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The advent of targeted therapies and personalized medicine in oncology has led in France to the settlement and organisation of a network of hospital molecular genetic platforms under the impetus of the National Cancer Institute (INCa). These platforms are, according to the concerned sites, integrated or not in pathology laboratories. The development of molecular biology methods, the choice of the procedures, the establishment of sample workflow, the quality control and the selection of the genomic alterations to be detected on each platform, have been left to the discretion of the different laboratories. Based on calls for project made by the INCa, hospital molecular genetic platforms were able to adapt their activity according to the assigned budgets. While the presence of some genomic alterations (i.e. KRAS gene mutations in metastatic colon adenocarcinoma or EGFR gene mutations in lung adenocarcinomas), may lead to administration of targeted therapies under the Marketing Authorization Application (MAA), others are associated with therapeutic clinical trials. However, increasing number of MAA for new molecules targeting genomic alterations is likely in the near future. In this context, it is necessary to quickly adapt the organisation of work of the hospital pathology laboratories performing molecular biology tests in order to meet the growing demand of oncologists in the field of targeted therapies. The purpose of this article is to describe the different steps of the settlement of a molecular genetic platform in an academic pathology laboratory (LPCE, CHU de Nice) and to show the experience of this laboratory specifically oriented on the support of the morphological and molecular diagnosis of lung cancer, thyroid cancer and malignant melanoma., (Copyright © 2013 Elsevier Masson SAS. All rights reserved.)

Over the last 10 years, significant financial support from the French National Institute of Cancer (INCa), the Ministry of Health (DGOS), and the Health and Research National Institute (Inserm) helped biobanks--of which tumour banks represent a prominent example of hospital-based infrastructures--to improve their operations, and in some instances to adopt the rules of Biological Ressource Centers as defined by OECD. Nowadays, the use of biological samples of human origin is strictly subordinated to regulations that integrate bioethical principles. However, in spite of the establishment of these regulations, requirement to obtain an authorisation and/or to register the biological collections with the Ministry of Research, many uncertainties persist. While French regulations mandate that samples can be used for research as long as patients did not oppose to such use, many biobank curators face practical and theoretical issues when establishing a Material Transfer Agreement with scientists, due to the lack of harmonization between national regulations--particularly due to a different perception of privacy and free will in anglo-american and other countries--and different demands on the side of private industry or editorial boards of scientific journals. The goal of this article is (1) to describe the procedure followed to collect patients' informed consent at the Biobank of CHU de Nice and (2) to assess the number of obtained consents in comparison to the number of collected samples between 01/09/2004 and 31/12/2009, the number of consents obtained before or after collecting the samples, and the number of patients' refusal to collect their biological resources. This balance-sheet is settled for the three major collections (thoracic, thyroid and head and neck tissues) from the Biobank of CHU de Nice. Results show that 88 % of consents were obtained during this period (82 % in a prospective manner and 6 % in a retrospective manner). Refusal was notified by writing in nine cases only. The percentage of consents varies slightly according to the collection involved and is stable from 2004 to 2009. Overall, our procedure is quite efficient at obtaining informed consents from a majority of patients for whom the tumour bank stores biological samples. This situation provides optimal conditions for the use of collected samples in the context of national and international research projects., (Copyright © 2010 Elsevier Masson SAS. All rights reserved.)

We report a case of lung infection caused by Pasteurella multocida in an immunocompetent patient. Diagnosis was made both on histological analysis of a lung wedge resection, showing pyoepithelioid granulomas, and on bacteriological cultures from lung tissue. Histological diagnosis of pulmonary pasteurellosis is difficult, and other etiological causes of pyoepithelioid granulomas of the lung have to be discussed. Pulmonary pasteurellosis is particularly severe in immunocompromised patients, and should be systematically suspected in patients exposed to pets, eventhough a percutaneous exposure is not usually found for these patients.

Mycobacterium tuberculosis infection remains a major health problem throughout the world. In France, tuberculosis is endemic, particularly in the Paris area (Ile-de-France) and in the south (Provence Alpes côte d'Azur) where immigration is greater than in other countries in northern Europe. Culture is the gold standard for diagnosis of tuberculosis and is the only method enabling a study of strain sensitivity to treatment. Histology contributes to diagnosis in most cases by revealing typical necrotizing granulomatous lesions. The diagnosis is then confirmed by the detection of acid-fast bacilli with Ziehl-Neelsen staining. However, the Ziehl-Neelsen stain is not sensitive and does not allow identification of different species. The polymerase chain reaction (PCR) DNA amplification method has been used to detect M. tuberculosis in formalin-fixed paraffin-embedded tissues. The aim of the present study was to investigate the value of this method for the diagnosis of M. tuberculosis infection. The results obtained with PCR assay were compared to those obtained with histological and microbiological methods (direct examination and culture). Sixty-three specimens (mainly lymph node and lung specimens) exhibiting a positive culture for M. tuberculosis were analyzed. Tuberculosis granulomas were noted in 32/63 cases, tuberculoid granulomas in 18/63, pyoepitheloid granuloms in 10/63, and non-specific inflammation in 3/63. Ziehl-Neelsen staining was positive in 11/63 cases. PCR assay on tissue sections was positive for M. tuberculosis in 58/63 cases. Controls of the PCR method (granulomas due to other mycobacterial species, foreign body granulomas, sarcoidosis granulomas) were all negative. This study shows that PCR from deparaffinized sections, 1) greatly increases the sensitivity of diagnosis of tuberculosis, 2) enables the diagnosis of M. tuberculosis infection. However, although this method reduces the time to diagnosis, culture remains the gold standard for identification of the mycobacterium and for determining the sensitivity of the isolated strain to treatment.