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clinical bioinformatics

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https://www.readbyqxmd.com/read/29227984/microrna-146b-5p-identified-in-porcine-liver-donation-model-is-associated-with-early-allograft-dysfunction-in-human-liver-transplantation
#1
Cheukfai Li, Qiang Zhao, Wei Zhang, Maogen Chen, Weiqiang Ju, Linwei Wu, Ming Han, Yi Ma, Xiaofeng Zhu, Dongping Wang, Zhiyong Guo, Xiaoshun He
BACKGROUND Poor transplant outcome was observed in donation after brain death followed by circulatory death (DBCD), since the donor organs suffered both cytokine storm of brain death and warm ischemia injury. MicroRNAs (miRNAs) have emerged as promising disease biomarkers, so we sought to establish a miRNA signature of porcine DBCD and verify the findings in human liver transplantation. MATERIAL AND METHODS MiRNA expression was determined with miRNA sequencing in 3 types of the porcine model of organ donation, including donation after brain death (DBD) group, donation after circulatory death (DCD) group, and DBCD group...
December 11, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29227308/medical-bioinformatics-in-melanoma
#2
Phil F Cheng
PURPOSE OF REVIEW: Bioinformatic insights from next-generation sequencing has been integral in understanding melanoma biology, resistance to treatment and provided new avenues for melanoma treatment. Whole-genome sequencing, whole-exome sequencing and RNA sequencing has redefined the molecular classification of melanoma, revealed distinct genetic aberrations that define clinical subtypes of melanoma and uncovered the diverse heterogeneity that resides in an individual tumor. RECENT FINDINGS: In this review, we will summarize the recent whole-genome study that catalogs the genomic landscape across many melanoma subtypes, the single-cell RNA sequencing studies that interrogates tumor heterogeneity and the personalized vaccine approaches to melanoma treatment...
December 8, 2017: Current Opinion in Oncology
https://www.readbyqxmd.com/read/29226910/towards-personalized-tumour-specific-therapeutic-vaccines-for-cancer
#3
REVIEW
Zhuting Hu, Patrick A Ott, Catherine J Wu
Cancer vaccines, which are designed to amplify tumour-specific T cell responses through active immunization, have long been envisioned as a key tool of effective cancer immunotherapy. Despite a clear rationale for such vaccines, extensive past efforts were unsuccessful in mediating clinically relevant antitumour activity in humans. Recently, however, next-generation sequencing and novel bioinformatics tools have enabled the systematic discovery of tumour neoantigens, which are highly desirable immunogens because they arise from somatic mutations of the tumour and are therefore tumour specific...
December 11, 2017: Nature Reviews. Immunology
https://www.readbyqxmd.com/read/29226007/houston-methodist-variant-viewer-an-application-to-support-clinical-laboratory-interpretation-of-next-generation-sequencing-data-for-cancer
#4
Paul A Christensen, Yunyun Ni, Feifei Bao, Heather L Hendrickson, Michael Greenwood, Jessica S Thomas, S Wesley Long, Randall J Olsen
Introduction: Next-generation-sequencing (NGS) is increasingly used in clinical and research protocols for patients with cancer. NGS assays are routinely used in clinical laboratories to detect mutations bearing on cancer diagnosis, prognosis and personalized therapy. A typical assay may interrogate 50 or more gene targets that encompass many thousands of possible gene variants. Analysis of NGS data in cancer is a labor-intensive process that can become overwhelming to the molecular pathologist or research scientist...
2017: Journal of Pathology Informatics
https://www.readbyqxmd.com/read/29220122/expression-profile-analysis-of-long-noncoding-rna-in-acute-myeloid-leukemia-by-microarray-and-bioinformatics
#5
Yuandong Feng, Ying Shen, Hongli Chen, Xiaman Wang, Ru Zhang, Yue Peng, Xiaoru Lei, Tian Liu, Jing Liu, Liufang Gu, Fangxia Wang, Yun Yang, Ju Bai, Jianli Wang, Wanhong Zhao, Aili He
Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides, which are involved in tumorigenesis and play a key role in cancer progression. To determine whether lncRNAs are involved in acute myeloid leukemia (AML), we analyzed the expression profile of lncRNAs and mRNAs in AML. 5 pairs of AML patients and iron deficiency anemia (IDA) controls were screened by microarray. Through co-expression analysis, differently expressed transcripts were done into modules, and lncRNAs got the functional annotations...
December 8, 2017: Cancer Science
https://www.readbyqxmd.com/read/29218953/-exploiture-and-application-of-an-internet-based-computation-platform-for-integrative-pharmacology-of-traditional-chinese-medicine
#6
Hai-Yu Xu, Zhen-Ming Liu, Yan Fu, Yan-Qiong Zhang, Jian-Jun Yu, Fei-Fei Guo, Shi-Huan Tang, Chuan-Yu Lv, Jin Su, Ru-Yi Cui, Hong-Jun Yang
Recently, integrative pharmacology(IP) has become a pivotal paradigm for the modernization of traditional Chinese medicines(TCM) and combinatorial drugs discovery, which is an interdisciplinary science for establishing the in vitro and in vivo correlation between absorption, distribution, metabolism, and excretion/pharmacokinetic(ADME/PK) profiles of TCM and the molecular networks of disease by the integration of the knowledge of multi-disciplinary and multi-stages. In the present study, an internet-based Computation Platform for IP of TCM(TCM-IP, www...
September 2017: Zhongguo Zhong Yao za Zhi, Zhongguo Zhongyao Zazhi, China Journal of Chinese Materia Medica
https://www.readbyqxmd.com/read/29217166/long-non-coding-rna-sox21-as1-sponges-mir-145-to-promote-the-tumorigenesis-of-colorectal-cancer-by-targeting-myo6
#7
An-Wei Wei, Li-Fang Li
Emerging evidences have proved that long non-coding RNAs (lncRNAs) act as important molecular regulator in the tumor progression, including colorectal cancer (CRC). LncRNA SOX21-AS1 has been verified as oncogenic molecular in other cancers and tumorigenesis. In present study, our team investigates the clinical characteristic and molecular function in CRC carcinogenesis. Results showed that lncRNA SOX21-AS1 expression was significantly over-expressed in CRC tissue samples and cells. The aberrant over-expression of SOX21-AS1 indicated poor prognosis of CRC patients...
December 4, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29217161/mir-1202-suppresses-hepatocellular-carcinoma-cells-migration-and-invasion-by-targeting-cyclin-dependent-kinase-14
#8
Bo Du, Peng Zhang, Zhiming Tan, Jifan Xu
Currently, hepatocellular carcinoma (HCC) patients still have poor survival outcomes mainly due to the powerful mobility of HCC cells. Increasing evidences hint that abnormally expressed miRNAs are capable to modulate HCC cells invasion and migration. MiR-1202 has been proposed as a ponderable molecular tumor marker in a variety of tumors. Here, results from real-time PCR indicated the decreased expression of miR-1202 in HCC. Clinically, statistical analysis showed that miR-1202 under-expression was closely associated with metastasis-related clinicopathologic characteristics...
December 4, 2017: Biomedicine & Pharmacotherapy, Biomédecine & Pharmacothérapie
https://www.readbyqxmd.com/read/29217154/production-of-a-chimeric-protein-and-its-potential-application-in-sero-diagnosis-of-mycoplasma-hominis-infection
#9
Saman Saadat, Mohammad M Sajadi, Mohammad Yousef Alikhani, Zahra Rikhtegaran Tehrani, Rasoul Yousefi Mashouf
INTRODUCTION: Mycoplasma hominis is an opportunistic pathogen of the human genital tract. Detection of antibodies against this organism in human serum or plasma is theoretically unreliable because of high variation in bacterial surface antigens. In this study, we applied the bioinformatics tools to design a chimeric protein constructed of specific, conserved and predicted immuno-dominant epitopes from two different membrane proteins, P120 and P80. MATERIAL AND METHODS: Linear B-cell epitopes of P120 and P80 were predicted and evaluated by bioinformatics tools and the designed chimeric protein was expressed in Escherichia coli...
December 4, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/29216878/adaptive-phenotype-drives-resistance-to-androgen-deprivation-therapy-in-prostate-cancer
#10
Nicoletta Ferrari, Ilaria Granata, Matteo Capaia, Marina Piccirillo, Mario Rosario Guarracino, Roberta Venè, Antonella Brizzolara, Andrea Petretto, Elvira Inglese, Martina Morini, Simonetta Astigiano, Adriana Agnese Amaro, Francesco Boccardo, Cecilia Balbi, Paola Barboro
BACKGROUND: Prostate cancer (PCa), the second most common cancer affecting men worldwide, shows a broad spectrum of biological and clinical behaviour representing the epiphenomenon of an extreme heterogeneity. Androgen deprivation therapy is the mainstay of treatment for advanced forms but after few years the majority of patients progress to castration-resistant prostate cancer (CRPC), a lethal form that poses considerable therapeutic challenges. METHODS: Western blotting, immunocytochemistry, invasion and reporter assays, and in vivo studies were performed to characterize androgen resistant sublines phenotype in comparison to the parental cell line LNCaP...
December 8, 2017: Cell Communication and Signaling: CCS
https://www.readbyqxmd.com/read/29216340/incorporating-blood-based-liquid-biopsy-information-into-cancer-staging-time-for-a-tnmb-system
#11
M Yang, M E Forbes, R L Bitting, S S O'Neill, P-C Chou, U Topaloglu, L D Miller, G A Hawkins, S C Grant, B R DeYoung, W J Petty, K Chen, B C Pasche, W Zhang
Tissue biopsy is the standard diagnostic procedure for cancer. Biopsy may also provide material for genotyping, which can assist in the diagnosis and selection of targeted therapies but may fall short in cases of inadequate sampling, particularly from highly heterogeneous tumors. Traditional tissue biopsy suffers greater limitations in its prognostic capability over the course of disease, most obviously as an invasive procedure with potential complications, but also with respect to probable tumor clonal evolution and metastasis over time from initial biopsy evaluation...
December 5, 2017: Annals of Oncology: Official Journal of the European Society for Medical Oncology
https://www.readbyqxmd.com/read/29215764/an-evaluation-of-the-challenges-to-developing-tumour-brca1-and-brca2-testing-methodologies-for-clinical-practice
#12
Gillian Ellison, Miika Ahdesmäki, Sally Luke, Paul M Waring, Andrew Wallace, Ronnie Wright, Benno Röthlisberger, Katja Ludin, Sabine Merkelbach-Bruse, Carina Heydt, Marjolijn J L Ligtenberg, Arjen R Mensenkamp, David Gonzalez Castro, Thomas Jones, Ana Vivancos, Olga Kondrashova, Patrick Pauwels, Christine Weyn, Eric Hahnen, Jan Hauke, Richie Soong, Zhongwu Lai, Brian Dougherty, T Hedley Carr, Justin Johnson, John Mills, J Carl Barrett
Ovarian cancer patients with germline or somatic pathogenic variants benefit from treatment with PARP inhibitors. Tumour BRCA1/2 testing is more challenging than germline testing as the majority of samples are formalin fixed paraffin embedded (FFPE), the tumour genome is complex and the allelic fraction of somatic variants can be low. We collaborated with 10 laboratories testing BRCA1/2 in tumours to compare different approaches to identify clinically important variants within FFPE tumour DNA samples. This was not a proficiency study but an inter-laboratory comparison to identify common issues...
December 7, 2017: Human Mutation
https://www.readbyqxmd.com/read/29215645/cherchez-la-femme-maternal-incidental-findings-can-explain-discordant-prenatal-cell-free-dna-sequencing-results
#13
REVIEW
Diana W Bianchi
Circulating DNA fragments in a pregnant woman's plasma derive from three sources: placenta, maternal bone marrow, and fetus. Prenatal sequencing to noninvasively screen for fetal chromosome abnormalities is performed on this mixed sample; results can therefore reflect the maternal as well as the fetoplacental DNA. Although it is recommended that pretest counseling include the possibility of detecting maternal genomic imbalance, this seldom occurs. Maternal abnormalities that can affect a prenatal screening test result include disorders that affect the size and metabolism of DNA, such as B12 deficiency, autoimmune disease, and intrahepatic cholestasis of pregnancy...
December 7, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29215605/cone-snails-a-big-store-of-conotoxins-for-novel-drug-discovery
#14
REVIEW
Bingmiao Gao, Chao Peng, Jiaan Yang, Yunhai Yi, Junqing Zhang, Qiong Shi
Marine drugs have developed rapidly in recent decades. Cone snails, a group of more than 700 species, have always been one of the focuses for new drug discovery. These venomous snails capture prey using a diverse array of unique bioactive neurotoxins, usually named as conotoxins or conopeptides. These conotoxins have proven to be valuable pharmacological probes and potential drugs due to their high specificity and affinity to ion channels, receptors, and transporters in the nervous systems of target prey and humans...
December 7, 2017: Toxins
https://www.readbyqxmd.com/read/29215599/systematic-analysis-of-transcriptomic-profile-of-renal-cell-carcinoma-under-long-term-hypoxia-using-next-generation-sequencing-and-bioinformatics
#15
Szu-Chia Chen, Feng-Wei Chen, Ya-Ling Hsu, Po-Lin Kuo
Patients with clear cell renal cell carcinoma (ccRCC) are often diagnosed with both von Hippel-Lindau (VHL) mutations and the constitutive activation of hypoxia-inducible factor-dependent signaling. In this study, we investigated the effects of long-term hypoxia in 786-O, a VHL-defective renal cell carcinoma cell line, to identify potential genes and microRNAs associated with tumor malignancy. The transcriptomic profiles of 786-O under normoxia, short-term hypoxia and long-term hypoxia were analyzed using next-generation sequencing...
December 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/29214632/thorough-analysis-of-unorthodox-abo-deletions-called-by-the-1000-genomes-project
#16
M Möller, Å Hellberg, M L Olsson
BACKGROUND AND OBJECTIVES: ABO remains the clinically most important blood group system, but despite earlier extensive research, significant findings are still being made. The vast majority of catalogued ABO null alleles are based on the c.261delG polymorphism. Apart from c.802G>A, other mechanisms for O alleles are rare. While analysing the data set from the 1000 Genomes (1000G) project, we encountered two previously uncharacterized deletions, which needed further exploration. MATERIALS AND METHODS: The Erythrogene database, complemented with bioinformatics software, was used to analyse ABO in 2504 individuals from 1000G...
December 6, 2017: Vox Sanguinis
https://www.readbyqxmd.com/read/29214011/long-non-coding-rna-h19-regulates-e2f1-expression-by-competitively-sponging-endogenous-mir-29a-3p-in-clear-cell-renal-cell-carcinoma
#17
Haowei He, Nana Wang, Xiaoming Yi, Chaopeng Tang, Dong Wang
Background: Numerous recent studies indicate that the long non-coding RNAs (lncRNAs) are frequently abnormal expressed and take critical roles in many cancers. Renal cell carcinoma is the secondary malignant tumors in the urinary system and has high mortality and morbidity. Around 80% of RCCs is clear cell renal cell carcinoma (ccRCC) and is characterized by high metastasis and relapse rate. However, the clinical significances of lncRNAs in ccRCC are still unknown. Methods: The human cancer lncRNA PCR array (Yingbio) was performed to detect the differentially expressed lncRNAs in human ccRCC samples...
2017: Cell & Bioscience
https://www.readbyqxmd.com/read/29211511/mitochondrial-trnaala-c5601t-mutation-may-modulate-the-clinical-expression-of-trnamet-a4435g-mutation-in-a-han-chinese-family-with-hypertension
#18
Ping Zheng, Shiliang Li, Chun Liu, Zhengbiao Zha, Xiang Wei, Yuan Yuan
Mutations in mitochondrial DNA, especially in mitochondrial tRNA (mt-tRNA) genes, are the important causes for maternally inherited hypertension. In this study, we reported the clinical, genetic, and molecular characterization of a Han Chinese family with hypertension. Most strikingly, this family exhibited a high penetrance and expressivity of hypertension. Sequence analysis of the complete mt-tRNA genes showed the presence of tRNAMet A4435G and tRNAAla C5601T mutations. The A4435G had already been reported as a pathogenic mutation associated with hypertension; in addition, the C5601T mutation, which was located at the highly conserved nucleotide of T arm of tRNAAla, created a novel Watson-Crick base pairing and may result in failure of tRNA metabolism...
December 6, 2017: Clinical and Experimental Hypertension: CHE
https://www.readbyqxmd.com/read/29209209/nonribosomal-peptides-from-marine-microbes-and-their-antimicrobial-and-anticancer-potential
#19
REVIEW
Shivankar Agrawal, Debabrata Acharya, Alok Adholeya, Colin J Barrow, Sunil K Deshmukh
Marine environments are largely unexplored and can be a source of new molecules for the treatment of many diseases such as malaria, cancer, tuberculosis, HIV etc. The Marine environment is one of the untapped bioresource of getting pharmacologically active nonribosomal peptides (NRPs). Bioprospecting of marine microbes have achieved many remarkable milestones in pharmaceutics. Till date, more than 50% of drugs which are in clinical use belong to the nonribosomal peptide or mixed polyketide-nonribosomal peptide families of natural products isolated from marine bacteria, cyanobacteria and fungi...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/29208367/the-role-of-epcam-in-tumor-progression-and-the-clinical-prognosis-of-endometrial-carcinoma
#20
Kuo-Chang Wen, Pi-Lin Sung, Yu-Ting Chou, Chih-Ming Pan, Peng-Hui Wang, Oscar Kuang-Sheng Lee, Cheng-Wen Wu
OBJECTIVE: EpCAM is a transmembrane glycoprotein that functions as an epithelial marker in endometrial tissues. However, the correlation between EpCAM and endometrial carcinoma (EC) is not clear. METHODS: This study investigated the association between EpCAM and EC. Immunohistochemistry staining and bioinformatics analysis disclosed the clinical importance of low EpCAM expression. The migratory ability of cells expressing low EpCAM levels was studied in transwell invasion assays in vitro and an orthotopic intra-uterine tumor injection model in vivo...
December 2, 2017: Gynecologic Oncology
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