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Clinical genomics

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https://www.readbyqxmd.com/read/29236174/oncotype-dx%C3%A2-in-breast-cancer-patients-clinical-experience-outcome-and-follow-up-a-case-control-study
#1
Michelle G Rath, Lorenz Uhlmann, Marita Fiedler, Joerg Heil, Michael Golatta, Christine Dinkic, Andre Hennigs, Sarah Schott, Veronika Ernst, Thorsten Koch, Christof Sohn, Cosima Brucker, Joachim Rom
PURPOSE: Breast cancer is the leading cause of death from cancer in women and the most common cancer in the world [1]. To date, many patients with estrogen-receptor-positive (ER+) breast cancer are overtreated with chemotherapy when the rationale for adjuvant chemotherapy is based on clinicopathologic parameters. Different studies were able to demonstrate that a 21-gene expression assay (Oncotype DX® Genomic Health, Redwood City, CA) can predict the benefit from adjuvant chemotherapy in ER+ breast cancers [2, 3] and provide additional prognostic information independent of clinicopathological features [4]...
December 13, 2017: Archives of Gynecology and Obstetrics
https://www.readbyqxmd.com/read/29236091/noncoding-copy-number-variations-are-associated-with-congenital-limb-malformation
#2
Ricarda Flöttmann, Bjørt K Kragesteen, Sinje Geuer, Magdalena Socha, Lila Allou, Anna Sowińska-Seidler, Laure Bosquillon de Jarcy, Johannes Wagner, Aleksander Jamsheer, Barbara Oehl-Jaschkowitz, Lars Wittler, Deepthi de Silva, Ingo Kurth, Idit Maya, Fernando Santos-Simarro, Wiebke Hülsemann, Eva Klopocki, Roger Mountford, Alan Fryer, Guntram Borck, Denise Horn, Pablo Lapunzina, Meredith Wilson, Bénédicte Mascrez, Denis Duboule, Stefan Mundlos, Malte Spielmann
PurposeCopy-number variants (CNVs) are generally interpreted by linking the effects of gene dosage with phenotypes. The clinical interpretation of noncoding CNVs remains challenging. We investigated the percentage of disease-associated CNVs in patients with congenital limb malformations that affect noncoding cis-regulatory sequences versus genes sensitive to gene dosage effects.MethodsWe applied high-resolution copy-number analysis to 340 unrelated individuals with isolated limb malformation. To investigate novel candidate CNVs, we re-engineered human CNVs in mice using clustered regularly interspaced short palindromic repeats (CRISPR)-based genome editing...
October 12, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29235940/slc9b1-methylation-predicts-fetal-intolerance-of-labor
#3
Anna K Knight, Karen N Conneely, Varun Kilaru, Dawayland Cobb, Jennifer L Payne, Samantha Meilman, Elizabeth J Corwin, Zachary A Kaminsky, Anne L Dunlop, Alicia K Smith
Fetal intolerance of labor is a common indication for delivery by Caesarean section. Diagnosis is based on the presence of category III fetal heart rate tracing, which is an abnormal heart tracing associated with increased likelihood of fetal hypoxia and metabolic acidemia. This study analyzed data from 177 unique women who, during their prenatal visits (7-15 weeks and/or 24-32 weeks) to Atlanta area prenatal care clinics, consented to provide blood samples for DNA methylation (HumanMethylation450 BeadChip) and gene expression (Human HT-12 v4 Expression BeadChip) analyses...
December 13, 2017: Epigenetics: Official Journal of the DNA Methylation Society
https://www.readbyqxmd.com/read/29235266/host-genetic-variations-associated-with-disease-progression-in-chronic-hepatitis-c-virus-infection
#4
REVIEW
Kentaro Matsuura, Yasuhito Tanaka
Treatment with recently-developed interferon-free oral regimens combining direct-acting antiviral agents (DAAs) results in the elimination of hepatitis C virus (HCV) in almost all chronic hepatitis C (CHC) patients. In the era of DAAs, surveillance of hepatocellular carcinoma (HCC) after eradication of HCV by anti-HCV therapy is particularly important. As is well known, an advanced state of hepatic fibrosis is the major risk factor for developing HCC. Therefore, an increased understanding of various factors associated with disease progression and development of HCC in CHC patients is essential for implementing personalized treatment and surveillance of disease progression and HCC...
December 13, 2017: Hepatology Research: the Official Journal of the Japan Society of Hepatology
https://www.readbyqxmd.com/read/29235051/development-of-the-cns-tap-tool-for-the-selection-of-precision-medicine-therapies-in-neuro-oncology
#5
Joseph R Linzey, Bernard L Marini, Amy Pasternak, Cory Smith, Zac Miklja, Lili Zhao, Chandan Kumar-Sinha, Alyssa Paul, Nicholas Harris, Patricia L Robertson, Lindsey M Hoffman, Arul Chinnaiyan, Rajen Mody, Carl Koschmann
The number of targeted therapies utilized in precision medicine are rapidly increasing. Neuro-oncology offers a unique challenge due to the varying blood brain barrier (BBB) penetration of each agent. Neuro-oncologists face a difficult task weighing the growing number of potential targeted therapies and their likelihood of BBB penetration. We developed the CNS TAP Working Group and performed an extensive literature review for the evidence-based creation of the CNS TAP tool, which was retrospectively validated by analyzing brain tumor patients who underwent therapy targeted based on genomic results from an academic sequencing study (MiOncoseq, n = 17) or private molecular profiling (Foundation One, n = 7)...
December 12, 2017: Journal of Neuro-oncology
https://www.readbyqxmd.com/read/29234618/carney-complex-eleven-open-heart-operations-in-a-single-family
#6
Sung Joon Han, Woosik Han, Min-Woong Kang, Jae Hyeon Yu, Shinkwang Kang, Myung Hoon Na
Herein, we report on a family with Carney complex. Four members of the family underwent a total of 11 open heart operations as well as 9 other operations to treat extrathoracic masses. All the family members met at least 2 major clinical criteria and 1 supplemental criterion. We analyzed their genomic loci, including the protein kinase A regulatory subunit 1 gene. The results revealed no specific mutations, except for a common single nucleotide polymorphism. This case series of Carney complex emphasizes the importance of close longitudinal follow-up because of the high rate of tumor recurrence irrespective of the site...
December 2017: Korean Journal of Thoracic and Cardiovascular Surgery
https://www.readbyqxmd.com/read/29234452/genetic-variations-of-cholesteryl-ester-transfer-protein-and-diet-interactions-in-relation-to-lipid-profiles-and-coronary-heart-disease-a-systematic-review
#7
REVIEW
Parvin Mirmiran, Zohre Esfandiar, Firoozeh Hosseini-Esfahani, Gelareh Koochakpoor, Maryam S Daneshpour, Bahar Sedaghati-Khayat, Fereidoun Azizi
Data on diet-genotype interactions in the prevention or treatment of dyslipidemia have increased remarkably. This systematic review aimed to assess nutrigenetic studies regarding the modulating effect of diet on cholesteryl ester transfer protein (CETP) polymorphisms in relation to metabolic traits. Data were collected through studies published between 2000 and SEP. 2016 using five electronic databases. The quality of eligible studies was assessed using a 12-item quality checklist, derived from the STrengthening the REporting of Genetic Association Studies (STREGA) statement...
2017: Nutrition & Metabolism
https://www.readbyqxmd.com/read/29234286/identification-of-biomarkers-correlated-with-the-tnm-staging-and-overall-survival-of-patients-with-bladder-cancer
#8
Sheng Li, Xiaoping Liu, Tongzu Liu, Xiangyu Meng, Xiaohong Yin, Cheng Fang, Di Huang, Yue Cao, Hong Weng, Xiantao Zeng, Xinghuan Wang
Objective: To identify candidate biomarkers correlated with clinical prognosis of patients with bladder cancer (BC). Methods: Weighted gene co-expression network analysis was applied to build a co-expression network to identify hub genes correlated with tumor node metastasis (TNM) staging of BC patients. Functional enrichment analysis was conducted to functionally annotate the hub genes. Protein-protein interaction network analysis of hub genes was performed to identify the interactions among the hub genes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/29233960/multiplexed-in-vivo-homology-directed-repair-and-tumor-barcoding-enables-parallel-quantification-of-kras-variant-oncogenicity
#9
Ian P Winters, Shin-Heng Chiou, Nicole K Paulk, Christopher D McFarland, Pranav V Lalgudi, Rosanna K Ma, Leszek Lisowski, Andrew J Connolly, Dmitri A Petrov, Mark A Kay, Monte M Winslow
Large-scale genomic analyses of human cancers have cataloged somatic point mutations thought to initiate tumor development and sustain cancer growth. However, determining the functional significance of specific alterations remains a major bottleneck in our understanding of the genetic determinants of cancer. Here, we present a platform that integrates multiplexed AAV/Cas9-mediated homology-directed repair (HDR) with DNA barcoding and high-throughput sequencing to simultaneously investigate multiple genomic alterations in de novo cancers in mice...
December 12, 2017: Nature Communications
https://www.readbyqxmd.com/read/29233927/comprehensive-mutation-and-copy-number-profiling-in-archived-circulating-breast-cancer-tumor-cells-documents-heterogeneous-resistance-mechanisms
#10
Costanza Paoletti, Andi K Cani, Jose M Larios, Daniel H Hovelson, Kimberly Aung, Elizabeth P Darga, Emily M Cannell, Paul J Baratta, Chia-Jen Liu, David Chu, Maryam Yazdani, Allen R Blevins, Valeria Sero, Nahomi Tokudome, Dafydd G Thomas, Christina Gersch, Anne F Schott, Yi-Mi Wu, Robert Lonigro, Dan R Robinson, Arul M Chinnaiyan, Farideh Z Bischoff, Michael D Johnson, Ben Ho Park, Daniel F Hayes, James M Rae, Scott A Tomlins
Addressing drug resistance is a core challenge in cancer research, but the degree of heterogeneity in resistance mechanisms in cancer is unclear. In this study, we conducted next-generation sequencing (NGS) of circulating tumor cells (CTC) from patients with advanced cancer, to assess mechanisms of resistance to targeted therapy and reveal opportunities for precision medicine. Comparison of the genomic landscapes of CTC and tissue metastases is complicated by challenges in comprehensive CTC genomic profiling and paired tissue acquisition, particularly in patients who progress after targeted therapy...
December 12, 2017: Cancer Research
https://www.readbyqxmd.com/read/29233925/a20-regulates-the-dna-damage-response-and-mediates-tumor-cell-resistance-to-dna-damaging-therapy
#11
Chuanzhen Yang, Weicheng Zang, Zefang Tang, Yapeng Ji, Ruidan Xu, Yongfeng Yang, Aiping Luo, Bin Hu, Zemin Zhang, Zhihua Liu, Xiaofeng Zheng
A competent DNA damage response (DDR) helps prevent cancer, but once cancer has arisen DDR can blunt the efficacy of chemotherapy and radiotherapy which cause lethal DNA breakage in cancer cells. Thus, blocking DDR may improve the efficacy of these modalities. Here we report a new DDR mechanism that interfaces with inflammatory signaling and might be blocked to improve anticancer outcomes. Specifically, we report that the ubiquitin-editing enzyme A20 binds and inhibits the E3 ubiquitin ligase RNF168, which is responsible for regulating histone H2A turnover critical for proper DNA repair...
December 12, 2017: Cancer Research
https://www.readbyqxmd.com/read/29233721/antitumor-mir-150-5p-and-mir-150-3p-inhibit-cancer-cell-aggressiveness-by-targeting-spock1-in-head-and-neck-squamous-cell-carcinoma
#12
Keiichi Koshizuka, Toyoyuki Hanazawa, Naoko Kikkawa, Koji Katada, Atsushi Okato, Takayuki Arai, Tetsuya Idichi, Yusaku Osako, Yoshitaka Okamoto, Naohiko Seki
OBJECTIVE: Our recent studies have revealed that both strands of pre-miRNAs, the guide strand and the passenger strand, are involved in cancer pathogenesis. Analyses of miRNA expression signatures by RNA sequencing in head and neck squamous cell carcinoma (HNSCC) showed that both of the strands of pre-miR-150 (miR-150-5p and miR-150-3p) were significantly downregulated, and that these miRNAs acted as antitumor miRNAs in HNSCC cells. The aim of this study was to identify oncogenic genes in HNSCC cells that were regulated by miR-150-5p and miR-150-3p...
December 9, 2017: Auris, Nasus, Larynx
https://www.readbyqxmd.com/read/29233637/compound-heterozygous-familial-hypercholesterolemia-in-a-chinese-boy-with-a-de%C3%A2-novo-and-transmitted-low-density-lipoprotein-receptor-mutation
#13
Yizhe Ma, Yingyun Gong, Abhimanyu Garg, Hongwen Zhou
BACKGROUND: Homozygous familial hypercholesterolemia is characterized by extremely elevated serum low-density lipoprotein cholesterol (LDL-C) levels and increased risk of cardiovascular complications due to biallelic mutations in LDL receptor (LDLR). OBJECTIVE: We present a 10-year-old Chinese homozygous familial hypercholesterolemia boy with biallelic LDLR mutations including an extremely rare de novo mutation. METHODS: Detailed family history and clinical and biochemical data were gathered from the pedigree...
October 26, 2017: Journal of Clinical Lipidology
https://www.readbyqxmd.com/read/29233588/changes-in-circulating-mirnas-in-healthy-overweight-and-obese-subjects-effect-of-diet-composition-and-weight-loss
#14
S Giardina, P Hernández-Alonso, A Díaz-López, A Salas-Huetos, J Salas-Salvadó, M Bulló
BACKGROUND: MicroRNAs (miRNAs) are small non-coding RNA molecules that can play an important role in several chronic metabolic conditions, including obesity. However, to date little is known about how they are regulated. Weight loss induced by surgical procedures has been effective at modulating specific circulating miRNAs, but the effect of energy-restricted diets with different macronutrient compositions on circulating miRNAs is not well understood. The objective of the present analysis was to explore the effect of three energy-restricted diets of different macronutrient composition and carbohydrate quality on plasma miRNA levels...
December 1, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/29233483/development-and-validation-of-a-modified-taqman-based-real-time-pcr-assay-targeting-the-lipl32-gene-for-detection-of-pathogenic-leptospira-in-canine-urine-samples
#15
Bruno Alonso Miotto, Aline Santana da Hora, Sueli Akemi Taniwaki, Paulo Eduardo Brandão, Marcos Bryan Heinemann, Mitika Kuribayashi Hagiwara
A modified TaqMan real-time polymerase chain reaction targeting a 138bp fragment within the lipl32 gene was developed to identify exclusively pathogenic Leptospira spp. in dog urine samples. Thirty-five samples from dogs with suspected clinical leptospirosis and 116 samples from apparently healthy dogs were tested for presence of leptospiral DNA using the TaqMan-based assay. The results were compared with those from a well-established conventional PCR targeting the 16S RNA encoding gene associated with nucleotide sequencing analysis...
December 2, 2017: Brazilian Journal of Microbiology: [publication of the Brazilian Society for Microbiology]
https://www.readbyqxmd.com/read/29233455/genetic-variation-of-cytochrome-p450-in-uyghur-chinese-population
#16
Guangzhao Qi, Duolu Li, Xiaojian Zhang
Interindividual and interethnic variability of drug responses could be attributed to the differences of genetic polymorphisms in the drug metabolizing enzymes and transporters genes among the populations. Here we reviewed the studies of genetic variations in Uyghur Chinese of fifteen CYP450 genes including CYP1A1, CYP1A2, CYP2A6, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1, CYP2J2, CYP2W1, CYP3A4, CYP3A5, CYP4A11, and CYP17A1, which totally covered 277 variants. We also collected the data of 277 variants covered in our study in two extensive population sequencing projects, the International HapMap Project (Hap-Map) and the 1000 Genomes Project and compared them with the data of Uyghur Chinese...
March 6, 2017: Drug Metabolism and Pharmacokinetics
https://www.readbyqxmd.com/read/29233452/downregulation-of-caspase-8-in-a-group-of-iranian-breast-cancer-patients-a-pilot-study
#17
Masoumeh Aghababazadeh, Najmeh Dorraki, Fahimeh Afzal Javan, Asieh Sadat Fattahi, Masoumeh Gharib, Alireza Pasdar
PURPOSE: It is now well known that evading apoptosis, as a cancer hallmark, can lead to tumour initiation, progression and metastasis. As a result of genome wide association studies, an initiator protease in this pathway, caspase 8 (CASP8), has been found to be an important gene regarding breast cancer susceptibility. The alterations of the expression of this gene have been reported in breast cancer cell lines. Given that in previous studies expression analysis of this gene had only been done in breast cancer cell lines, in this study we aimed to evaluate the expression of this gene in breast cancer tissues versus adjacent normal tissues, using real-time quantitative method...
December 7, 2017: Journal of the Egyptian National Cancer Institute
https://www.readbyqxmd.com/read/29233255/burkholderia-stabilis-outbreak-associated-with-contaminated-commercially-available-washing-gloves-switzerland-may-2015-to-august-2016
#18
Rami Sommerstein, Urs Führer, Elia Lo Priore, Carlo Casanova, Dominik M Meinel, Helena Mb Seth-Smith, Andreas Kronenberg, On Behalf Of Anresis, Daniel Koch, Laurence Senn, Andreas F Widmer, Adrian Egli, Jonas Marschall, On Behalf Of Swissnoso
We describe an outbreak of Burkholderia stabilis associated with contaminated washing gloves, a commercially available Class I medical device. Triggered by an increase in Burkholderia cepacia complex (BCC) bacteremias and the detection of BCC in unopened packages of washing gloves, an ad hoc national outbreak committee comprising representatives of a public health organisation, a regulatory agency, and an expert association convened and commissioned an outbreak investigation. The investigation included retrospective case finding across Switzerland and whole genome sequencing (WGS) of isolates from cases and gloves...
December 2017: Euro Surveillance: Bulletin Européen sur les Maladies Transmissibles, European Communicable Disease Bulletin
https://www.readbyqxmd.com/read/29232918/population-specific-associations-of-deleterious-rare-variants-in-coding-region-of-p2ry1-p2ry12-purinergic-receptor-genes-in-large-vessel-ischemic-stroke-patients
#19
Piotr K Janicki, Ceren Eyileten, Victor Ruiz-Velasco, Khaled Anwar Sedeek, Justyna Pordzik, Anna Czlonkowska, Iwona Kurkowska-Jastrzebska, Shigekazu Sugino, Yuka Imamura-Kawasawa, Dagmara Mirowska-Guzel, Marek Postula
The contribution of low-frequency and damaging genetic variants associated with platelet function to ischemic stroke (IS) susceptibility remains unknown. We employed a deep re-sequencing approach in Polish patients in order to investigate the contribution of rare variants (minor allele frequency, MAF < 1%) to the IS genetic susceptibility in this population. The genes selected for re-sequencing consisted of 26 genes coding for proteins associated with the surface membrane of platelets. Targeted pooled re-sequencing (Illumina HiSeq 2500) was performed on genomic DNA of 500 cases (patients with history of clinically proven diagnosis of large-vessel IS) and 500 controls...
December 11, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29232904/an-expanded-multi-organ-disease-phenotype-associated-with-mutations-in-yars
#20
Anna Tracewska-Siemiątkowska, Lonneke Haer-Wigman, Danielle G M Bosch, Deborah Nickerson, Michael J Bamshad, Maartje van de Vorst, Nanna Dahl Rendtorff, Claes Möller, Ulrika Kjellström, Sten Andréasson, Frans P M Cremers, Lisbeth Tranebjærg
Whole exome sequence analysis was performed in a Swedish mother-father-affected proband trio with a phenotype characterized by progressive retinal degeneration with congenital nystagmus, profound congenital hearing impairment, primary amenorrhea, agenesis of the corpus callosum, and liver disease. A homozygous variant c.806T > C, p.(F269S) in the tyrosyl-tRNA synthetase gene (YARS) was the only identified candidate variant consistent with autosomal recessive inheritance. Mutations in YARS have previously been associated with both autosomal dominant Charcot-Marie-Tooth syndrome and a recently reported autosomal recessive multiorgan disease...
December 11, 2017: Genes
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