Technical reproducibility of single-nucleotide and size-based DNA biomarker assessment using DNA extracted from formalin-fixed, paraffin-embedded tissues.

DNA extracted from formalin-fixed, paraffin-embedded (FFPE) tissues has been used in the past to analyze genetic polymorphisms. We evaluated the technical reproducibility of different types of assays for gene polymorphisms using DNA extracted from FFPE material. By using the MassARRAY iPLEX system, we investigated polymorphisms in DPYD (rs1801159 and rs3918290), UMPS (rs1801019), ERCC1 (rs11615), ERCC1 (rs3212986), and ERCC2 (rs13181) in 56 FFPE DNA samples. By using PCR, followed by size-based gel electrophoresis, we also examined TYMS 5' untranslated region 2R/3R repeats and GSTT1 deletions in 50 FFPE DNA samples and 34 DNAs extracted from fresh-frozen tissues and cell lines. Each polymorphism was analyzed by two independent runs. We found that iPLEX biomarker assays measuring single-nucleotide polymorphisms provided consistent concordant results. However, by using FFPE DNA, size-based PCR biomarkers (GSTT1 and TYMS 5' untranslated region) were discrepant in 32.7% (16/49, with exact 95% CI, 19.9%-47.5%; exact binomial confidence limit test) and 4.2% (2/48, with exact 95% CI, 0.5%-14.3%) of cases, respectively, whereas no discrepancies were observed using intact genomic DNA. Our findings suggest that DNA from FFPE material can be used to reliably test single-nucleotide polymorphisms. However, results based on size-based PCR biomarkers, and particularly GSTT1 deletions, using FFPE DNA need to be interpreted with caution. Independent repeated assays should be performed on all cases to assess potential discrepancies.

Ethnic differences in survival outcome in patients with advanced stage non-small cell lung cancer: results of a meta-analysis of randomized controlled trials.

INTRODUCTION: Although interethnic differences in survival to cytotoxic chemotherapy in patients with non-small cell lung cancer exist, an analysis of survival outcomes based on ethnicity has not yet been fully evaluated systematically using large patient cohorts. Furthermore, recent trial results may be confounded by the use of the epidermal growth factor receptor (EGFR) tyrosine kinase inhibitor (TKI). METHODS: A meta-analysis was performed using trials identified through MEDLINE. Summary data on median overall survival (OS), time to progression, progression-free survival, and overall response rate (ORR) were collected from randomized controlled trials. Outcomes were compared between Asian and Caucasian studies. RESULTS: Of the 1182 citations identified, 391 treatment arms (Asian 90 and Caucasian 301) were analyzed. The median OS and ORR in Asian and Caucasian studies for all chemotherapy regimens was 10.1 and 8.0 months (p < 0.001) and 32.2 and 25.9% (p < 0.001), respectively. The median OS in Asian and Caucasian studies for monotherapy, platinum doublets, and three drugs or more combination was 9.9 and 6.8 months, 10.4 and 8.6 months, and 9.4 and 8.0 months, respectively (all p < 0.001). In studies published pre-EGFR TKI, the median OS and ORR in Asian and Caucasian studies for all chemotherapy regimens was 9.1 versus 7.3 months (p < 0.001), respectively, and 29.0 and 23.0% (p < 0.006), respectively. The median OS in Asian and Caucasian studies for monotherapy, platinum doublets, and three drugs or more combination pre-EGFR TKI was 8.9 and 6.5 months (p < 0.005), 9.1 and 7.5 months (p < 0.001), and 9.3 and 7.6 months (p < 0.003), respectively. In third-generation platinum doublets, the median OS in Asian and Caucasian studies was 11.3 and 9.5 months (p < 0.001), respectively, and ORR was 35.0 and 29.8% (p < 0.001), respectively. CONCLUSION: Ethnic differences in survival and response rate to chemotherapy exist and should be considered in clinical trial designs especially in the global context.

Detection of BRAF V600E mutation by pyrosequencing.

INTRODUCTION: Detection of the V600E hotspot mutation in BRAF oncogene is extremely useful for the screening of hereditary non-polyposis colorectal cancer (Lynch's syndrome) and for the prediction of sensitivity to MEK inhibitors. Here we describe a method for detecting this mutation based upon pyrosequencing technology. METHODS: The efficiency of pyrosequencing for detecting BRAF V600E mutations was compared with the conventional dideoxy sequencing method in 12 tumour cell lines and in 108 colorectal tumours. RESULTS: The results from pyrosequencing were 100% concordant with those from dideoxy sequencing. This method was capable of detecting BRAF V600E mutations at a much lower ratio of mutant to wild-type alleles (1:50) than dideoxy sequencing (1:5) while being considerably faster and less expensive. CONCLUSIONS: Pyrosequencing offers a specific, sensitive, rapid and cost-effective alternative to dideoxy sequencing for the detection of BRAF V600E mutations in clinical tumour specimens.

Detection of epidermal growth factor receptor variations by partially denaturing HPLC.

BACKGROUND: Epidermal growth factor receptor gene (EGFR) variants may be useful markers for identifying responders to gefitinib and erlotinib, small-molecule tyrosine kinase inhibitors of EGFR; therefore, sensitive and cost-effective assays are needed to detect EGFR variants in routine clinical samples. We have developed a partially denaturing HPLC (pDHPLC) assay that is superior to direct sequencing with respect to detection limits, costs, and time requirements. METHODS: Primers, temperatures, and buffer conditions were optimized for PCR-pDHPLC analysis of EGFR exons 18-21. We evaluated the detection limits of pDHPLC and direct sequencing by analyzing mixtures of wild-type and variant EGFR DNA and screened 192 lung cancer samples to examine the diversity of pDHPLC-detectable variants. To assess amenability to routine analysis, we tested lung and pleural tissue specimens from 14 lung cancer patients treated with gefitinib. RESULTS: The detection limits for variant alleles were 1:100 for pDHPLC and 1:5 for direct sequencing. pDHPLC analysis detected 26 unique EGFR variants, including the common deletions in exon 19 and substitutions in codons 787 and 858. Direct sequencing could not identify 30% (18 of 60) of the variant amplicons identified by pDHPLC. We identified these 18 amplicons by fraction collection after pDHPLC analysis. Analysis of a limited series of lung biopsy samples detected EGFR variants more frequently in gefitinib responders than in nonresponders. pDHPLC analysis was 56% less expensive and 39% faster than direct sequencing. CONCLUSIONS: pDHPLC-based analysis detects EGFR variations in routine clinical samples with a better detection limit and lower cost and time requirement than direct sequencing.