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https://www.readbyqxmd.com/read/29050365/mitochondrial-genome-variation-and-prostate-cancer-a-review-of-the-mutational-landscape-and-application-to-clinical-management
#1
REVIEW
Anton M F Kalsbeek, Eva K F Chan, Niall M Corcoran, Christopher M Hovens, Vanessa M Hayes
Prostate cancer is a genetic disease. While next generation sequencing has allowed for the emergence of molecular taxonomy, classification is restricted to the nuclear genome. Mutations within the maternally inherited mitochondrial genome are known to impact cancer pathogenesis, as a result of disturbances in energy metabolism and apoptosis. With a higher mutation rate, limited repair and increased copy number compared to the nuclear genome, the clinical relevance of mitochondrial DNA (mtDNA) variation requires deeper exploration...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050331/a-glo10-score-for-the-prediction-of-prognosis-in-high-grade-gliomas
#2
Feng Chen, Peng Peng, Yi Zhou, Zhen-Yu Yang, Hai-Quan Zhang, Xiang-Sheng Ao, Da-Quan Zhou, Chun-Xiang Xiang
Gliomas are the most common lethal brain tumours and remain great heterogeneity in terms of histopathology and clinical outcomes. Among them, glioblastomas are the most aggressive tumours that lead to a median of less than one-year survival in patients. Despite the little improvement of in diagnosis and treatments for last decades, there is an urgent need for prognostic markers to distinguish high- and low-risk patients before treatment.Here, we generated a list of genes associated with glioblastoma progressions and then performed a comprehensive statistical modelling strategy to derive a 10-gene (GLO10) score from genome wide expression profiles of a large glioblastoma cohort (n=844)...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050264/the-microrna-expression-signature-of-pancreatic-ductal-adenocarcinoma-by-rna-sequencing-anti-tumour-functions-of-the-microrna-216-cluster
#3
Keiichi Yonemori, Naohiko Seki, Tetsuya Idichi, Hiroshi Kurahara, Yusaku Osako, Keiichi Koshizuka, Takayuki Arai, Atsushi Okato, Yoshiaki Kita, Takaaki Arigami, Yuko Mataki, Yuko Kijima, Kosei Maemura, Shoji Natsugoe
We analysed the RNA sequence-based microRNA (miRNA) signature of pancreatic ductal adenocarcinoma (PDAC). Aberrantly expressed miRNAs were successfully identified in this signature. Using the PDAC signature, we focused on 4 clustered miRNAs, miR-216a-5p, miR-216a-3p, miR-216b-5p and miR-216b-3p on human chromosome 2p16.1. All members of the miR-216 cluster were significantly reduced in PDAC specimens. Ectopic expression of these miRNAs suppressed cancer cell aggressiveness, suggesting miR-216 cluster as anti-tumour miRNAs in PDAC cells...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050249/profiling-cancer-associated-genetic-alterations-and-molecular-classification-of-cancer-in-korean-gastric-cancer-patients
#4
Yoonjung Kim, Mee-Yon Cho, Juwon Kim, Sung Nam Kim, Seoung Chul Oh, Kyung-A Lee
Recently, the Cancer Genome Atlas (TCGA) Research Network and Asian Cancer Research Group provided a new classification of gastric cancer (GC) to aid the development of biomarkers for targeted therapy and predict prognosis. We studied associations between genetically aberrant profiles of cancer-related genes, environmental factors, and histopathological features in 107 paired gastric tumor-non-tumor tissue GC samples. 6.5% of our GC cases were classified as the EBV subtype, 17.8% as the MSI subtype, 43.0% as the CIN subtype, and 32...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050228/mutation-landscape-and-intra-tumor-heterogeneity-of-two-manecs-of-the-esophagus-revealed-by-multi-region-sequencing
#5
Wenqing Yuan, Zhen Liu, Wanjun Lei, Li Sun, Haijun Yang, Yu Wang, Shweta Ramdas, Xiao Dong, Ruiping Xu, Hong Cai, Jun Z Li, Yang Ke
Mixed adenoneuroendocrine carcinoma (MANEC) in the esophagus is an infrequent but highly malignant cancer with few known genomic alterations. We conducted whole-exome sequencing and whole-genome SNP genotyping for 4-6 tumor subregions and 5-6 adjacent normal tissue sites and 1-3 lymph node metastases in two esophageal MANECs to detect somatic mutations and copy number alterations, and to explore their spatial heterogeneity and underlying clonal structure. TP53 mutation, RB1 deletion or LOH, and PIK3CA, PTEN, KRAS, SOX2, DVL3, TP63 amplification appeared in all regions in both tumors...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29050227/identification-of-two-novel-biomarkers-of-rectal-carcinoma-progression-and-prognosis-via-co-expression-network-analysis
#6
Min Sun, Taojiao Sun, Zhongshi He, Bin Xiong
mRNA expression profiles provide important insights on a diversity of biological processes involved in rectal carcinoma (RC). Our aim was to comprehensively map complex interactions between the mRNA expression patterns and the clinical traits of RC. We employed the integrated analysis of five microarray datasets and The Cancer Genome Atlas rectal adenocarcinoma database to identify 2118 consensual differentially expressed genes (DEGs) in RC and adjacent normal tissue samples, and then applied weighted gene co-expression network analysis to parse DEGs and eight clinical traits in 66 eligible RC samples...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29049858/adolescents-and-young-adults-with-brain-tumors-in-the-context-of-molecular-advances-in-neuro-oncology
#7
REVIEW
Michal Zapotocky, Vijay Ramaswamy, Alvaro Lassaletta, Eric Bouffet
Adolescents and young adults (AYA) comprise a specific group of oncology patients with a distinct biological and epidemiological spectrum of central nervous system neoplasms. It has been well documented that they differ clinically, especially in relation to prognosis and chemotherapy tolerance; however, the underlying reasons for this are unclear. Recent advances in the genomics of both childhood and adult brain tumors have provided new explanations and insights into the previously described age-dependent heterogeneity...
October 19, 2017: Pediatric Blood & Cancer
https://www.readbyqxmd.com/read/29049801/search-for-genetic-factors-in-bicuspid-aortic-valve-disease-acta2-mutations-do-not-play-a-major-role
#8
Giada Tortora, Anita Wischmeijer, Paolo Berretta, Jacopo Alfonsi, Luca Di Marco, Andrea Barbieri, Caterina Marconi, Federica Isidori, Cesare Rossi, Ornella Leone, Roberto Di Bartolomeo, Marco Seri, Davide Pacini
OBJECTIVES: Mutations in ACTA2 have been reported as a cause of familiar thoracic aortic aneurysm (TAA) with associated bicuspid aortic valve (BAV) in some individuals. Our aim is to investigate the role of ACTA2 mutations in BAV associated with TAA in 20 patients. METHODS: We recruited 20 patients who underwent surgery for BAV and TAA; clinical genetic evaluation and ACTA2 mutation analysis were performed on each patient, along with next-generation sequencing analysis of BAV-related genes...
July 27, 2017: Interactive Cardiovascular and Thoracic Surgery
https://www.readbyqxmd.com/read/29049454/association-of-mitochondrial-dna-copy-number-with-cardiovascular-disease
#9
Foram N Ashar, Yiyi Zhang, Ryan J Longchamps, John Lane, Anna Moes, Megan L Grove, Josyf C Mychaleckyj, Kent D Taylor, Josef Coresh, Jerome I Rotter, Eric Boerwinkle, Nathan Pankratz, Eliseo Guallar, Dan E Arking
Importance: Mitochondrial dysfunction is a core component of the aging process and may play a key role in atherosclerotic cardiovascular disease. Mitochondrial DNA copy number (mtDNA-CN), which represents the number of mitochondria per cell and number of mitochondrial genomes per mitochondrion, is an indirect biomarker of mitochondrial function. Objective: To determine whether mtDNA-CN, measured in an easily accessible tissue (buffy coat/circulating leukocytes), can improve risk classification for cardiovascular disease (CVD) and help guide initiation of statin therapy for primary prevention of CVD...
October 11, 2017: JAMA Cardiology
https://www.readbyqxmd.com/read/29049378/immune-modulatory-genomic-properties-differentiate-gut-microbiota-of-infants-with-and-without-eczema
#10
Seungdae Oh, Gaik Chin Yap, Pei-Ying Hong, Chiung-Hui Huang, Marion M Aw, Lynette Pei-Chi Shek, Wen-Tso Liu, Bee Wah Lee
Gut microbiota play an important role in human immunological processes, potentially affecting allergic diseases such as eczema. The diversity and structure of gut microbiota in infants with eczema have been previously documented. This study aims to evaluate by comparative metagenomics differences in genetic content in gut microbiota of infants with eczema and their matched controls. Stools were collected at the age of one month old from twelve infants from an at risk birth cohort in a case control manner. Clinical follow up for atopic outcomes were carried out at the age of 12 and 24 months...
2017: PloS One
https://www.readbyqxmd.com/read/29049138/graph-theoretical-analysis-of-genome-scale-data-examination-of-gene-activation-occurring-in-the-setting-of-community-acquired-pneumonia
#11
Octavia M Peck Palmer, Gary Rogers, Sachin Yende, Derek C Angus, Michael A Langston, Gilles Clermont
INTRODUCTION: We have previously reported evidence that black individuals appear to have a significantly higher incidence of infection-related hospitalizations compared to white individuals. It is possible that the host immune response is responsible for this vital difference. In support such a hypothesis, the aim of this study was to determine whether black and white individuals exhibit differential whole blood gene network activation. METHODS: We examined whole blood network activation in a subset of patients (n = 22 pairs, propensity score matched (1:1) black and white patients) with community-acquired pneumonia (CAP) from the Genetic and Inflammatory Markers of Sepsis study...
October 18, 2017: Shock
https://www.readbyqxmd.com/read/29049014/transcriptomic-guided-drug-repositioning-supported-by-a-new-bioinformatics-search-tool-genexpharma
#12
Beste Turanli, Gizem Gulfidan, Kazim Yalcin Arga
Drug repositioning is an innovative approach to identify new therapeutic indications for existing drugs. Drug repositioning offers the promise of reducing drug development timeframes and costs, and because it involves drugs that are already in the clinic, it might remedy some of the drug safety challenges traditionally associated with drug candidates that are not yet available in the clinic. The gene-by-drug interactions are an important dimension of optimal drug repositioning and development strategies. While gene-by-drug interactions have been curated and presented in various databases, novel bioinformatics tools and approaches are timely, and required with a specific focus to support drug positioning...
October 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/29048660/canonical-and-non-canonical-wnt-signaling-in-cancer-stem-cells-and-their-niches-cellular-heterogeneity-omics-reprogramming-targeted-therapy-and-tumor-plasticity-review
#13
Masaru Katoh
Cancer stem cells (CSCs), which have the potential for self-renewal, differentiation and de-differentiation, undergo epigenetic, epithelial-mesenchymal, immunological and metabolic reprogramming to adapt to the tumor microenvironment and survive host defense or therapeutic insults. Intra-tumor heterogeneity and cancer-cell plasticity give rise to therapeutic resistance and recurrence through clonal replacement and reactivation of dormant CSCs, respectively. WNT signaling cascades cross-talk with the FGF, Notch, Hedgehog and TGFβ/BMP signaling cascades and regulate expression of functional CSC markers, such as CD44, CD133 (PROM1), EPCAM and LGR5 (GPR49)...
September 19, 2017: International Journal of Oncology
https://www.readbyqxmd.com/read/29048555/an-architecture-for-genomics-analysis-in-a-clinical-setting-using-galaxy-and-docker
#14
W Digan, H Countouris, M Barritault, D Baudoin, P Laurent-Puig, H Blons, A Burgun, B Rance
Background: Next Generation Sequencing is used on a daily basis to perform molecular analysis to determine subtypes of disease (e.g., in cancer) and to assist in the selection of the optimal treatment. Clinical bioinformatics handles the manipulation of the data generated by the sequencer, from the generation to the analysis and interpretation. Reproducibility and traceability are crucial issues in a clinical setting. Results: We have designed an approach based on the Docker container technology and Galaxy, the popular bioinformatics analysis support open-source software...
October 18, 2017: GigaScience
https://www.readbyqxmd.com/read/29048510/donor-derived-mycoplasma-hominis-and-an-apparent-cluster-of-m-hominis-cases-in-solid-organ-transplant-recipients
#15
Olivia C Smibert, Heather L Wilson, Asma Sohail, Shanti Narayanasamy, Mark B Schultz, Susan A Ballard, Jason C Kwong, Jim de Boer, C Orla Morrissey, Anton Y Peleg, Greg I Snell, Miranda A Paraskeva, Adam W J Jenney
Background: Invasive and disseminated Mycoplasma hominis infections are well recognized but uncommon complications in solid organ transplant recipients. In a single center, a cluster of M. hominis infections were identified in lung transplant recipients from the same thoracic intensive care unit (ICU). We sought to determine the source(s) of these infections. Methods: Medical records of the donor and infected transplant recipients were reviewed for clinical characteristics...
October 16, 2017: Clinical Infectious Diseases: An Official Publication of the Infectious Diseases Society of America
https://www.readbyqxmd.com/read/29048296/chlamydia-trachomatis-biovar-l2-infection-in-women-in-south-africa
#16
Remco P H Peters, Ronan Doyle, Mathys J Redelinghuys, James A McIntyre, Georges M Verjans, Judith Breuer, Marleen M Kock
We detected Chlamydia trachomatis biovar L2 in vaginal swab specimens of 7 women with vaginal discharge in South Africa. Whole-genome sequencing directly from clinical specimens identified a closely related cluster of strains. The clinical role of this infection in the context of syndromic management should be clarified.
November 2017: Emerging Infectious Diseases
https://www.readbyqxmd.com/read/29047251/a-novel-1-13-mb-interstitial-duplication-at-19q13-32-causing-developmental-delay-and-microcephaly-in-a-pediatric-patient-the-first-asian-case-reports
#17
John Hoon Rim, Jeong A Kim, Jongha Yoo
Only 6 patients with partial trisomy of the long arm of chromosome 19 (19q), caused by direct interstitial duplications, have been reported until today. Herein, we report a pediatric patient with a novel 1.13 Mb direct interstitial duplication within 19q13.32, which is the smallest fragment affected so far. A five-year old Korean boy of healthy parents presented with microcephaly, growth retardation, developmental delay, and craniofacial dysmorphism. Even though G-banded chromosome analysis at resolution of 550-band revealed normal karyotype, duplication of 1...
November 2017: Yonsei Medical Journal
https://www.readbyqxmd.com/read/29047098/emerging-role-of-micrornas-and-long-noncoding-rnas-in-healthy-and-diseased-lung
#18
Jun-Hua Xiao, Qiong-Yu Hao, Katie Wang, Jes Paul, Yong-Xiao Wang
Pulmonary hypertension (PH) is a complex and multifactorial disease. An inability to fully unravel the molecular complexities has led to various clinical challenges in developing new therapies for this disease. Noncoding RNAs (ncRNAs) are RNA molecules with limited ability of coding proteins. The amount of ncRNAs is up to 98% of the whole genome's transcripts. Many ncRNAs with a regulatory function of genes have been identified to date and found to act at various steps along the protein biosynthetic process, which includes transcription, RNA maturation, translation, and protein degradation...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/29046940/gastric-cancer-immunohistochemical-classification-of-molecular-subtypes-and-their-association-with-clinicopathological-characteristics
#19
Eva-Maria Birkman, Naziha Mansuri, Samu Kurki, Annika Ålgars, Minnamaija Lintunen, Raija Ristamäki, Jari Sundström, Olli Carpén
Gastric cancer is traditionally divided into intestinal and diffuse histological subtypes, but recent molecular analyses have led to novel classification proposals based on genomic alterations. While the intestinal- and diffuse-type tumours are distinguishable from each other at the molecular level, intestinal-type tumours have more diverse molecular profile. The technology required for comprehensive molecular analysis is expensive and not applicable for routine clinical diagnostics. In this study, we have used immunohistochemistry and in situ hybridisation in molecular classification of gastric adenocarcinomas with an emphasis on the intestinal subtype...
October 19, 2017: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29046784/the-role-of-gene-variants-in-the-pathogenesis-of-neurodegenerative-disorders-as-revealed-by-next-generation-sequencing-studies-a-review
#20
REVIEW
Shirley Yin-Yu Pang, Kay-Cheong Teo, Jacob Shujui Hsu, Richard Shek-Kwan Chang, Miaoxin Li, Pak-Chung Sham, Shu-Leong Ho
The clinical diagnosis of neurodegenerative disorders based on phenotype is difficult in heterogeneous conditions with overlapping symptoms. It does not take into account the disease etiology or the highly variable clinical course even amongst patients diagnosed with the same disorder. The advent of next generation sequencing (NGS) has allowed for a system-wide, unbiased approach to identify all gene variants in the genome simultaneously. With the plethora of new genes being identified, genetic rather than phenotype-based classification of Mendelian diseases such as spinocerebellar ataxia (SCA), hereditary spastic paraplegia (HSP) and Charcot-Marie-Tooth disease (CMT) has become widely accepted...
2017: Translational Neurodegeneration
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