Clinical pharmacogenomic testing of KRAS, BRAF and EGFR mutations by high resolution melting analysis and ultra-deep pyrosequencing

BACKGROUND: Epidermal growth factor receptor (EGFR) and its downstream factors KRAS and BRAF are mutated in several types of cancer, affecting the clinical response to EGFR inhibitors. Mutations in the EGFR kinase domain predict sensitivity to the tyrosine kinase inhibitors gefitinib and erlotinib in lung adenocarcinoma, while activating point mutations in KRAS and BRAF confer resistance to the anti-EGFR monoclonal antibody cetuximab in colorectal cancer. The development of new generation methods for systematic mutation screening of these genes will allow more appropriate therapeutic choices. METHODS: We describe a high resolution melting (HRM) assay for mutation detection in EGFR exons 19-21, KRAS codon 12/13 and BRAF V600 using formalin-fixed paraffin-embedded samples. Somatic variation of KRAS exon 2 was also analysed by massively parallel pyrosequencing of amplicons with the GS Junior 454 platform. RESULTS: We tested 120 routine diagnostic specimens from patients with colorectal or lung cancer. Mutations in KRAS, BRAF and EGFR were observed in 41.9%, 13.0% and 11.1% of the overall samples, respectively, being mutually exclusive. For KRAS, six types of substitutions were detected (17 G12D, 9 G13D, 7 G12C, 2 G12A, 2 G12V, 2 G12S), while V600E accounted for all the BRAF activating mutations. Regarding EGFR, two cases showed exon 19 deletions (delE746-A750 and delE746-T751insA) and another two substitutions in exon 21 (one showed L858R with the resistance mutation T590M in exon 20, and the other had P848L mutation). Consistent with earlier reports, our results show that KRAS and BRAF mutation frequencies in colorectal cancer were 44.3% and 13.0%, respectively, while EGFR mutations were detected in 11.1% of the lung cancer specimens. Ultra-deep amplicon pyrosequencing successfully validated the HRM results and allowed detection and quantitation of KRAS somatic mutations. CONCLUSIONS: HRM is a rapid and sensitive method for moderate-throughput cost-effective screening of oncogene mutations in clinical samples. Rather than Sanger sequence validation, next-generation sequencing technology results in more accurate quantitative results in somatic variation and can be achieved at a higher throughput scale.

Genetic diversity of Toscana virus

Distribution of Toscana virus (TOSV) is evolving with climate change, and pathogenicity may be higher in nonexposed populations outside areas of current prevalence (Mediterranean Basin). To characterize genetic diversity of TOSV, we determined the coding sequences of isolates from Spain and France. TOSV is more diverse than other well-studied phleboviruses (e.g.,Rift Valley fever virus).

Fracturas femorales periprotésicas de rodilla tratadas con clavo intramedular retrógrado y osteosíntesis con placa: comparación de resultados a medio-largo plazo

INTRODUCTION: The femoral periprosthetic fracture of the knee is one of the most feared complications because of its repercussions. Incidence are more and more likely due to the increase of total implanted arthroplasty of the knee, due to the increasing lifespan among the general population. The objective of this study is to analyze some of the perioperative aspects of the treatment of these fractures, comparing the use of osteosynthesis with plates and the retrograde nailing in those patients with femoral periprosthetic knee fractures with a stable implant. MATERIAL AND METODS: The study retrospectively examines 18 cases treated consecutively in our hospital (3 men and 15 women, average age of 72.7 years) between the years of 2000 and 2009. All fractures were located in the distal femur and on a stable implant. Eight were treated through retrograde nailing (Group I) and ten with plates (Group II). The cases are analyzed through the tests of the University of Mann-Withney and the exact Fischer test, with significant values of p≤0.05, the variables of median hospital stay, necessity of transfusion indicated with values of hemoglobin less than 8 mg/ml, preoperative radiological alignment and postoperative alignment of the total knee prosthesis (TKR), measured following the anatomical tibiofemoral axis, time of consolidation and incidence of localized complications in both groups. RESULTS: We did not find any statistically significant differences between the two groups in any of the variables analyzed. Localized complications are more frequent in Group I (62.5 percent of patients) than in Group II (10 percent of patients). The need for transfusion is greater in Group II (40 percent) than in Group I (12.5 percent). CONCLUSIONS: The type of implant used in treatment of femoral periprosthetic knee fracture does not significantly influence perioperative factors. The treatment for this type of fractures should be individually chosen in relation to the type of fracture, characteristics of the patient and stability and prosthesis model of the primary knee.

Liver safety assessment: required data elements and best practices for data collection and standardization in clinical trials.

A workshop was convened to discuss best practices for the assessment of drug-induced liver injury (DILI) in clinical trials. In a breakout session, workshop attendees discussed necessary data elements and standards for the accurate measurement of DILI risk associated with new therapeutic agents in clinical trials. There was agreement that in order to achieve this goal the systematic acquisition of protocol-specified clinical measures and lab specimens from all study subjects is crucial. In addition, standard DILI terms that address the diverse clinical and pathologic signatures of DILI were considered essential. There was a strong consensus that clinical and lab analyses necessary for the evaluation of cases of acute liver injury should be consistent with the US Food and Drug Administration (FDA) guidance on pre-marketing risk assessment of DILI in clinical trials issued in 2009. A recommendation that liver injury case review and management be guided by clinicians with hepatologic expertise was made. Of note, there was agreement that emerging DILI signals should prompt the systematic collection of candidate pharmacogenomic, proteomic and/or metabonomic biomarkers from all study subjects. The use of emerging standardized clinical terminology, CRFs and graphic tools for data review to enable harmonization across clinical trials was strongly encouraged. Many of the recommendations made in the breakout session are in alignment with those made in the other parallel sessions on methodology to assess clinical liver safety data, causality assessment for suspected DILI, and liver safety assessment in special populations (hepatitis B, C, and oncology trials). Nonetheless, a few outstanding issues remain for future consideration.