Comparative analysis of four methods to extract DNA from paraffin-embedded tissues: effect on downstream molecular applications

<p>Abstract</p> <p>Background</p> <p>A large portion of tissues stored worldwide for diagnostic purposes is formalin-fixed and paraffin-embedded (FFPE). These FFPE-archived tissues are an extremely valuable source for retrospective (genetic) studies. These include mutation screening in cancer-critical genes as well as pathogen detection. In this study we evaluated the impact of several widely used DNA extraction methods on the quality of molecular diagnostics on FFPE tissues.</p> <p>Findings</p> <p>We compared 4 DNA extraction methods from 4 identically processed FFPE mammary-, prostate-, colon- and lung tissues with regard to PCR inhibition, real time SNP detection and amplifiable fragment size. The extraction methods, with and without proteinase K pre-treatment, tested were: 1) heat-treatment, 2) QIAamp DNA-blood-mini-kit, 3) EasyMAG NucliSens and 4) Gentra Capture-Column-kit.</p> <p>Amplifiable DNA fragment size was assessed by multiplexed 200-400-600 bp PCR and appeared highly influenced by the extraction method used. Proteinase K pre-treatment was a prerequisite for proper purification of DNA from FFPE. Extractions with QIAamp, EasyMAG and heat-treatment were found suitable for amplification of fragments up to 400 bp from all tissues, 600 bp amplification was marginally successful (best was QIAamp). QIAamp and EasyMAG extracts were found suitable for downstream real time SNP detection. Gentra extraction was unsuitable. Hands-on time was lowest for heat-treatment, followed by EasyMAG.</p> <p>Conclusions</p> <p>We conclude that the extraction method plays an important role with regard to performance in downstream molecular applications.</p

Comparison of EGFR and K-RAS gene status between primary tumours and corresponding metastases in NSCLC

In non-small-cell lung cancer (NSCLC), epidermal growth factor receptor (EGFR) and K-RAS mutations of the primary tumour are associated with responsiveness and resistance to tyrosine kinase inhibitors (TKIs), respectively. However, the EGFR and K-RAS mutation status in metastases is not well studied. We compared the mutation status of these genes between the primary tumours and the corresponding metastases of 25 patients. Epidermal growth factor receptor and K-RAS mutation status was different between primary tumours and corresponding metastases in 7 (28%) and 6 (24%) of the 25 patients, respectively. Among the 25 primary tumours, three ‘hotspot' and two non-classical EGFR mutations were found; none of the corresponding metastases had the same mutation pattern. Among the five (20%) K-RAS mutations detected in the primary tumours, two were maintained in the corresponding metastasis. Epidermal growth factor receptor and K-RAS mutations were detected in the metastatic tumours of three (12%) and five (20%) patients, respectively. The expressions of EGFR and phosphorylated EGFR showed 10 and 50% discordance, in that order. We conclude that there is substantial discordance in EGFR and K-RAS mutational status between the primary tumours and corresponding metastases in patients with NSCLC and this might have therapeutic implications when treatment with TKIs is considered

Scrotal neoplasia: would truck drivers be at greater risk?

OBJECTIVE: To analyze how scrotal neoplasias have been managed during the past decade and to question possible factors or professions associated to its presence. MATERIALS AND METHODS: We retrospectively evaluated every case reported from 1995 to 2005 at our hospital. We described the clinical scenario, complementary exams, treatments and outcomes. We also tried to verify if there was any risk, predisposing factors or professions that would explain the cancer origin. RESULTS: Six cases were reviewed. Out of these, three patients were truck drivers. Five of them showed restricted lesions without inguinal lymph nodes enlargement. Histologically, six patients presented squamous carcinoma, with two of them having the verrucous type. The median age of patients was 52 years old (31 to 89). The five patients who are still alive had their lesions completely removed with safety margin and primary closure. CONCLUSIONS: We have noticed that the scrotal carcinoma behavior is similar to that of the penis, where removal of the lesion and study of the regional lymph nodes help to increase the patient survival rate. The outstanding fact was that three out of six patients were truck drivers, raising the hypothesis that such profession, maybe due to the contact or attrition with the diesel exhaust expelled by the engine or to sexual promiscuity, would imply in a larger risk of developing this rare neoplasia