratory medicine. Methods: We have developed a chip-based platform for detection of SNP’s of the thiopurine S-methyltransferase (TPMT), N-acetyltransferase (NAT2) and cytochrome 3A4 (CYP3A4). In addition, all SNP’s were validated using SNP detection by real-time PCR. Results: Low-density microarrays are ideally suited for analyzing limited number of genes in routine laboratory medicine. We used a microarray technology platform for SNP analysis in addition with automatically genotyping. Results for SNP genotyping agreed with results of real time PCR and sequencing for each single nucleotide polymorphism. In addition, results of SNP detection of TPMT, NAT2 and CYP3A4 were automatically combined with the individual report of the detected genotype. CONCLUSIONS: This integrated microarray technology platform is adaptable and versatile, while offering the automatically genotyping and reporting for routine analysis in the laboratory medicine.

KEY WORDS: Microarray, pharmacogenetic diagnosis, genotyping.

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Paper presented at the International Symposium on Predictive Oncology and Intervention Strategies; Paris, France; February 9 - 12, 2002; in the section on Prognostic Markers.