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https://www.readbyqxmd.com/read/29168748/variety-and-dynamics-of-proteoforms-in-the-human-proteome-aspects-of-markers-for-hepatocellular-carcinoma
#1
Stanislav Naryzhny, Victor Zgoda, Artur Kopylov, Elena Petrenko, Olga Kleist, Аlexander Archakov
We have previously developed an approach, where two-dimensional gel electrophoresis (2DE) was used, followed by sectional analysis of the whole gel using high-resolution nano-liquid chromatography-mass spectrometry (ESI LC-MS/MS). In this study, we applied this approach on the panoramic analysis of proteins and their proteoforms from normal (liver) and cancer (HepG2) cells. This allowed us to detect, in a single proteome, about 20,000 proteoforms coded by more than 4000 genes. A set of 3D-graphs showing distribution of these proteoforms in 2DE maps (profiles) was generated...
November 23, 2017: Proteomes
https://www.readbyqxmd.com/read/29167940/the-prognostic-value-of-circulating-myeloblasts-in-patients-with-myelodysplastic-syndromes
#2
Vu H Duong, Eric Padron, Najla H Al Ali, Jeffrey E Lancet, Jeff Hall, Brian Kwok, Ling Zhang, Pearlie K Epling-Burnette, Alan F List, Rami S Komrokji
The prognostic value of peripheral blasts (PB) is not well-studied in patients with myelodysplastic syndromes (MDS). We evaluated the impact of PB on overall survival (OS) and transformation to acute myeloid leukemia (AML) in a large cohort. The MDS database at the Moffitt Cancer Center was retrospectively reviewed to identify patients with ≥ 1% PB (PB-MDS) and those without PB (BM-MDS). We also assessed the correlation between PB and gene mutations. One thousand seven hundred fifty-eight patients were identified, among whom 13% had PB near the time of diagnosis...
November 22, 2017: Annals of Hematology
https://www.readbyqxmd.com/read/29167272/direct-testing-for-allele-specific-expression-differences-between-conditions
#3
Luis Leon-Novelo, Alison R Gerken, Rita M Graze, Lauren M McIntyre, Fabio Marroni
Allelic imbalance (AI) indicates the presence of functional variation in cis regulatory regions. Detecting cis regulatory differences using AI is widespread, yet there is no formal statistical methodology that tests whether AI differs between conditions. Here we present a novel model and formally test differences in AI across conditions using Bayesian credible intervals. The approach tests AI by environment (GxE) interactions and can be used to test AI between environments, genotypes, sex, and any other condition...
November 22, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/29165888/molecular-pathology-and-thyroid-fna
#4
REVIEW
D N Poller, S Glaysher
This review summarises molecular pathological techniques applicable to thyroid FNA. The molecular pathology of thyroid tumours is now fairly well understood. Molecular methods may be used as a rule-in test for diagnosis of malignancy in thyroid nodules, eg BRAF V600E point mutation, use of a seven-gene mutational panel (BRAF V600E, RAS genes, RET/PTC or PAX8/PPARG rearrangement), or as a comprehensive multigene next-generation sequencing panel, eg ThyroSeq v2. Molecular methods can also be applied as rule-out tests for malignancy in thyroid nodules, eg Afirma or ThyroSeq v2 or as markers of prognosis, eg TERT promoter mutation or other gene mutations including BRAF V600E, TP53 and AKT1, and as tests for newly defined tumour entities such as non-invasive follicular thyroid neoplasm with papillary like nuclei, or as a molecular marker(s) for targeted therapies...
December 2017: Cytopathology: Official Journal of the British Society for Clinical Cytology
https://www.readbyqxmd.com/read/29165790/physician-interpretation-of-genomic-test-results-and-treatment-selection
#5
Lauren L Brusco, Chetna Wathoo, Kenna R Mills Shaw, Vijaykumar R Holla, Ann M Bailey, Amber M Johnson, Yekaterina B Khotskaya, Beate C Litzenburger, Nora S Sanchez, Jia Zeng, Elmer V Bernstam, Cathy Eng, Bryan K Kee, Rodabe N Amaria, Mark J Routbort, Gordon B Mills, John Mendelsohn, Funda Meric-Bernstam
BACKGROUND: Genomic testing is increasingly performed in oncology, but concerns remain regarding the clinician's ability to interpret results. In the current study, the authors sought to determine the agreement between physicians and genomic annotators from the Precision Oncology Decision Support (PODS) team at The University of Texas MD Anderson Cancer Center in Houston regarding actionability and the clinical use of test results. METHODS: On a prospective protocol, patients underwent clinical genomic testing for hotspot mutations in 46 or 50 genes...
November 22, 2017: Cancer
https://www.readbyqxmd.com/read/29165578/clues-for-polygenic-inheritance-of-pituitary-stalk-interruption-syndrome-by-exome-sequencing-in-20-patients
#6
Nitash Zwaveling-Soonawala, Marielle Alders, Aldo Jongejan, Lidija Kovacic, Floor A Duijkers, Saskia M Maas, Eric Fliers, A S Paul van Trotsenburg, Raoul C Hennekam
Context: Pituitary stalk interruption syndrome (PSIS) consists of a small/absent anterior pituitary lobe, interrupted/absent pituitary stalk, and an ectopic posterior pituitary lobe. Mendelian forms of PSIS are detected infrequently (< 5%), and a polygenic etiology has been suggested. GLI2 variants have been reported in a relatively high frequency in PSIS. Objective: To provide further evidence for a non-Mendelian, polygenic etiology of PSIS. Methods: Exome sequencing (trio approach) in 20 patients with isolated PSIS...
November 20, 2017: Journal of Clinical Endocrinology and Metabolism
https://www.readbyqxmd.com/read/29165010/dnmt3a-co-mutation-is-required-for-flt3-itd-as-an-adverse-prognostic-indicator-in-intermediate-risk-cytogenetic-group-aml
#7
Juan Ma, Jennifer Dunlap, Aleksandra Paliga, Elie Traer, Richard Press, Lisong Shen, Guang Fan
This single institution cohort study of 132 AML patients investigated the clinical implications of co-mutations detected with a 42-gene NGS panel. In the intermediate-risk cytogenetic group, FLT3-ITD is an adverse prognostic indicator only in the presence of a DNMT3A co-mutation, regardless of NPM1 mutation status. In the absence of a concomitant DNMT3A mutation, there was no significant difference in overall survival between FLT3-ITD positive and FLT3-ITD negative patients. Furthermore, mutation analysis on post-induction specimens showed that residual FLT3-ITD and/or DNMT3A mutations were associated with a high frequency of therapy resistance or relapse in AML...
November 22, 2017: Leukemia & Lymphoma
https://www.readbyqxmd.com/read/29163588/genome-wide-analysis-of-japonica-rice-performance-under-limited-water-and-permanent-flooding-conditions
#8
Andrea Volante, Francesca Desiderio, Alessandro Tondelli, Rosaria Perrini, Gabriele Orasen, Chiara Biselli, Paolo Riccardi, Alessandra Vattari, Daniela Cavalluzzo, Simona Urso, Manel Ben Hassen, Agostino Fricano, Pietro Piffanelli, Paolo Cozzi, Filippo Biscarini, Gian Attilio Sacchi, Luigi Cattivelli, Giampiero Valè
A rice GWAS panel of 281 accessions of japonica rice was phenotypically characterized for 26 traits related to phenology, plant and seed morphology, physiology and yield for 2 years in field conditions under permanent flooding (PF) and limited water (LW). A genome-wide analysis uncovered a total of 160 significant marker-trait associations (MTAs), of which 32 were LW-specific, 59 were PF-specific, and 69 were in common between the two water management systems. LW-specific associations were identified for several agronomic traits including days to maturation, days from flowering to maturation, leaf traits, plant height, panicle and seed traits, hundred grain weight, yield and tillering...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163559/genome-wide-association-study-of-calcium-accumulation-in-grains-of-european-wheat-cultivars
#9
Dalia Z Alomari, Kai Eggert, Nicolaus von Wirén, Klaus Pillen, Marion S Röder
Mineral concentrations in cereals are important for human health, especially for people who depend mainly on consuming cereal diet. In this study, we carried out a genome-wide association study (GWAS) of calcium concentrations in wheat (Triticum aestivum L.) grains using a European wheat diversity panel of 353 varieties [339 winter wheat (WW) plus 14 of spring wheat (SW)] and phenotypic data based on two field seasons. High genotyping densities of single-nucleotide polymorphism (SNP) markers were obtained from the application of the 90k iSELECT ILLUMINA chip and a 35k Affymetrix chip...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29163495/human-cd141-dendritic-cell-and-cd1c-dendritic-cell-undergo-concordant-early-genetic-programming-after-activation-in-humanized-mice-in-vivo
#10
Yoshihito Minoda, Isaac Virshup, Ingrid Leal Rojas, Oscar Haigh, Yide Wong, John J Miles, Christine A Wells, Kristen J Radford
Human immune cell subsets develop in immunodeficient mice following reconstitution with human CD34(+) hematopoietic stem cells. These "humanized" mice are useful models to study human immunology and human-tropic infections, autoimmunity, and cancer. However, some human immune cell subsets are unable to fully develop or acquire full functional capacity due to a lack of cross-reactivity of many growth factors and cytokines between species. Conventional dendritic cells (cDCs) in mice are categorized into cDC1, which mediate T helper (Th)1 and CD8(+) T cell responses, and cDC2, which mediate Th2 and Th17 responses...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/29163336/two-novel-mutations-associated-with-ataxia-telangiectasia-identified-using-an-ion-ampliseq-inherited-disease-panel
#11
Maria V Kuznetsova, Dmitry Yu Trofimov, Ekaterina S Shubina, Taisiya O Kochetkova, Natalia A Karetnikova, Ilya Yu Barkov, Vladimir A Bakharev, Oleg A Gusev, Gennady T Sukhikh
Ataxia-telangiectasia (A-T), or Louis-Bar syndrome, is a rare neurodegenerative disorder associated with immunodeficiency. For families with at least one affected child, timely A-T genotyping during any subsequent pregnancy allows the parents to make an informed decision about whether to continue to term when the fetus is affected. Mutations in the ATM gene, which is 150 kb long, give rise to A-T; more than 600 pathogenic variants in ATM have been characterized since 1990 and new mutations continue to be discovered annually...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/29163333/mutation-analysis-of-consanguineous-moroccan-patients-with-parkinson-s-disease-combining-microarray-and-gene-panel
#12
Ahmed Bouhouche, Christelle Tesson, Wafaa Regragui, Mounia Rahmani, Valérie Drouet, Houyam Tibar, Zouhayr Souirti, Rafiqua Ben El Haj, Naima Bouslam, Mohamed Yahyaoui, Alexis Brice, Ali Benomar, Suzanne Lesage
During the last two decades, 15 different genes have been reported to be responsible for the monogenic form of Parkinson's disease (PD), representing a worldwide frequency of 5-10%. Among them, 10 genes have been associated with autosomal recessive PD, with PRKN and PINK1 being the most frequent. In a cohort of 145 unrelated Moroccan PD patients enrolled since 2013, 19 patients were born from a consanguineous marriage, of which 15 were isolated cases and 4 familial. One patient was homozygous for the common LRRK2 G2019S mutation and the 18 others who did not carry this mutation were screened for exon rearrangements in the PRKN gene using Affymetrix Cytoscan HD microarray...
2017: Frontiers in Neurology
https://www.readbyqxmd.com/read/29163177/assessment-of-pharmacogenomic-panel-assay-for-prediction-of-taxane-toxicities-preliminary-results
#13
Raffaele Di Francia, Luigi Atripaldi, Salvo Di Martino, Carla Fierro, Tommaso Muto, Anna Crispo, Sabrina Rossetti, Gaetano Facchini, Massimiliano Berretta
Backbone: Paclitaxel and docetaxel are the primary taxane anticancer drugs regularly used to treat, breast, gastric, ovarian, head/neck, lung, and genitourinary neoplasm. Suspension of taxane treatments compromising patient benefits is more frequently caused by peripheral neuropathy and allergy, than to tumor progression. Several strategies for preventing toxicity have been investigated so far. Recently, findings on the genetic variants associated with toxicity and resistance to taxane-based chemotherapy have been reported...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29162897/gwas-qtl-mapping-and-gene-expression-analyses-in-brassica-napus-reveal-genetic-control-of-branching-morphogenesis
#14
Yajun He, Daoming Wu, Dayong Wei, Ying Fu, Yixin Cui, Hongli Dong, Chuandong Tan, Wei Qian
Branch number is an important trait in plant architecture that can influence crop yield and quality in Brassica napus. Here, we detected the QTLs responsible for branch number in a DH population and its reconstructed F2 population over two years. Further, a GWAS research on branch number was performed using a panel of 327 accessions with 33186 genomic SNPs from the 60 K Brassica Illumina® Infinium SNP array. Through combining linkage analysis and association mapping, a new QTL was fine mapped onto C03. Subsequently, we tested the correlations between the SNP polymorphisms and mRNA expression levels of genes in the target interval to identify potential loci or genes that control branch number through expression...
November 21, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29162694/an-endogenous-retroviral-envelope-syncytin-and-its-cognate-receptor-identified-in-the-viviparous-placental-mabuya-lizard
#15
Guillaume Cornelis, Mathis Funk, Cécile Vernochet, Francisca Leal, Oscar Alejandro Tarazona, Guillaume Meurice, Odile Heidmann, Anne Dupressoir, Aurélien Miralles, Martha Patricia Ramirez-Pinilla, Thierry Heidmann
Syncytins are envelope genes from endogenous retroviruses that have been captured during evolution for a function in placentation. They have been found in all placental mammals in which they have been searched, including marsupials. Placental structures are not restricted to mammals but also emerged in some other vertebrates, most frequently in lizards, such as the viviparous Mabuya Scincidae. Here, we performed high-throughput RNA sequencing of a Mabuya placenta transcriptome and screened for the presence of retroviral env genes with a full-length ORF...
November 21, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29162654/the-impact-of-hereditary-cancer-gene-panels-on-clinical-care-and-lessons-learned
#16
Volkan Okur, Wendy K Chung
Mutations in hereditary cancer syndromes account for a modest fraction of all cancers; however, identifying patients with these germline mutations offers tremendous health benefits to both patients and their family members. There are about 60 genes that confer a high lifetime risk of specific cancers, and this information can be used to tailor prevention, surveillance, and treatment. With advances in next-generation sequencing technologies and the elimination of gene patents for evaluating genetic information, we are now able to analyze multiple genes simultaneously, leading to the widespread clinical use of gene panels for germline cancer testing...
November 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29160301/new-insights-into-the-pharmacogenomics-of-antidepressant-response-from-the-gendep-and-star-d-studies-rare-variant-analysis-and-high-density-imputation
#17
C Fabbri, K E Tansey, R H Perlis, J Hauser, N Henigsberg, W Maier, O Mors, A Placentino, M Rietschel, D Souery, G Breen, C Curtis, L Sang-Hyuk, S Newhouse, H Patel, M Guipponi, N Perroud, G Bondolfi, M O'Donovan, G Lewis, J M Biernacka, R M Weinshilboum, A Farmer, K J Aitchison, I Craig, P McGuffin, R Uher, C M Lewis
Genome-wide association studies have generally failed to identify polymorphisms associated with antidepressant response. Possible reasons include limited coverage of genetic variants that this study tried to address by exome genotyping and dense imputation. A meta-analysis of Genome-Based Therapeutic Drugs for Depression (GENDEP) and Sequenced Treatment Alternatives to Relieve Depression (STAR*D) studies was performed at the single-nucleotide polymorphism (SNP), gene and pathway levels. Coverage of genetic variants was increased compared with previous studies by adding exome genotypes to previously available genome-wide data and using the Haplotype Reference Consortium panel for imputation...
November 21, 2017: Pharmacogenomics Journal
https://www.readbyqxmd.com/read/29158814/dna-methylation-of-mir-7-is-a-mechanism-involved-in-platinum-response-through-mafg-overexpression-in-cancer-cells
#18
Olga Vera, Julia Jimenez, Olga Pernia, Carlos Rodriguez-Antolin, Carmen Rodriguez, Fatima Sanchez Cabo, Javier Soto, Rocio Rosas, Sara Lopez-Magallon, Isabel Esteban Rodriguez, Ana Dopazo, Federico Rojo, Cristobal Belda, Rafael Alvarez, Jaime Valentin, Javier Benitez, Rosario Perona, Javier De Castro, Inmaculada Ibanez de Caceres
One of the major limitations associated with platinum use is the resistance that almost invariably develops in different tumor types. In the current study, we sought to identify epigenetically regulated microRNAs as novel biomarkers of platinum resistance in lung and ovarian cancers, the ones with highest ratios of associated chemo-resistance. Methods: We combined transcriptomic data from microRNA and mRNA under the influence of an epigenetic reactivation treatment in a panel of four paired cisplatin -sensitive and -resistant cell lines, followed by real-time expression and epigenetic validations for accurate candidate selection in 19 human cancer cell lines...
2017: Theranostics
https://www.readbyqxmd.com/read/29158785/breast-cancer-cell-line-classification-and-its-relevance-with-breast-tumor-subtyping
#19
REVIEW
Xiaofeng Dai, Hongye Cheng, Zhonghu Bai, Jia Li
Breast cancer cell lines have been widely used for breast cancer modelling which encompasses a panel of diseases with distinct phenotypical associations. Though cell lines provide unlimited homogenous materials for tumor studies and are relatively easy to culture, they are known to accumulate mutations duringthe initial establishment and subsequent series of cultivations. Thus, whether breast cancer cell line heterogeneity reflects that of carcinoma remains an important issue to resolve before drawing any reliable conclusion at the tumor level using cell lines...
2017: Journal of Cancer
https://www.readbyqxmd.com/read/29158550/exome-pool-seq-in-neurodevelopmental-disorders
#20
Bernt Popp, Arif B Ekici, Christian T Thiel, Juliane Hoyer, Antje Wiesener, Cornelia Kraus, André Reis, Christiane Zweier
High throughput sequencing has greatly advanced disease gene identification, especially in heterogeneous entities. Despite falling costs this is still an expensive and laborious technique, particularly when studying large cohorts. To address this problem we applied Exome Pool-Seq as an economic and fast screening technology in neurodevelopmental disorders (NDDs). Sequencing of 96 individuals can be performed in eight pools of 12 samples on less than one Illumina sequencer lane. In a pilot study with 96 cases we identified 27 variants, likely or possibly affecting function...
November 20, 2017: European Journal of Human Genetics: EJHG
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