scholarly journals Explore the Rare—Molecular Identification and Wine Evaluation of Two Autochthonous Greek Varieties: “Karnachalades” and “Bogialamades”

Plants ◽  
2021 ◽  
Vol 10 (8) ◽  
pp. 1556
Author(s):  
Dimitrios Evangelos Miliordos ◽  
Georgios Merkouropoulos ◽  
Charikleia Kogkou ◽  
Spyridon Arseniou ◽  
Anastasios Alatzas ◽  
...  
Keyword(s):  
Molecular Data ◽  
Molecular Profiling ◽  
Scientific Data ◽  
Financial Impact ◽  
Molecular Profile ◽  
Red Wines ◽  
Grape Berries ◽  
Quality Aspects ◽  
Commercial Vineyard ◽  
Of Greece

Wines produced from autochthonous Vitis vinifera varieties have an essential financial impact on the national economy of Greece. However, scientific data regarding characteristics and quality aspects of these wines is extremely limited. The aim of the current study is to define the molecular profile and to describe chemical and sensory characteristics of the wines produced by two autochthonous red grapevine varieties—“Karnachalades” and “Bogialamades”—grown in the wider area of Soufli (Thrace, Greece). We used seven microsatellites to define the molecular profile of the two varieties, and then we compared their profile to similar molecular data from other autochthonous as well as international varieties. Grape berries were harvested at optimum technological maturity from a commercial vineyard for two consecutive vintages (2017–2018) and vilification was performed using a common vinification protocol: the 2017 vintage provided wines, from both varieties, with greater rates of phenolics and anthocyanins than 2018, whereas regarding the sensory analysis, “Bogialamades” wine provided a richer profile than “Karnachalades”. To our knowledge, this is the first study that couples both molecular profiling and exploration of the enological potential of the rare Greek varieties “Karnachalades” and “Bogialamades”; they represent two promising varieties for the production of red wines in the historic region of Thrace.

scholarly journals Wolbachia: endosymbiont of onchocercid nematodes and their vectors

2021 ◽  
Vol 14 (1) ◽  
Author(s):  
Ranju Ravindran Santhakumari Manoj ◽  
Maria Stefania Latrofa ◽  
Sara Epis ◽  
Domenico Otranto
Keyword(s):  
Control Strategies ◽  
Molecular Data ◽  
Scientific Data ◽  
Growth And Survival ◽  
Vector Borne Diseases ◽  
Wide Range ◽  
Veterinary Importance ◽  
Wolbachia Endosymbiont ◽  
Vector Borne ◽  
And Control

Abstract Background Wolbachia is an obligate intracellular maternally transmitted, gram-negative bacterium which forms a spectrum of endosymbiotic relationships from parasitism to obligatory mutualism in a wide range of arthropods and onchocercid nematodes, respectively. In arthropods Wolbachia produces reproductive manipulations such as male killing, feminization, parthenogenesis and cytoplasmic incompatibility for its propagation and provides an additional fitness benefit for the host to protect against pathogens, whilst in onchocercid nematodes, apart from the mutual metabolic dependence, this bacterium is involved in moulting, embryogenesis, growth and survival of the host. Methods This review details the molecular data of Wolbachia and its effect on host biology, immunity, ecology and evolution, reproduction, endosymbiont-based treatment and control strategies exploited for filariasis. Relevant peer-reviewed scientic papers available in various authenticated scientific data bases were considered while writing the review. Conclusions The information presented provides an overview on Wolbachia biology and its use in the control and/or treatment of vectors, onchocercid nematodes and viral diseases of medical and veterinary importance. This offers the development of new approaches for the control of a variety of vector-borne diseases. Graphic Abstract

scholarly journals EPEN-45. NORMALIZING AND FACILITATING GENOMIC TESTING AT DIAGNOSIS IN PEDIATRIC EPENDYMOMA

2020 ◽  
Vol 22 (Supplement_3) ◽  
pp. iii317-iii317
Author(s):  
Emily Owens Pickle ◽  
Ana Aguilar-Bonilla ◽  
Amy Smith
Keyword(s):  
Current Practice ◽  
Molecular Classification ◽  
Molecular Data ◽  
Molecular Profiling ◽  
Genomic Testing ◽  
Molecular Testing ◽  
Newly Diagnosed ◽  
Pediatric Ependymoma ◽  
Need Support ◽  
Almost All

Abstract The current consensus is that diagnosis and treatment of ependymoma should be based upon clinical and molecular classification. As we move into this paradigm, it is important all ependymoma cases undergo tumor collection, preservation, and molecular profiling at diagnosis. Our group of 6 sites gathered data on a cohort of 72 ependymoma cases. Sites were asked to report known molecular findings; 60/68 eligible cases (88%) did not include genetic findings. The low number of cases with molecular findings was surprising and since cases were diagnosed from as early as 2004, we asked collaborators to share their current practice in profiling (e.g., how frequently; in what setting were ependymomas sent for testing) to try and better understand current practice at sites. Since the publication of ependymoma molecular data, sites with a neuro-oncology program report sending almost all newly diagnosed ependymomas for molecular testing, whereas current practices at sites without dedicated neuro-oncology were less consistent. Profiling in the setting of relapse was more frequently reported at all centers. The implementation of molecular testing at diagnosis may need support at sites without dedicated neuro-oncology. Lead investigators for upcoming ependymoma clinical trials will need to think carefully about the logistics of profiling at centers where this is not standard practice at diagnosis.

scholarly journals Six new cases confirm the clinical molecular profile of complete combined 17α-hydroxylase/ 17,20-lyase deficiency in Brazil

2010 ◽  
Vol 54 (8) ◽  
pp. 711-716 ◽  
Author(s):  
Daiane Rodrigues Barbosa Belgini ◽  
Maricilda Palandi de Mello ◽  
Maria Tereza Matias Baptista ◽  
Daniel Minutti de Oliveira ◽  
Fernanda Canova Denardi ◽  
...  
Keyword(s):  
Present Report ◽  
Molecular Data ◽  
The Other ◽  
Renin Activity ◽  
Inguinal Region ◽  
Molecular Profile ◽  
Hydroxylase Deficiency ◽  
Lyase Deficiency ◽  
Frequent Mutations ◽  
Low Levels

In 2004, Costa-Santos and cols. reported 24 patients from 19 Brazilian families with 17α-hydroxylase deficiency and showed that p.W406R and p.R362C corresponded to 50% and 32% of CYP17A1 mutant alleles, respectively. The present report describes clinical and molecular data of six patients from three inbred Brazilian families with 17α-hydroxlyse deficiency. All patients had hypogonadism, amenorrhea and hypertension at diagnosis. Two sisters were found to be 46,XY with both gonads palpable in the inguinal region. All patients presented hypergonadotrophic hypogonadism, with high levels of ACTH (> 104 ng/mL), suppressed plasmatic renin activity, low levels of potassium (< 2.8 mEq/L) and elevated progesterone levels (> 4.4 ng/mL). Three of them, including two sisters, were homozygous for p.W406R mutation and the other three (two sisters and one cousin) were homozygous for p.R362C. The finding of p.W406R and p.R362C in the CYP17A1 gene here reported in additional families, confirms them as the most frequent mutations causing complete combined 17α-hydroxylase/17,20-lyase deficiency in Brazilian patients.

scholarly journals Investigating the clinical, pathological and molecular profile of oncocytic adrenocortical neoplasms

2021 ◽  
Author(s):  
Eleanor Fewings ◽  
Serena Khoo Sert Kim ◽  
Alexey Larionov ◽  
Alison Marker ◽  
Olivier Giger ◽  
...  
Keyword(s):  
Treatment Strategies ◽  
Case Series ◽  
Missense Variant ◽  
Molecular Profiling ◽  
The Cancer Genome Atlas ◽  
Biological Behavior ◽  
Molecular Profile ◽  
Mutation Burden ◽  
Rare Tumours ◽  
Paired Tumour

Background: Malignant oncocytic adrenocortical neoplasms (OANs) are rare tumours with a distinctive biological behavior compared to conventional adrenocortical carcinoma (ACC). The current prognostic systems overestimate the malignant potential of these tumours and guidance for surveillance and treatment strategies are lacking. Aim: To evaluate the utility of clinical, pathological and molecular markers in predicting the biological behavior and outcomes of malignant OANs. Methods: A retrospective clinicopathological review of ten histologically confirmed OANs was carried out. Whole exome sequencing (WES) of germline and paired tumour samples was performed for four of the ten OAN cases and compared to WES data from five cases of conventional ACC and data from The Cancer Genome Atlas (TCGA). We reviewed all cases of malignant OAN reported in the literature and compared to our case series. Results: Eight (80%) tumours were classified as malignant, one borderline and one benign (Lin-Weiss-Bisceglia criteria: LWB). The malignant OAN were larger tumours and had higher MIB index and Helsinki scores. Molecular profiling identified a pathogenic germline variant in MSH6 in an individual in the OAN group. The OAN samples had a lower mutation burden compared to the ACC samples. Somatic driver variants were identified in OAN and ACC samples including a pathogenic missense variant in CTNNB1. Conclusion: In this study, the LWB classification demonstrated sensitivity for the differentiation of benign from malignant OAN. Molecular profiling identified dysregulation in DNA repair and Wnt signaling pathways in both OAN and ACC samples, suggesting a molecular overlap between OAN and conventional ACC.

Use of Molecular Profiling to Guide Treatment Decisions in Patients with Neuroendocrine Tumors: Preliminary Results

2016 ◽  
Vol 82 (4) ◽  
pp. 369-375 ◽  
Author(s):  
Holt S. Cutler ◽  
Paul Ogando ◽  
Joshua H. Uhr ◽  
Dani O. Gonzalez ◽  
Richard R.P. Warner ◽  
...  
Keyword(s):  
Neuroendocrine Tumors ◽  
Clinical Symptoms ◽  
Case Series ◽  
Molecular Profiling ◽  
Serum Markers ◽  
Carcinoid Tumors ◽  
Molecular Profile ◽  
Chemotherapy Response ◽  
Choice Of Treatment ◽  
Selection Of

This case series demonstrates the potential of molecular profiling to improve selection of anti-tumor therapies in the treatment of patients with neuroendocrine and carcinoid tumors. Carcinoid tumors resected at one institution over a 3-year period were sent for molecular profiling to guide choice of treatment. Potentially beneficial therapies were identified based on the measured expression of 20 proteins and oncogenes and a comprehensive review of the chemotherapy response literature. The clinical charts of 41 patients were reviewed retrospectively, and 12 were selected as representatives of the range of effects molecular profiling has on carcinoid treatment. Their presentation, molecular profile results, treatment, and disease progression is reviewed in the following case series. A total of nine patients were treated with drugs identified as potentially beneficial by molecular profile reports. These include capecitabine, 5-fluorouracil, temozolomide, oxaliplatin, and gemcitabine. Based on clinical symptoms, serum markers of disease, and radio-graphic evidence five of nine patients responded to treatment, two had mixed responses, and two did not respond to treatment. At this early juncture, our critique of molecular profiling for neuroendocrine tumors is favorable, as a significant number of our patients responded to drugs identified by molecular profiling as potentially beneficial.

Approaching individualized care with a clinical tissue proteomics methodology.

2013 ◽  
Vol 31 (15_suppl) ◽  
pp. e22180-e22180
Author(s):  
Donald Joseph Johann ◽  
Sumana Mukherjee ◽  
DaRue Prieto ◽  
Josip Blonder
Keyword(s):  
Molecular Data ◽  
Molecular Profiling ◽  
Similarity Score ◽  
Normal Breast ◽  
Molecular Heterogeneity ◽  
Cancer Pathways ◽  
Tumor Subtypes ◽  
Individualized Care ◽  
Time Requirements ◽  
Molecular Circuitry

e22180 Background: The vast majority of therapy plans for cancer patients are derived categorically. Currently, large and time lengthy clinical trials supply the oncology community with aggregate population and survival statistics. Although this approach has been successful there are known shortfalls. More specifically, since the inherent molecular heterogeneity of the solid tumor under study has not been examined, it is not surprising that results may vary widely across individual patients. Therefore, what is needed is a rationally-based molecular profiling of an individual patient's tumor, in a timely manner. The aim is to link the best drug(s) to the individual patient's cancer based on objective molecular data, thus maximizing therapeutic efficacy and minimizing toxicity. Methods: Presented is a new form of a protein-based molecular profiling approach developed utilizing LC/MS-MS. Importantly, this method has the same tissue and time requirements as IHC. A total of 30 breast tumors and 10 normal breast samples were analyzed. Tumors consisted of 10 ER+, 10 HER2+, and 10 triple negative. Custom software was developed. First, to better illustrate the molecular circuitry of the tumor, proteomic data was rendered as a virtual wiring diagram. This was done on a per tumor basis thus graphically illustrating the molecular traffic intensities. Second, computationally deriving a numeric similarity score to allow for easier comparison of molecular circuitry. Results: Biologically relevant proteins (p53, ER, HER2, Ki67) including driver oncoproteins were found. Effective molecular profiling of breast cancer at the protein level was achieved and the established clinical tumor subtypes were discriminated by unsupervised clustering. A visualized simulation of an estrogen carcinogenesis network was also developed. Experimentally identified proteins and expression levels were mapped and objectified onto known cancer pathways contained in the network. Conclusions: Since the tissue quantity and time requirements are the same as IHC the approach is clinically practical. The approach is discovery based and complementary to IHC but is not dependent on antibodies. This method shows promise as a research tool in a clinical trial.

Next-generation sequencing: Profiling gallbladder cancer (GBC).

2015 ◽  
Vol 33 (3_suppl) ◽  
pp. 286-286 ◽  
Author(s):  
Joanne Wing-Yan Chiu ◽  
Stefano Serra ◽  
Suzanne Kamel-Reid ◽  
Tong Zhang ◽  
Mairead Geraldine McNamara ◽  
...  
Keyword(s):  
Pik3ca Mutation ◽  
Tumor Grade ◽  
Illumina Miseq ◽  
Molecular Profiling ◽  
Ampullary Cancer ◽  
Idh1 Mutation ◽  
Molecular Profile ◽  
Biliary Cancer ◽  
Formalin Fixed Paraffin Embedded ◽  
Frequent Mutations

286 Background: Molecular profiling data of GBC is scant and it is often included with other biliary cancers for analysis, which may hinder advancing drug discovery. Methods: Archival formalin fixed paraffin embedded (FFPE) tissue of GBC from 2 research hospitals in Toronto (n=21) and Hong Kong (n=21) were analyzed by MassARRAY Sequenom panel (23 genes, 279 mutations), or by next general sequencing (NGS) using Proton or Illumina MiSeq TruSeq Amplicon Cancer Panel (48 genes, 212 amplicons, ≥500x coverage). Results of other biliary cancer and ampullary cancer from an ongoing profiling project were also reported. Results: Twelve biliary cancer samples first analyzed with Sequenom revealed no mutations. Reanalysis with NGS of these yielded mutations in 5. All subsequent samples were analyzed with NGS (n=57). Mutations were identified in 80% [53 mutations in 42 GBC, 8 mutations in 9 intrahepatic cholangiocarcinoma (IHC), 7 mutations in 6 hilar/distal bile duct cancers (DBD)]. The most frequent mutations in GBC were TP53 and SMAD4, and KRAS mutation was found in 7% (Table). PIK3CA mutation was found in 5% of GBC but not the other biliary cancers, and IDH1 mutation was exclusive for IHC, in agreement with published literature. TP53 mutations in GBC patients did not correlate with gender, tumor grade, survival, or treatment response to gemcitabine-based chemotherapy. There was no difference in mutation patterns in GBC between 2 institutions/countries. Conclusions: NGS can be utilized for molecular profiling of biliary cancer, detecting potentially actionable targets in the majority of cases. Our preliminary data suggests GBC may have its own molecular profile, deserving special consideration in trial design for biliary cancer. To our knowledge the current study is the biggest cohort of NGS analysis for GBC. [Table: see text]

Evaluation of liquid biopsies for molecular profiling in patients with advanced non-small cell lung cancer (NSCLC) in the relapse treatment setting.

2017 ◽  
Vol 35 (15_suppl) ◽  
pp. 11532-11532
Author(s):  
Jordi Remon ◽  
Benjamin Besse ◽  
Ludovic Lacroix ◽  
Laura Mezquita ◽  
Cecile Jovelet ◽  
...  
Keyword(s):  
Liquid Biopsy ◽  
Dynamic Change ◽  
Molecular Profiling ◽  
Molecular Profile ◽  
Blood Collection ◽  
Liquid Biopsies ◽  
Molecular Abnormalities ◽  
Nsclc Patients ◽  
Tumor Dna ◽  
Allele Fraction

11532 Background: Molecular profiling is limited by access to sufficient tumor tissue for comprehensive analysis and due to tumor heterogeneity, the complete range of tumor DNA abnormalities may not be represented nor accurately reflect the clinical evolution of disease. Circulating tumor DNA (ctDNA) can be used as a minimally-invasive liquid biopsy for the detection, quantification and monitoring of molecular abnormalities for personalized treatment strategies. Methods: In a prospectively designed program, to date, we have recruited 227 advanced NSCLC patients having received prior therapy, with unknown molecular profile at time of blood collection. Blood collections (10ml K2-EDTA) were performed to assess molecular profile prior to or at time of relapse. Repeat samples were performed on patients initiated on treatment and followed for up to 18months. Patient samples were analyzed with InVision (enhanced tagged-amplicon sequencing) using a 34 gene panel. Interim analysis performed with full descriptive summary statistical analyses to be presented at conference. Results: ctDNA profiling detected somatic mutations in 182pts (80.2%), predominantly located in TP53 (46%), EGFR (28%), KRAS (11%) and STK11 (7%, half of which had concurrent KRAS). Of note, clinically actionable mutations were detected: T790M (25pts, median 1.4% AF), ERBB2 (8 pts), MET (8pts) and BRAF (4pts) providing eligibility for new therapy options. 20pts including 12 EGFR/T790M+ve were evaluated for ctDNA monitoring up to 18 months (median 10m); correlation between dynamic change in mutation allele fraction and clinical response was observed, especially predictive of relapse to treatment. 10 patients demonstrated SD/PR response to osimertinib treatment with T790M detection at low allele fraction (7/10 < 1% AF with 1pt at 0.08% AF). Conclusions: ctDNA can be used as a non-invasive ‘liquid biopsy’ for molecular profiling of NSCLC patients to detect clinically relevant and actionable mutations when tissue biopsy is unavailable. Liquid biopsies can be repeated as needed where tissue is not feasible, providing real-time information to support personalised treatment.

Additional data on Iranian trichodorids (Triplonchida: Trichodoridae) and first record of a rare species, Trichodorus variabilis Roca, 1998

Nematology ◽  
2017 ◽  
Vol 19 (2) ◽  
pp. 121-129 ◽  
Author(s):  
Majid Pedram ◽  
Ali Roshan-Bakhsh ◽  
Ebrahim Pourjam ◽  
Mohammad Reza Atighi ◽  
Wilfrida Decraemer ◽  
...  
Keyword(s):  
Phylogenetic Analyses ◽  
First Record ◽  
Molecular Data ◽  
Slight Variation ◽  
Natural Forests ◽  
Northern Iran ◽  
Phylogenetic Studies ◽  
Molecular Phylogenetic ◽  
First Time ◽  
Of Greece

Trichodorus variabilis, recovered from three separate locations in natural forests of northern Iran, was studied using morphological, morphometric and molecular data. Variation in position of the ventromedian cervical papillae (CP1 and CP2) with respect to the onchiostyle base in the resting position, and spicule characters (having or lacking striation in distal blade region and bristles in proximal blade region) were observed. Variation was also observed in the nature of the pharyngo-intestinal junction (offset to slight overlapping). The secretory-excretory pore of females also showed slight variation in placement. Molecular phylogenetic studies, using partial 28S rDNA D2-D3 sequences of three studied populations and one sequenced isolate of the species from Greece, revealed T. variabilis has variation in the sequences of this genomic fragment. The similarity percent of four sequences ranged from 96.7 to 99.7%. The species was found for the first time outside of Greece, the country from which it was originally described. A newly recovered population of T. persicus, originally described from Iran, was also included in the molecular phylogenetic analyses.

The PLATON pilot-study “Platform for analyzing targetable tumor mutations”: A PLATON network study.

2021 ◽  
Vol 39 (15_suppl) ◽  
pp. TPS6598-TPS6598
Author(s):  
Arndt Vogel ◽  
Bianca Zäpf ◽  
Thorsten Oliver Goetze ◽  
Benedikt Westphalen ◽  
Lothar Müller ◽  
...  
Keyword(s):  
Clinical Trials ◽  
Pilot Study ◽  
Web Application ◽  
Treatment Options ◽  
Molecular Profiling ◽  
Tumor Board ◽  
Molecular Profile ◽  
Curative Therapy ◽  
Esophagogastric Cancer ◽  
Study Sites

TPS6598 Background: PLATON Network is designed as a platform to improve personalized therapy based on genomic profiles in gastrointestinal cancer patients. PLATON’s study-design focuses on patient’s molecular profiling and will provide a network web application for interlinking PLATON investigators which integrates information of the participating centers, their patients, the molecular profiles and available clinical trials at PLATON`s study-sites. Methods: The PLATON Network is designed as a permanent open, multicenter, prospective, cohort study with biobanking, with a shared platform infrastructure for associated sub-studies. In a first approach the PLATON Network enrolls within its pilot-study 200 patients in Germany of both sexes and ages over 18 at 40 study sites (NCT04484636) with signed informed consent. All patients of the pilot-study are diagnosed with hepatocellular cancer (HCC), intra- and extrahepatic cholangiocellular carcinoma (CCA), gallbladder carcinoma (GBCA), pancreatic cancer (PDCA) or esophagogastric cancer (EC/GC). At the time of enrolment, patients are within their first-line therapy and no local curative therapy is available. Molecular profiling will be performed with the Foundation Medicine Assays FoundationOne CDx and FoundationOne Liquid CDx. Investigators may use the platform for searching clinical trials matching the individual molecular profile of their patients or may identify a patient, who may be eligible for a study or other treatment options available at the corresponding centers of the PLATON network. The interactive network web application will comprise a dashboard and a moderated chat room to interact for example in a virtual Molecular Tumor Board. The first patient was included on the 25th of November 2020. Up to 12th of February 2021, a total of 36 patients HCC (N = 1), CCA (N = 6), PDCA (N = 12), GBCA (N = 0) and EC/GC (N = 16) were enrolled at 11 study-sites and the results of 29 genetic analyses were completed. All cohorts of the pilot-study are open for recruitments up to a maximum of 40 individuals per diagnostic group. Clinical trial information: NCT04484636.

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