RESUMO
PURPOSE: Fresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS. METHODS: We conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples. RESULTS: We found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs). CONCLUSION: We present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.
Assuntos
Variações do Número de Cópias de DNA/genética , Genoma Humano/genética , Neoplasias/genética , Sequenciamento Completo do Genoma/métodos , Tomada de Decisões , Feminino , Humanos , Masculino , Neoplasias/sangue , Neoplasias/patologia , Inclusão em Parafina , Polimorfismo de Nucleotídeo Único/genéticaRESUMO
Embedding stratified cancer medicine into the patient pathway will require adaptation of the diagnostic pathway to incorporate predictive molecular analysis, presenting challenges of accessing tumour samples of sufficient quality and quantity for analysis and ensuring the timeliness, accuracy, and clinical validity of results. In 2010, Cancer Research UK (CRUK), in partnership with AstraZeneca and Pfizer, set up the Stratified Medicine Programme (SMP1) to work collaboratively with a small number of hospital and genetics laboratories to demonstrate the feasibility of testing large volumes of samples, while working towards more standardised and efficient processes. By June 2013, 9010 patient samples had been sent for genetic testing and here we present an overview of our experience and the wealth of insights that have been generated into the complexities of attempting this transformation of National Health Service (NHS) care.