Quantitative detection of circulating tumor DNA by droplet-based digital PCR.

Droplet-based digital PCR is used to detect and quantify the seven most frequent KRAS mutations in circulating tumor DNA of patients with advanced colorectal cancer.- The droplet-based digital PCR method is versatile and two modes of analysis are demonstrated: o Duplex analysis enables sensitive detection of wild-type DNA plus one KRAS or BRAF mutation. o Multiplex analysis enables simultaneous detection of wild-type DNA plus 3 or 4 KRAS mutations.- Detection of rare sequences is highly sensitive compared to the same Taqman assay in bulk (10 % LLOD bulk vs 0.0005 % LLOD droplets).- Biomarkers detection is quantitative: the fraction of mutated DNA in patient samples ranges from 0.1 % to 42%.- Results from circulating tumor DNA analysis match the tumor DNA characterization in most cases, and discordant results reveal need for further studies. Copy and paste your text content here, adjusting the font size to fit Background Circulating tumor DNA (ctDNA) is present in plasma of individuals with advanced cancers. 1 ctDNA is a prognostic marker for patients with colorectal cancer (CRC) and it might also be used for predicting the response to targeted therapy. For example, mutations in KRAS indicate which patients will fail to respond to specific therapies (cetuximab, panitunimab). 2 Although ctDNA is characterized by the presence of a somatic mutation, direct quantitative detection through a simple workflow of such mutant DNA is not feasible by current technologies because the ratio of ctDNA to wildtype DNA can be as low as 1/10,000. This study describes the use of droplet-based digital PCR for detection and quantitation of one of the seven most frequent KRAS mutations in ctDNA from plasm

Pharmacogenetic assessment of toxicity and outcome in patients with metastatic colorectal cancer treated with LV5FU2, FOLFOX, and FOLFIRI: FFCD 2000-05

L’objectif de ce travail était la recherche de biomarqueurs moléculaires prédictifs de la tolérance et de l’efficacité des chimio– thérapies utilisées dans le colorectal (CCR) métastatique. Nous avons effectué le génotypage de 20 polymorphismes présents au sein de 9 gènes connus ou suspectés d’être impliqués dans la voie du 5FU, de l’oxaliplatine, ou de l’irinotécan, à partir de l’ADN extrait du sang de 346 patients traités dans le cadre d’un essai de phase III. Cet essai comparait une chimiothérapie séquentielle par 5FU (schéma LV5FU2) suivie d’une association 5FU plus oxali– platine (schéma FOLFOX) à une chimiothérapie combinée de type FOLFOX d’emblée en première ligne de traitement. Nous avons trouvé un risque de toxicité hématologique sévère sous FOLFOX significativement augmenté chez les patients porteurs de l’allèle ERCC2-K751QC. La présence de l’allèle TS-5’UTR3RG du gène de la thymidylate synthase était associée à un taux de réponse significativement plus élevé sous LV5FU2. Le taux de réponse au FOLFOX en 2e ligne était significativement supérieur chez les patients porteurs de l’allèle ERCC1-IVS3+74G, et chez ceux ayant au moins un allèle de GSTT1 présent. L’analyse prédictive a montré un effet dépendant du traitement de certains polymorphismes. En effet, une survie sans progression significativement allongée par l’ajout de l’oxaliplatine en 1re ligne a été observée uniquement chez les patients ayant un génotype TS-5’UTR2R/2R ou 2R/3R, suggérant l’absence de bénéfice d’une bithérapie par FOLFOX d’emblée en première ligne chez les patients TS-5’UTR3R/3R. Ces résultats montrent que l’étude des polymorphismes constitutionnels permettent de prédire non seulement la toxicité mais aussi l’efficacité des chimiothérapies antitumorales du cancer colorectal, et ainsi (sous réserve d’une validation sur une population indépendante) d’orienter la stratégie thérapeutique à l’échelle de l’individu

Genome wide SNP comparative analysis between EGFR and KRAS mutated NSCLC and characterization of two models of oncogenic cooperation in non-small cell lung carcinoma

<p>Abstract</p> <p>Background</p> <p>Lung cancer with EGFR mutation was shown to be a specific clinical entity. In order to better understand the biology behind this disease we used a genome wide characterization of loss of heterozygosity and amplification by Single Nucleotide Polymorphism (SNP) Array analysis to point out chromosome segments linked to <it>EGFR </it>mutations. To do so, we compared genetic profiles between <it>EGFR </it>mutated adenocarcinomas (ADC) and <it>KRAS </it>mutated ADC from 24 women with localized lung cancer.</p> <p>Results</p> <p>Patterns of alterations were different between <it>EGFR </it>and <it>KRAS </it>mutated tumors and specific chromosomes alterations were linked to the <it>EGFR </it>mutated group. Indeed chromosome regions 14q21.3 (p = 0.027), 7p21.3-p21.2 (p = 0.032), 7p21.3 (p = 0.042) and 7p21.2-7p15.3 (p = 0.043) were found significantly amplified in EGFR mutated tumors. Within those regions 3 genes are of special interest <it>ITGB8</it>, <it>HDAC9 </it>and <it>TWIST1</it>. Moreover, homozygous deletions at <it>CDKN2A </it>and LOH at <it>RB1 </it>were identified in <it>EGFR </it>mutated tumors. We therefore tested the existence of a link between EGFR mutation, CDKN2A homozygous deletion and cyclin amplification in a larger series of tumors. Indeed, in a series of non-small-cell lung carcinoma (n = 98) we showed that homozygous deletions at <it>CDKN2A </it>were linked to <it>EGFR </it>mutations and absence of smoking whereas cyclin amplifications (<it>CCNE1 </it>and <it>CCND1</it>) were associated to <it>TP53 </it>mutations and smoking habit.</p> <p>Conclusion</p> <p>All together, our results show that genome wide patterns of alteration differ between <it>EGFR </it>and <it>KRAS </it>mutated lung ADC, describe two models of oncogenic cooperation involving either <it>EGFR </it>mutation and <it>CDKN2A </it>deletion or cyclin amplification and <it>TP53 </it>inactivating mutations and identified new chromosome regions at 7p and 14q associated to EGFR mutations in lung cancer.</p

Genetic polymorphisms of MMP1, MMP3 and MMP7 gene promoter and risk of colorectal adenoma

BACKGROUND: Matrix metalloproteinases (MMP) have been shown to play a role in colorectal cancer (CRC). More recently, MMP1, MMP3 and MMP7 functional gene promoter polymorphisms have been found to be associated with CRC occurrence and prognosis. To document the role of MMP polymorphisms in the early step of colorectal carcinogenesis, we investigated their association with colorectal adenoma risk in a case-control study comprising 295 patients with large adenomas (LA), 302 patients with small adenomas (SA) and 568 polyp-free (PF) controls. METHODS: Patients were genotyped using automated fragment analysis for MMP1 -1607 ins/del G and MMP3 -1612 ins/delA (MMP3.1) polymorphisms and allelic discrimination assay for MMP3 -709 A/G (MMP3.2) and MMP7 -181 A/G polymorphisms. Association between MMP genotypes and colorectal adenomas was first tested for each polymorphism separately and then for combined genotypes using the combination test. Adjustment on relevant variables and estimation of odds ratios were performed using unconditional logistic regression. RESULTS: No association was observed between the polymorphisms and LA when compared to PF or SA. When comparing SA to PF controls, analysis revealed a significant association between MMP3 -1612 ins/delA polymorphism and SA with an increased risk associated with the 6A/6A genotype (OR = 1.67, 95%CI: 1.20–2.34). Using the combination test, the best association was found for MMP3.1-MMP1 (p = 0.001) with an OR of 1.88 (95%CI: 1.08–3.28) for the combined genotype 2G/2G-6A/6A estimated by logistic regression. CONCLUSION: These data show a relation between MMP1 -1607 ins/del G and MMP3 -1612 ins/delA combined polymorphisms and risk of SA, suggesting their potential role in the early steps of colorectal carcinogenesis

Simultaneous detection of lung fusions using a multiplex RT-PCR next generation sequencing-based approach:A multi-institutional research study

Contains fulltext : 195300.pdf (publisher's version ) (Open Access

Exome sequencing identifies germline variants in DIS3 in familial multiple myeloma

[Excerpt] Multiple myeloma (MM) is the third most common hematological malignancy, after Non-Hodgkin Lymphoma and Leukemia. MM is generally preceded by Monoclonal Gammopathy of Undetermined Significance (MGUS) [1], and epidemiological studies have identified older age, male gender, family history, and MGUS as risk factors for developing MM [2]. The somatic mutational landscape of sporadic MM has been increasingly investigated, aiming to identify recurrent genetic events involved in myelomagenesis. Whole exome and whole genome sequencing studies have shown that MM is a genetically heterogeneous disease that evolves through accumulation of both clonal and subclonal driver mutations [3] and identified recurrently somatically mutated genes, including KRAS, NRAS, FAM46C, TP53, DIS3, BRAF, TRAF3, CYLD, RB1 and PRDM1 [3,4,5]. Despite the fact that family-based studies have provided data consistent with an inherited genetic susceptibility to MM compatible with Mendelian transmission [6], the molecular basis of inherited MM predisposition is only partly understood. Genome-Wide Association (GWAS) studies have identified and validated 23 loci significantly associated with an increased risk of developing MM that explain ~16% of heritability [7] and only a subset of familial cases are thought to have a polygenic background [8]. Recent studies have identified rare germline variants predisposing to MM in KDM1A [9], ARID1A and USP45 [10], and the implementation of next-generation sequencing technology will allow the characterization of more such rare variants. [...]French National Cancer Institute (INCA) and the Fondation Française pour la Recherche contre le Myélome et les Gammapathies (FFMRG), the Intergroupe Francophone du Myélome (IFM), NCI R01 NCI CA167824 and a generous donation from Matthew Bell. This work was supported in part through the computational resources and staff expertise provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai. Research reported in this paper was supported by the Office of Research Infrastructure of the National Institutes of Health under award number S10OD018522. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health. The authors thank the Association des Malades du Myélome Multiple (AF3M) for their continued support and participation. Where authors are identified as personnel of the International Agency for Research on Cancer / World Health Organization, the authors alone are responsible for the views expressed in this article and they do not necessarily represent the decisions, policy or views of the International Agency for Research on Cancer / World Health Organizatio

Le syndrome de Capgras et autres délires d'identification des personnes (approche historique, clinique et psychopathologique)

L'illusion des sosies ou syndrome de Capgras a été décrit en 1923 par Joseph Capgras et son interne Jean Reboul-Lachaux. Ce " curieux petit syndrome " se caractérise par une méconnaissance délirante de l'identité de certains proches très investis affectivement. Le sujet reconnaît l'apparence physique d'autrui, mais il ne peut accéder à son identité. Il est convaincu qu'il affaire à un sosie, un imposteur. Le syndrome de Frégoli, l'intermétamorphose et le syndrome du double subjectif constituent, avec le syndrome de Capgras, les quatre principaux délires d'identification des personnes. Ces syndromes mettent en évidence une dissociation des registres de la reconnaissance et de l'identification. La découverte, vers le milieu des années 1970, de cas de patients développant un syndrome de Capgras dans un contexte organique et l'avènement des techniques d'imagerie cérébrale ont contribué au développement des hypothèses en neuropsychologie cognitive, modifiant ainsi le champ de la psychopathologie, où prédominaient les interprétations psychodynamiques. Nous avons, dans ce travail, étudié le syndrome de Cpagras sous ses aspects historiques, cliniques et psychopathologiques.PARIS7-Xavier Bichat (751182101) / SudocPARIS-BIUM (751062103) / SudocSudocFranceF

Pharmacokinetic drug-drug interactions of tyrosine kinase inhibitors: A focus on cytochrome P450, transporters, and acid suppression therapy

International audienceThe extensive use of tyrosine kinase inhibitors (TKI's) in hematology and oncology has shown that these drugs have a significant potential for drug-drug interactions. Since these drugs have a rather low therapeutic window, some drug interactions are of particular clinical relevance either on drug toxicity or on patient's response. Significant interactions occur with concomitant use of acid-suppressive therapy leading to a decreased oral bioavailability. However, such interactions are drug dependent according to their solubility pattern and to the duration of action of acid-suppressive therapy, which is coprescribed. Significant interactions occur by inhibition or induction of CYP450 3A4 which is the main metabolic pathway of TKIs. However, minor metabolic pathways should also be paid attention to. Interactions involving efflux and influx transporters should also be considered occurring for some TKIs. Genetic polymorphism in drug metabolism as well as in drug transport is a factor of variability in drug exposure, which could modulate the magnitude of drug-drug interactions (DDIs). It should be noticed that TKIs can also be at the origin of drug interactions by altering the pharmacokinetics of coprescribed drugs. Since cancer patients are given many drugs either for supportive care or for the treatment of drug toxicity, and to the fact that the oldest patients are polymedicated, a clear understanding of DDIs with TKIs is of interest. The objectives of this review are to provide an overview of the mechanisms of DDIs with TKIs and to provide to physicians and pharmacists recommendations to manage these DDIs in their clinical practice

Modélisation des effets des systèmes de culture sur la dynamique de la plante parasite orobanche rameuse en interaction avec la flore adventice

National audienc

Les vallées fossiles de la baie de la Vilaine : nature et évolution du prisme sédimentaire côtier du Pléistocène armoricain

International audienceL'étude d(un maillage serré de profils sismiques Sparker haute résolution, obtenus en baie de Vilaine (mission INSU-CNRS Géovill), a permis de mettre en évidence la structure du prisme sédimentaire côtier, préservé entre les côte et l'isobathe -50 m, en Bretagne sud. Ce prisme repose sur un substratum qui montre trois entités sismiques U1, U2, U3 attribuées respectivement au socle métamorphique et magmatique, aux grès et calcaires gréseux yprésiens et lutétiens et aux séries sédimentaires post-éocènes. le prisme côtier comprend trois unités sismiques principales. Une unité basale (U4), interprétée comme des dépôts fluviatiles en tresse, qui pourrait correspondre aux séries datée à terre de 600 à 317 ka BP. Une unité médiane (U5) d'âge inconnu correspondant à des dépôts fluviatiles méandriformes et estuariens passant vers l'ouest à des dépôts d'embouchure. Une unité sommitale (U6) comprenant des argilites marines et des systèmes littoraux de type barrière dont la base est datée de 8 110±200 ans. Ces trois dernières unités sont séparées par deux discontinuités majeures. Une "unconformity" ou limite de séquence entre U4 et U5 et une surface de ravinement par la houle et les marées entre les unités 5 et 6. Ces surfaces limitent deux séquences à l'intérieur du prisme côtier : une séquence basale (U4) et une séquence sommitale (U5 et U6).Par analogie avec l'évolution décrite à terre, la séquence basale est attribuée au cycle glaciaire saalien et/ou elstérien et la séquence sommitale au cycle weichsélien (cortège de bas niveau) et à la transgression marine holocène (cortège transgressif). Toutefois, le passage d'une séquence à l'autre correspond à un changement de 60°, des directions d'écoulement des paléofleuves bretons en baie de Vilaine dont l'orientation suit celle des principaux réseaux de fractures régionaux. Ainsi, l'activité de la Bretagne au Pléistocène, liée aux contraintes intraplaques, pourrait être à l'origine de la distribution des corps sédimentaires dans le prisme côtier sud breton. En effet, le basculement du Massif Armoricain au cours de cette période a provoqué un rajeunissement complet des profils fluviatiles régionaux et peut-être la fin de la capture de la Paléovilaine par la Paléoloire