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ATLAS Biolabs Expands Services in Molecular Genetics to High-Throughput SNP-genotyping Based on MS

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By introducing  Sequenom’s MassARRAY® Analyzer* for use in DNA analysis, ATLAS Biolabs GmbH aims to expand its range of services in molecular genetics. Sequenom’s MassARRAY® system comprises a high-throughput platform which utilizes matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) for genotyping of single nucleotide polymorphisms (SNPs).

The system can be used for validating potential biomarkers identified by next-generation sequencing, for fine mapping of  genome-wide association study (GWAS) data and for applications that employ defined SNP panels. The exceptional flexibility of the system allows for the quick adoption of newly discovered biomarkers into novel or existing biomarker panels.

Mass spectrometry requires only very small amounts of genomic DNA and delivers precise quantitative results, thereby providing substantial benefits for the analysis of genetic material. With the direct detection method it is possible to find even low frequency mutations, which might otherwise go undetected. Moreover, genotyping can be carried out not only with fresh and frozen material, but also with formalin-fixed, paraffin-embedded (FFPE) tissue samples. Since DNA purified from FFPE material is usually highly degraded and available only in small quantities, the molecular analysis of these samples is limited when using conventional methods.

“We are excited about the MassARRAY® system, which will help us to offer a valuable service to our customers. The system is an ideal complement to our range of services,“ said Professor Peter Nuernberg, Chief Executive Officer of ATLAS Biolabs. For example, MALDI-TOF MS is extremely valuable in SNP genotyping following GWAS, a field in which ATLAS Biolabs is one of the leading service providers in Europe, due to its proven experience with the whole-genome SNP chip technologies from Affymetrix and Illumina. In addition, by combining the MassARRAY® system with Sequenom’s OncoCarta™ panel**, ATLAS Biolabs is now able to rapidly monitor oncogene mutations in somatic cells.

“OncoCarta™ is currently the only panel for rare somatic mutation profiling that offers rapid parallel analysis of 238 mutations in 19 common oncogenes,” said Michael Monko, Senior Vice President, Sales & Marketing at Sequenom. “We look forward to close cooperation with ATLAS Biolabs to ensure that even more researchers in Europe have access to these innovative technologies, regardless of whether they are working in basic or clinical research or in drug development.”

The MassARRAY System for SNP Genotyping

The MassARRAY® platform with the iPLEX® Gold genotyping assay** is a complete genotyping solution for the validation and fine mapping of SNPs and somatic mutations. The system includes software that can automatically design primers for multiplexed assays.

In a subsequent reaction, primers are extended to detect sequence differences at the single nucleotide level. Following extension, products are spotted onto chip arrays, which are then placed in the MALDI-TOF mass spectrometer. A 384-position array is typically processed in 45-60 minutes.

The results are automatically loaded into a database that allows convenient data analysis. Genotyping reactions can be multiplexed with up to 40 SNPs in each individual reaction, resulting in throughput levels of up to 150,000 genotypes per instrument per day.