High resolution melting analysis for the rapid and sensitive detection of mutations in clinical samples: KRAS codon 12 and 13 mutations in non-small cell lung cancer

BACKGROUND: The development of targeted therapies has created a pressing clinical need for the rapid and robust molecular characterisation of cancers. We describe here the application of high-resolution melting analysis (HRM) to screen for KRAS mutations in clinical cancer samples. In non-small cell lung cancer, KRAS mutations have been shown to identify a group of patients that do not respond to EGFR targeted therapies and the identification of these mutations is thus clinically important. METHODS: We developed a high-resolution melting (HRM) assay to detect somatic mutations in exon 2, notably codons 12 and 13 of the KRAS gene using the intercalating dye SYTO 9. We tested 3 different cell lines with known KRAS mutations and then examined the sensitivity of mutation detection with the cell lines using 189 bp and 92 bp amplicons spanning codons 12 and 13. We then screened for KRAS mutations in 30 non-small cell lung cancer biopsies that had been previously sequenced for mutations in EGFR exons 18–21. RESULTS: Known KRAS mutations in cell lines (A549, HCT116 and RPMI8226) were readily detectable using HRM. The shorter 92 bp amplicon was more sensitive in detecting mutations than the 189 bp amplicon and was able to reliably detect as little as 5–6% of each cell line DNA diluted in normal DNA. Nine of the 30 non-small cell lung cancer biopsies had KRAS mutations detected by HRM analysis. The results were confirmed by standard sequencing. Mutations in KRAS and EGFR were mutually exclusive. CONCLUSION: HRM is a sensitive in-tube methodology to screen for mutations in clinical samples. HRM will enable high-throughput screening of gene mutations to allow appropriate therapeutic choices for patients and accelerate research aimed at identifying novel mutations in human cancer

Integrated mutation, copy number and expression profiling in resectable non-small cell lung cancer

<p>Abstract</p> <p>Background</p> <p>The aim of this study was to identify critical genes involved in non-small cell lung cancer (NSCLC) pathogenesis that may lead to a more complete understanding of this disease and identify novel molecular targets for use in the development of more effective therapies.</p> <p>Methods</p> <p>Both transcriptional and genomic profiling were performed on 69 resected NSCLC specimens and results correlated with mutational analyses and clinical data to identify genetic alterations associated with groups of interest.</p> <p>Results</p> <p>Combined analyses identified specific patterns of genetic alteration associated with adenocarcinoma vs. squamous differentiation; <it>KRAS </it>mutation; <it>TP53 </it>mutation, metastatic potential and disease recurrence and survival. Amplification of 3q was associated with mutations in <it>TP53 </it>in adenocarcinoma. A prognostic signature for disease recurrence, reflecting <it>KRAS </it>pathway activation, was validated in an independent test set.</p> <p>Conclusions</p> <p>These results may provide the first steps in identifying new predictive biomarkers and targets for novel therapies, thus improving outcomes for patients with this deadly disease.</p

Endobronchial Ultrasound-Guided Transbronchial Needle Aspiration for the Evaluation of Suspected Lymphoma

BackgroundEvidence regarding the utility of endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) in the assessment of isolated mediastinal lymphadenopathy (IMLN) is evolving. Its diagnostic accuracy in the evaluation of suspected lymphoma remains uncertain.MethodsWe reviewed a prospectively recorded database of consecutive patients with suspected lymphoma who underwent EBUS-TBNA to evaluate IMLN. Patients in whom EBUS-TBNA was nondiagnostic subsequently underwent surgical biopsy or a minimum of 6 months radiologic surveillance.ResultsNinety-eight patients underwent EBUS-TBNA for evaluation of IMLN. Clinicoradiologic features suggested sarcoidosis as the likely diagnosis in 43 patients. In the remaining 55 patients, EBUS-TBNA achieved definitive diagnosis in 42 patients (76%; 95% confidence interval [CI] 55–90). Lymphoma was ultimately diagnosed in 21 of 55 patients (38%). EBUS-TBNA demonstrated lymphoma in 16 (76%) patients; however, four patients required further surgical biopsy to completely characterize lymphoma subtypes. Surgical biopsy was required to diagnose specific lymphoma subtypes not readily amenable to diagnosis with low volume specimens. Sensitivity and specificity for definitive diagnosis of lymphoma were 57% (95% CI 37–76) and 100% (95% CI 91–100), respectively.ConclusionsAlthough the diagnostic accuracy of EBUS-TBNA for lymphoma is lower than that for the lung cancer staging, the procedure is an appropriate investigative technique for the patients with IMLN because of the low incidence of lymphoma in this population, and the significant proportion of such patients (76%) in whom surgical biopsy is obviated

Validity of the assessment of quality of life (AQoL) utility instrument in patients with operable and inoperable lung cancer

There have been few longitudinal studies of quality of life in patients with all stages of lung cancer, particularly those that have included measures of utility. The purpose of this study was to examine the psychometric properties of the Assessment of Quality of Life instrument (AQoL) in patients with lung cancer. The AQoL is a health-related quality of life questionnaire and provides a descriptive system for a multi-attribute utility instrument (MAU), so that scores can be used in cost-utility evaluations. In the present study the reliability (internal consistency) of the AQoL was examined and the concurrent validity was assessed using the Medical Outcomes 36-item Short Form Health Survey (SF-36) as the comparator instrument. The sensitivity to different health states of the AQoL and the responsiveness to change over time was also examined. A prospective, non-experimental cohort study was undertaken. Ninety-two participants with all stages of lung cancer were recruited from a tertiary multi-disciplinary lung cancer clinic. Ninety participants had non-small cell lung cancer (NSCLC) and two had limited stage small cell lung cancer. The AQOL and SF-36 surveys were administered concurrently at baseline. In patients with NSCLC the surveys were then repeated 3 and 6 months later. Correlations between the baseline AQoL summary scales and SF-36 summary scales support the divergent and convergent validity of the AQoL. Reliability was also found to be sufficient (Cronbach\u27s Alpha = 0.76). In addition, in patients with inoperable NSCLC, baseline AQoL scores were found to be predictive of survival at 6 months in Cox proportional hazards multivariate analysis. However, the physical components summary score of the SF-36 was more sensitive to differences in health states between patients with different stages of NSCLC at 6 months of follow-up and more responsive to change over time in both operable and inoperable patients with NSCLC than the AQoL. The findings support the construct validity and reliability of the AQoL in this population. However, there remains some uncertainty about whether the AQoL has sufficient sensitivity to different health states in this population. Further studies using other MAU instruments may determine whether alternative instruments are more sensitive to different health states in individuals with lung cancer.<br /

Sex-dependent staging in non–small-cell lung cancer; analysis of the effect of sex differences in the eighth edition of the tumor, node, metastases staging system

Introduction: Non–small-cell lung cancer (NSCLC) has disproportionately negative outcomes in men compared with women. The importance of the relationship between sex and tumor, node, metastases (TNM) staging system remains unknown. The objective of this study was to investigate the effect of sex on NSCLC survival for each stage in the eighth edition of the TNM staging system in NSCLC. Patients and Methods: Two cohorts treated surgically with curative intent between 2000 and 2010 were analyzed. The primary cohort was from Australia with a second population set from the Surveillance, Epidemiology, and End Results (SEER) database. Univariate and multivariate analyses of putative and validated prognostic factors were undertaken to investigate sex-dependent prognostication with detailed analyses of sex differences in each TNM stage. The primary outcome was disease-specific survival (DSS) at 5 years. Results: Inclusion criteria were met by 555 patients in the Australian cohort, 335 men (60.4%) and 220 (39.6%) women; and 47,706 patients from the SEER cohort, 24,671 men (51.7%) and 23,035 women (48.3%). Five-year DSS was significantly worse for men in multivariate analyses for the Australian (hazard ratio [HR], 1.44; 95% confidence interval [CI], 1.04-1.98; P =.026) and SEER (HR, 1.24; 95% CI, 1.20-1.28;