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Tuononen K.,University of Helsinki | Maki-Nevala S.,University of Helsinki | Sarhadi V.K.,University of Helsinki | Wirtanen A.,University of Helsinki | And 9 more authors.
Genes Chromosomes and Cancer | Year: 2013

The development of tyrosine kinase inhibitor treatments has made it important to test cancer patients for clinically significant gene mutations that influence the benefit of treatment. Targeted next-generation sequencing (NGS) provides a promising method for diagnostic purposes by enabling the simultaneous detection of multiple mutations in various genes in a single test. The aim of our study was to screen EGFR, KRAS, and BRAF mutations by targeted NGS and commonly used real-time polymerase chain reaction (PCR) methods to evaluate the feasibility of targeted NGS for the detection of the mutations. Furthermore, we aimed to identify potential novel mutations by targeted NGS. We analyzed formalin-fixed, paraffin-embedded (FFPE) tumor tissue specimens from 81 non-small cell lung carcinoma patients. We observed a significant concordance (from 96.3 to 100%) of the EGFR, KRAS, and BRAF mutation detection results between targeted NGS and real-time PCR. Moreover, targeted NGS revealed seven nonsynonymous single-nucleotide variations and one insertion-deletion variation in EGFR not detectable by the real-time PCR methods. The potential clinical significance of these variants requires elucidation in future studies. Our results support the use of targeted NGS in the screening of EGFR, KRAS, and BRAF mutations in FFPE tissue material. © 2012 Wiley Periodicals, Inc.

Tuononen K.,University of Helsinki | Sarhadi V.K.,University of Helsinki | Wirtanen A.,University of Helsinki | Ronty M.,University of Helsinki | And 7 more authors.
BioMed Research International | Year: 2013

Anaplastic lymphoma receptor tyrosine kinase (ALK) gene rearrangements occur in a subgroup of non-small cell lung carcinomas (NSCLCs). The identification of these rearrangements is important for guiding treatment decisions. The aim of our study was to screen ALK gene fusions in NSCLCs and to compare the results detected by targeted resequencing with results detected by commonly used methods, including fluorescence in situ hybridization (FISH), immunohistochemistry (IHC), and real-time reverse transcription-PCR (RT-PCR). Furthermore, we aimed to ascertain the potential of targeted resequencing in detection of ALK-rearranged lung carcinomas. We assessed ALK fusion status for 95 formalin-fixed paraffin-embedded tumor tissue specimens from 87 patients with NSCLC by FISH and real-time RT-PCR, for 57 specimens from 56 patients by targeted resequencing, and for 14 specimens from 14 patients by IHC. All methods were performed successfully on formalin-fixed paraffin-embedded tumor tissue material. We detected ALK fusion in 5.7% (5 out of 87) of patients examined. The results obtained from resequencing correlated significantly with those from FISH, real-time RT-PCR, and IHC. Targeted resequencing proved to be a promising method for ALK gene fusion detection in NSCLC. Means to reduce the material and turnaround time required for analysis are, however, needed. © 2013 Katja Tuononen et al.

Telaranta-Keerie A.,Lab21 Ltd | Clarke B.,Lab21 Ltd
Pharmacogenomics | Year: 2012

Pharmacogenetics is essential in the discovery of individual differences in metabolism and response to drugs, as well as in increasing the understanding of disease mechanisms. In addition, the use of biomarker assays is now critical in personalized medicine as specific variations in therapeutic targets can determine whether a drug is effective, particularly in oncology. Lab21 Ltd provides comprehensive and flexible biomarker assay development and commercialization services with an integrated structure that includes a full global development and commercialization capability together with accredited clinical service laboratories in both Europe and the USA. Lab21 adopts a platform and technology agnostic approach to molecular and immunodiagnostic development, and has an established and successful history of partnering with major pharmaceutical companies. Lab21 is becoming a significant global provider of diagnostic products and services, and is an ideal strategic partner for pharmaceutical and larger diagnostic companies to successfully deliver their biomarker assays to the patient. © 2012 Future Medicine Ltd.

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