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https://www.readbyqxmd.com/read/28635624/effects-of-type-1-diabetes-risk-alleles-on-immune-cell-gene-expression
#1
REVIEW
Ramesh Ram, Grant Morahan
Genetic studies have identified 61 variants associated with the risk of developing Type 1 Diabetes (T1D). The functions of most of the non-HLA (Human Leukocyte Antigen) genetic variants remain unknown. We found that only 16 of these risk variants could potentially be linked to a protein-coding change. Therefore, we investigated whether these variants affected susceptibility by regulating changes in gene expression. To do so, we examined whole transcriptome profiles of 600 samples from the Type 1 Diabetes Genetics Consortium (T1DGC)...
June 21, 2017: Genes
https://www.readbyqxmd.com/read/28635424/genome-wide-linkage-and-haplotype-sharing-analysis-implicates-the-mcdr3-locus-as-a-candidate-region-for-a-developmental-macular-disorder-in-association-with-digit-abnormalities
#2
Valentina Cipriani, Ambreen Kalhoro, Gavin Arno, Raquel S Silva, Nikolas Pontikos, Virginie Puech, Michelle E McClements, David M Hunt, Veronica van Heyningen, Michel Michaelides, Andrew R Webster, Anthony T Moore, Bernard Puech
BACKGROUND: Developmental macular disorders are a heterogeneous group of rare retinal conditions that can cause significant visual impairment from childhood. Among these disorders, autosomal dominant North Carolina macular dystrophy (NCMD) has been mapped to 6q16 (MCDR1) with recent support for a non-coding disease mechanism of PRDM13. A second locus on 5p15-5p13 (MCDR3) has been implicated in a similar phenotype, but the disease-causing mechanism still remains unknown. METHODS: Two families affected by a dominant developmental macular disorder that closely resembles NCMD in association with digit abnormalities were included in the study...
March 2, 2017: Ophthalmic Genetics
https://www.readbyqxmd.com/read/28634180/a-mutyh-germline-mutation-is-associated-with-small-intestinal-neuroendocrine-tumors
#3
Jan P Dumanski, Chiara Rasi, Peyman Björklund, Hanna Davies, Abir Salwa Ali, Malin Grönberg, Staffan Welin, Halfdan Sorbye, Henning Grønbæk, Janet Cunningham, Lars A Forsberg, Lars Lind, Erik Ingelsson, Peter Stalberg, Per Hellman, Eva Tiensuu Janson
The genetics behind predisposition to small intestinal neuroendocrine tumors (SI-NETs) is largely unknown, but there is growing awareness of a familial form of the disease. We aimed to identify germline mutations involved in the carcinogenesis of SI-NETs. The strategy included next-generation sequencing of exome- and/or whole-genome of blood DNA, and in selected cases tumor DNA, from 24 patients from 15 families with the history of SI-NETs. We identified seven candidate mutations in six genes that were further studied using 215 sporadic SI-NET patients...
June 20, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28633944/gene-expression-analysis-identify-a-metabolic-and-cell-function-alterations-as-a-hallmark-of-obesity-without-metabolic-syndrome-in-peripheral-blood-a-pilot-study
#4
Daniel Antonio de Luis, Raquel Almansa, Rocío Aller, Olatz Izaola, E Romero
BACKGROUND: Understanding molecular basis involved in overweight is an important first step in developing therapeutic pathways against excess in body weight gain. OBJECTIVE: The purpose of our pilot study was to evaluate the gene expression profiles in the peripheral blood of obese patients without other metabolic complications. DESIGN: A sample of 17 obese patients without metabolic syndrome and 15 non obese control subjects was evaluated in a prospective way...
June 10, 2017: Clinical Nutrition: Official Journal of the European Society of Parenteral and Enteral Nutrition
https://www.readbyqxmd.com/read/28632820/the-nexus-of-stem-cell-derived-beta-cells-and-genome-engineering
#5
Sara D Sackett, Aida Rodriguez, Jon S Odorico
Diabetes, type 1 and type 2 (T1D and T2D), are diseases of epidemic proportions, which are complicated and defined by genetics, epigenetics, environment, and lifestyle choices. Current therapies consist of whole pancreas or islet transplantation. However, these approaches require life-time immunosuppression, and are compounded by the paucity of available donors. Pluripotent stem cells have advanced research in the fields of stem cell biology, drug development, disease modeling, and regenerative medicine, and importantly allows for the interrogation of therapeutic interventions...
2017: Review of Diabetic Studies: RDS
https://www.readbyqxmd.com/read/28630326/reconstruction-and-evolutionary-history-of-eutherian-chromosomes
#6
Jaebum Kim, Marta Farré, Loretta Auvil, Boris Capitanu, Denis M Larkin, Jian Ma, Harris A Lewin
Whole-genome assemblies of 19 placental mammals and two outgroup species were used to reconstruct the order and orientation of syntenic fragments in chromosomes of the eutherian ancestor and six other descendant ancestors leading to human. For ancestral chromosome reconstructions, we developed an algorithm (DESCHRAMBLER) that probabilistically determines the adjacencies of syntenic fragments using chromosome-scale and fragmented genome assemblies. The reconstructed chromosomes of the eutherian, boreoeutherian, and euarchontoglires ancestor each included >80% of the entire length of the human genome, whereas reconstructed chromosomes of the most recent common ancestor of simians, catarrhini, great apes, and humans and chimpanzees included >90% of human genome sequence...
June 19, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28629316/a-multiplex-primer-design-algorithm-for-target-amplification-of-continuous-genomic-regions
#7
Ahmet Rasit Ozturk, Tolga Can
BACKGROUND: Targeted Next Generation Sequencing (NGS) assays are cost-efficient and reliable alternatives to Sanger sequencing. For sequencing of very large set of genes, the target enrichment approach is suitable. However, for smaller genomic regions, the target amplification method is more efficient than both the target enrichment method and Sanger sequencing. The major difficulty of the target amplification method is the preparation of amplicons, regarding required time, equipment, and labor...
June 19, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28625393/establishment-and-characterization-of-uterine-sarcoma-and-carcinosarcoma-patient-derived-xenograft-models
#8
Tine Cuppens, Jeroen Depreeuw, Daniela Annibali, Debby Thomas, Els Hermans, Ellen Gommé, Xuan Bich Trinh, David Debruyne, Philippe Moerman, Diether Lambrechts, Frédéric Amant
OBJECTIVE: Uterine sarcomas (US) and carcinosarcomas (CS) are rare, aggressive cancers. The lack of reliable preclinical models hampers the search for new treatment strategies and predictive biomarkers. To this end, we established and characterized US and CS patient-derived xenograft (PDX) models. METHODS: Tumor fragments of US and CS were subcutaneously implanted into immunocompromised mice. Engrafted xenograft and original tumors were compared by means of histology, immunohistochemistry, whole-genome low-coverage sequencing for copy number variations, and RNA sequencing...
June 16, 2017: Gynecologic Oncology
https://www.readbyqxmd.com/read/28623054/detection-of-yellow-fever-virus-genomes-from-four-imported-cases-in-china
#9
Shujuan Cui, Yang Pan, Yanning Lyu, Zhichao Liang, Jie Li, Yulan Sun, Xiangfeng Dou, Lili Tian, Da Huo, Lijuan Chen, Xinyu Li, Quanyi Wang
Yellow fever virus (YFV), as the first proven human-pathogenic virus, is still a major public health problem with a dramatic upsurge in recent years. This is a report on four imported cases of yellow fever virus into China identified by whole genome sequencing. Phylogenetic analysis was performed and the results showed that these four viruses were highly homologous with Angola 71 strains (AY968064). In addition, effective mutations of amino acids were not observed in the E protein domain of four viruses, thus confirming the effectiveness of the YFV-17D vaccine (X03700)...
June 13, 2017: International Journal of Infectious Diseases: IJID
https://www.readbyqxmd.com/read/28622368/minimal-genetic-change-in-vibrio-cholerae-in-mozambique-over-time-multilocus-variable-number-tandem-repeat-analysis-and-whole-genome-sequencing
#10
Marcelino Garrine, Inácio Mandomando, Delfino Vubil, Tacilta Nhampossa, Sozinho Acacio, Shan Li, Joseph N Paulson, Mathieu Almeida, Daryl Domman, Nicholas R Thomson, Pedro Alonso, Oscar Colin Stine
Although cholera is a major public health concern in Mozambique, its transmission patterns remain unknown. We surveyed the genetic relatedness of 75 Vibrio cholerae isolates from patients at Manhiça District Hospital between 2002-2012 and 3 isolates from river using multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS). MLVA revealed 22 genotypes in two clonal complexes and four unrelated genotypes. WGS revealed i) the presence of recombination, ii) 67 isolates descended monophyletically from a single source connected to Wave 3 of the Seventh Pandemic, and iii) four clinical isolates lacking the cholera toxin gene...
June 16, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28622346/flavivirus-and-filovirus-evoprinters-new-alignment-tools-for-the-comparative-analysis-of-viral-evolution
#11
Thomas Brody, Amarendra S Yavatkar, Dong Sun Park, Alexander Kuzin, Jermaine Ross, Ward F Odenwald
BACKGROUND: Flavivirus and Filovirus infections are serious epidemic threats to human populations. Multi-genome comparative analysis of these evolving pathogens affords a view of their essential, conserved sequence elements as well as progressive evolutionary changes. While phylogenetic analysis has yielded important insights, the growing number of available genomic sequences makes comparisons between hundreds of viral strains challenging. We report here a new approach for the comparative analysis of these hemorrhagic fever viruses that can superimpose an unlimited number of one-on-one alignments to identify important features within genomes of interest...
June 16, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28620085/a-sine-insertion-in-atp1b2-in-belgian-shepherd-dogs-affected-by-spongy-degeneration-with-cerebellar-ataxia-sdca2
#12
Nico Mauri, Miriam Kleiter, Elisabeth Dietschi, Michael Leschnik, Sandra Högler, Michaela Wiedmer, Joëlle Dietrich, Diana Henke, Frank Steffen, Simone Schuller, Corinne Gurtner, Nadine Stokar-Regenscheit, Donal O'Toole, Thomas Bilzer, Christiane Herden, Anna Oevermann, Vidhya Jagannathan, Tosso Leeb
Spongy degeneration with cerebellar ataxia (SDCA) is a genetically heterogeneous neurodegenerative disorder with autosomal recessive inheritance in Malinois dogs, one of the four varieties of the Belgian Shepherd breed. Using a combined linkage and homozygosity mapping approach we identified a ~10.6 Mb critical interval on chromosome 5 in a Malinois family with four puppies affected by cerebellar dysfunction. Visual inspection of the 10.6 Mb interval in whole genome sequencing data from one affected puppy revealed a 227 bp SINE insertion into the ATP1B2 gene encoding the β2 subunit of the Na(+)/K(+)-ATPase holoenzyme (ATP1B2:c...
June 15, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28619810/complete-genome-sequence-of-the-campylobacter-cuniculorum-type-strain-lmg-24588
#13
William G Miller, Emma Yee, Joana Revez, James L Bono, Mirko Rossi
Campylobacter cuniculorum is a thermotolerant species isolated from farmed rabbits (Oryctolagus cuniculus). Although C. cuniculorum is highly prevalent in rabbits farmed for human consumption, the pathogenicity of this organism in humans is still unknown. This study describes the whole-genome sequence of the C. cuniculorum type strain LMG 24588 (=CCUG 56289(T)).
June 15, 2017: Genome Announcements
https://www.readbyqxmd.com/read/28618935/heterogeneous-dna-methylation-status-in-same-cell-subpopulations-of-ovarian-cancer-tissues
#14
Qiling Li, Xue Xue, Wenzhi Li, Qi Wang, Lu Han, Tiffany Brunson, Wei Xu, Isfahan Chambers-Harris, Qing Wang, Xu Li, Li Ma, Qing Song
This study aims to explore the heterogeneous DNA methylation differences between individual single ovarian cancer cells isolated from the same formalin-fixed and paraffin-embedded human ovarian cancer tissue. Single cells were isolated by laser microdissection. Whole genome amplification and polymerase chain reaction purification were performed on the converted genomic DNA. Target primers designed for checking DNA methylation were used in polymerase chain reaction reactions to amplify special fragments. Sequencing was performed to analyze the heterogeneous DNA methylation statuses of different single ovarian cancer cells...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28618934/identification-of-curcumin-inhibited-extracellular-matrix-receptors-in-non-small-cell-lung-cancer-a549-cells-by-rna-sequencing
#15
Huiping Li, Hongjin Wu, Hongfang Zhang, Ying Li, Shuang Li, Qiang Hou, Shixiu Wu, Shuan-Ying Yang
Curcumin is a potent anti-cancer drug in several types of human cancers. Despite of several preclinical and clinical studies of curcumin, the precise mechanism of curcumin in cancer prevention has remained unclear. In our study, we for the first time investigated whole transcriptome alteration in A549 non-small cell lung cancer (NSCLC) cell lines after treatment with curcumin using RNA sequencing. We found that lots of genes and signaling pathways were significantly altered after curcumin treatment in A549 cells...
June 2017: Tumour Biology: the Journal of the International Society for Oncodevelopmental Biology and Medicine
https://www.readbyqxmd.com/read/28618417/cholesterol-enhances-colorectal-cancer-progression-via-ros-elevation-and-mapk-signaling-pathway-activation
#16
Caihua Wang, Peiwei Li, Junmei Xuan, Chunpeng Zhu, Jingjing Liu, Lizhen Shan, Qin Du, Yuezhong Ren, Jun Ye
BACKGROUND/AIMS: Elevated serum cholesterol levels were linked to a higher risk of colorectal adenoma and colorectal cancer (CRC), while the effect of cholesterol on CRC metastasis has not been widely studied. METHODS: CRC patients were enrolled to evaluate the association between low-density lipoprotein cholesterol (LDL) and CRC metastases, and LDL receptor (LDLR) level of the CRC tissue was assessed by immunohistochemistry. The effects of LDL on cell proliferation, migration and stemness were assessed in CRC cells in vitro, and the effects of high fat diet (HFD) on tumor growth and intestinal tumorigenicity were investigated in vivo...
June 15, 2017: Cellular Physiology and Biochemistry
https://www.readbyqxmd.com/read/28617800/whole-genome-sequencing-distinguishes-between-relapse-and-reinfection-in-recurrent-leprosy-cases
#17
Mariane M A Stefani, Charlotte Avanzi, Samira Bührer-Sékula, Andrej Benjak, Chloé Loiseau, Pushpendra Singh, Maria A A Pontes, Heitor S Gonçalves, Emerith M Hungria, Philippe Busso, Jérémie Piton, Maria I S Silveira, Rossilene Cruz, Antônio Schetinni, Maurício B Costa, Marcos C L Virmond, Suzana M Diorio, Ida M F Dias-Baptista, Patricia S Rosa, Masanori Matsuoka, Maria L F Penna, Stewart T Cole, Gerson O Penna
BACKGROUND: Since leprosy is both treated and controlled by multidrug therapy (MDT) it is important to monitor recurrent cases for drug resistance and to distinguish between relapse and reinfection as a means of assessing therapeutic efficacy. All three objectives can be reached with single nucleotide resolution using next generation sequencing and bioinformatics analysis of Mycobacterium leprae DNA present in human skin. METHODOLOGY: DNA was isolated by means of optimized extraction and enrichment methods from samples from three recurrent cases in leprosy patients participating in an open-label, randomized, controlled clinical trial of uniform MDT in Brazil (U-MDT/CT-BR)...
June 15, 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28616646/molecular-genetic-diagnostics-for-ventricular-arrhythmias-and-sudden-cardiac-death-syndromes
#18
B Stallmeyer, S Dittmann, G Seebohm, J Müller, E Schulze-Bahr
Inherited forms of ventricular arrhythmias are rare diseases, but a major cause for severe cardiac events, sudden unexplained death syndromes, and death in young adults, infants, and children. Each disorder is genetically heterogeneous (5-20 genes per disease) and molecular testing may include both core genes and less common disease genes as well. Owing to the rapid development and feasibility of sequencing technologies enabling a parallel analysis of several hundred genes up to a whole exome, disease mutations can be identified very efficiently, but have to be seen in the complexity and natural variance of the human genome...
June 14, 2017: Herz
https://www.readbyqxmd.com/read/28615624/circulation-of-hadv-41-with-diverse-genome-types-and-recombination-in-acute-gastroenteritis-among-children-in-shanghai
#19
Peng Li, Lang Yang, Jiayin Guo, Wenwei Zou, Xuebin Xu, Xiaoxia Yang, Xinying Du, Shaofu Qiu, Hongbin Song
Human adenovirus F (HAdV-F) is one of the major causative species detected in acute gastroenteritis in children worldwide. HAdV-F is composed of serotypes 40 and 41. Most studies have reported the prevalence of HAdV-41 and focused on its epidemiologic characteristics. In this study, seventeen samples were identified as HAdV-41 out of 273 fecal specimens from children with acute diarrhea in Shanghai. Five isolates were isolated and subjected to whole genome sequencing and analysis to characterize the genetic variation and evolution...
June 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28614801/dna-methyltransferase-3b-regulates-articular-cartilage-homeostasis-by-altering-metabolism
#20
Jie Shen, Cuicui Wang, Daofeng Li, Taotao Xu, Jason Myers, John M Ashton, Ting Wang, Michael J Zuscik, Audrey McAlinden, Regis J O'Keefe
Osteoarthritis (OA) is the most common form of arthritis worldwide. It is a complex disease affecting the whole joint but is generally characterized by progressive degradation of articular cartilage. Recent genome-wide association screens have implicated distinct DNA methylation signatures in OA patients. We show that the de novo DNA methyltransferase (Dnmt) 3b, but not Dnmt3a, is present in healthy murine and human articular chondrocytes and its expression decreases in OA mouse models and in chondrocytes from human OA patients...
June 15, 2017: JCI Insight
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