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Genome Medicine

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https://www.readbyqxmd.com/read/28738906/next-generation-sequencing-to-monitor-the-spread-of-antimicrobial-resistance
#1
Michael Otto
Next-generation sequencing is increasingly being used to monitor current and historic events related to the emergence and spread of antimicrobial resistance. In a recent publication, researchers analyzed the rise of methicillin-resistant Staphylococcus aureus in the 1960s, emphasizing that adaptations conferring antibiotic resistance might pre-date the introduction of novel antibiotic derivatives. Other researchers have evaluated the role of transmission within a healthcare network, using the example of extended-spectrum beta-lactamase-resistant Escherichia coli...
July 25, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28738847/longitudinal-genomic-surveillance-of-multidrug-resistant-escherichia-coli-carriage-in-a-long-term-care-facility-in-the-united-kingdom
#2
Hayley J Brodrick, Kathy E Raven, Teemu Kallonen, Dorota Jamrozy, Beth Blane, Nicholas M Brown, Veronique Martin, M Estée Török, Julian Parkhill, Sharon J Peacock
BACKGROUND: Residents of long-term care facilities (LTCF) may have high carriage rates of multidrug-resistant pathogens, but are not currently included in surveillance programmes for antimicrobial resistance or healthcare-associated infections. Here, we describe the value derived from a longitudinal epidemiological and genomic surveillance study of drug-resistant Escherichia coli in a LTCF in the United Kingdom (UK). METHODS: Forty-five of 90 (50%) residents were recruited and followed for six months in 2014...
July 25, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28738853/host-gene-microbiome-interactions-molecular-mechanisms-in-inflammatory-bowel-disease
#3
Hiutung Chu
Recent studies have identified links between host genetic variants and microbial recognition of the microbiome. Defects in host-microbiome interactions in individuals harboring inflammatory bowel disease risk alleles may result in imbalances of the microbial community, impaired pathogen clearance, and failure to sense beneficial commensal microbes. These findings highlight the importance of maintaining bi-directional communication at the mucosal interface during intestinal homeostasis.
July 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28724449/novel-promoters-and-coding-first-exons-in-dlg2-linked-to-developmental-disorders-and-intellectual-disability
#4
Claudio Reggiani, Sandra Coppens, Tayeb Sekhara, Ivan Dimov, Bruno Pichon, Nicolas Lufin, Marie-Claude Addor, Elga Fabia Belligni, Maria Cristina Digilio, Flavio Faletra, Giovanni Battista Ferrero, Marion Gerard, Bertrand Isidor, Shelagh Joss, Florence Niel-Bütschi, Maria Dolores Perrone, Florence Petit, Alessandra Renieri, Serge Romana, Alexandra Topa, Joris Robert Vermeesch, Tom Lenaerts, Georges Casimir, Marc Abramowicz, Gianluca Bontempi, Catheline Vilain, Nicolas Deconinck, Guillaume Smits
BACKGROUND: Tissue-specific integrative omics has the potential to reveal new genic elements important for developmental disorders. METHODS: Two pediatric patients with global developmental delay and intellectual disability phenotype underwent array-CGH genetic testing, both showing a partial deletion of the DLG2 gene. From independent human and murine omics datasets, we combined copy number variations, histone modifications, developmental tissue-specific regulation, and protein data to explore the molecular mechanism at play...
July 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28720124/defining-the-role-of-lgr5-stem-cells-in-colorectal-cancer-from-basic-research-to-clinical-applications
#5
Masayuki Fujii, Toshiro Sato
Intestinal epithelium is structured by two distinct components: the villi and the crypts. The crypts harbor stem cells expressing Lgr5 and thus have been a representative model to study tissue stem cell functions. Recent advances in organoid technology and analytical modalities have enabled precise characterization of Lgr5(+) intestinal stem cells, providing insights into their roles in homeostasis and cancer.
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28720120/interrogating-the-unsequenceable-genomic-trinucleotide-repeat-disorders-by-long-read-sequencing
#6
Qian Liu, Peng Zhang, Depeng Wang, Weihong Gu, Kai Wang
Microsatellite expansion, such as trinucleotide repeat expansion (TRE), is known to cause a number of genetic diseases. Sanger sequencing and next-generation short-read sequencing are unable to interrogate TRE reliably. We developed a novel algorithm called RepeatHMM to estimate repeat counts from long-read sequencing data. Evaluation on simulation data, real amplicon sequencing data on two repeat expansion disorders, and whole-genome sequencing data generated by PacBio and Oxford Nanopore technologies showed superior performance over competing approaches...
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28716134/detecting-protein-variants-by-mass-spectrometry-a-comprehensive-study-in-cancer-cell-lines
#7
Javier A Alfaro, Alexandr Ignatchenko, Vladimir Ignatchenko, Ankit Sinha, Paul C Boutros, Thomas Kislinger
BACKGROUND: Onco-proteogenomics aims to understand how changes in a cancer's genome influences its proteome. One challenge in integrating these molecular data is the identification of aberrant protein products from mass-spectrometry (MS) datasets, as traditional proteomic analyses only identify proteins from a reference sequence database. METHODS: We established proteomic workflows to detect peptide variants within MS datasets. We used a combination of publicly available population variants (dbSNP and UniProt) and somatic variations in cancer (COSMIC) along with sample-specific genomic and transcriptomic data to examine proteome variation within and across 59 cancer cell-lines...
July 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28687074/strength-of-functional-signature-correlates-with-effect-size-in-autism
#8
Sara Ballouz, Jesse Gillis
BACKGROUND: Disagreements over genetic signatures associated with disease have been particularly prominent in the field of psychiatric genetics, creating a sharp divide between disease burdens attributed to common and rare variation, with study designs independently targeting each. Meta-analysis within each of these study designs is routine, whether using raw data or summary statistics, but combining results across study designs is atypical. However, tests of functional convergence are used across all study designs, where candidate gene sets are assessed for overlaps with previously known properties...
July 7, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28683826/identification-and-characterization-of-a-foxa2-regulated-transcriptional-enhancer-at-a-type-2-diabetes-intronic-locus-that-controls-gckr-expression-in-liver-cells
#9
Maykel López Rodríguez, Dorota Kaminska, Kati Lappalainen, Jussi Pihlajamäki, Minna U Kaikkonen, Markku Laakso
BACKGROUND: Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes (T2D). However, the underlying biological mechanisms for many of these associations remain unknown. GWAS signals close to the glucokinase regulatory protein gene (GCKR) have been reported for lipid and glucose metabolism traits and the risk of T2D. We investigated the regulatory function of an intronic locus at GCKR represented by the lead single nucleotide polymorphism (SNP) rs780094...
July 6, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28662719/erratum-to-functional-implications-of-microbial-and-viral-gut-metagenome-changes-in-early-stage-l-dopa-na%C3%A3-ve-parkinson-s-disease-patients
#10
J R Bedarf, F Hildebrand, L P Coelho, S Sunagawa, M Bahram, F Goeser, P Bork, U Wüllner
No abstract text is available yet for this article.
June 29, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28659176/isown-accurate-somatic-mutation-identification-in-the-absence-of-normal-tissue-controls
#11
Irina Kalatskaya, Quang M Trinh, Melanie Spears, John D McPherson, John M S Bartlett, Lincoln Stein
BACKGROUND: A key step in cancer genome analysis is the identification of somatic mutations in the tumor. This is typically done by comparing the genome of the tumor to the reference genome sequence derived from a normal tissue taken from the same donor. However, there are a variety of common scenarios in which matched normal tissue is not available for comparison. RESULTS: In this work, we describe an algorithm to distinguish somatic single nucleotide variants (SNVs) in next-generation sequencing data from germline polymorphisms in the absence of normal samples using a machine learning approach...
June 29, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28655327/advances-in-the-delivery-of-rna-therapeutics-from-concept-to-clinical-reality
#12
REVIEW
James C Kaczmarek, Piotr S Kowalski, Daniel G Anderson
The rapid expansion of the available genomic data continues to greatly impact biomedical science and medicine. Fulfilling the clinical potential of genetic discoveries requires the development of therapeutics that can specifically modulate the expression of disease-relevant genes. RNA-based drugs, including short interfering RNAs and antisense oligonucleotides, are particularly promising examples of this newer class of biologics. For over two decades, researchers have been trying to overcome major challenges for utilizing such RNAs in a therapeutic context, including intracellular delivery, stability, and immune response activation...
June 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28633659/computing-patient-data-in-the-cloud-practical-and-legal-considerations-for-genetics-and-genomics-research-in-europe-and-internationally
#13
Fruzsina Molnár-Gábor, Rupert Lueck, Sergei Yakneen, Jan O Korbel
Biomedical research is becoming increasingly large-scale and international. Cloud computing enables the comprehensive integration of genomic and clinical data, and the global sharing and collaborative processing of these data within a flexibly scalable infrastructure. Clouds offer novel research opportunities in genomics, as they facilitate cohort studies to be carried out at unprecedented scale, and they enable computer processing with superior pace and throughput, allowing researchers to address questions that could not be addressed by studies using limited cohorts...
June 20, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28629429/linked-read-sequencing-resolves-complex-genomic-rearrangements-in-gastric-cancer-metastases
#14
Stephanie U Greer, Lincoln D Nadauld, Billy T Lau, Jiamin Chen, Christina Wood-Bouwens, James M Ford, Calvin J Kuo, Hanlee P Ji
BACKGROUND: Genome rearrangements are critical oncogenic driver events in many malignancies. However, the identification and resolution of the structure of cancer genomic rearrangements remain challenging even with whole genome sequencing. METHODS: To identify oncogenic genomic rearrangements and resolve their structure, we analyzed linked read sequencing. This approach relies on a microfluidic droplet technology to produce libraries derived from single, high molecular weight DNA molecules, 50 kb in size or greater...
June 19, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28615076/dissecting-the-human-microbiome-with-single-cell-genomics
#15
Andrew C Tolonen, Ramnik J Xavier
Recent advances in genome sequencing of single microbial cells enable the assignment of functional roles to members of the human microbiome that cannot currently be cultured. This approach can reveal the genomic basis of phenotypic variation between closely related strains and can be applied to the targeted study of immunogenic bacteria in disease.
June 14, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28595657/brain-cox-investigating-and-visualising-gene-co-expression-in-seven-human-brain-transcriptomic-datasets
#16
Saskia Freytag, Rosemary Burgess, Karen L Oliver, Melanie Bahlo
BACKGROUND: The pathogenesis of neurological and mental health disorders often involves multiple genes, complex interactions, as well as brain- and development-specific biological mechanisms. These characteristics make identification of disease genes for such disorders challenging, as conventional prioritisation tools are not specifically tailored to deal with the complexity of the human brain. Thus, we developed a novel web-application-brain-coX-that offers gene prioritisation with accompanying visualisations based on seven gene expression datasets in the post-mortem human brain, the largest such resource ever assembled...
June 8, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28592326/the-genomic-road-to-invasion-examining-the-similarities-and-differences-in-the-genomes-of-associated-oral-pre-cancer-and-cancer-samples
#17
Henry M Wood, Catherine Daly, Rebecca Chalkley, Burcu Senguven, Lisa Ross, Philip Egan, Preetha Chengot, Jennifer Graham, Neeraj Sethi, Thian K Ong, Kenneth MacLennan, Pamela Rabbitts, Caroline Conway
BACKGROUND: It is frequently assumed that pre-invasive lesions are simpler precursors of cancer and will contain a limited subset of the genomic changes seen in their associated invasive disease. Driver mutations are thought to occur early, but it is not known how many of these are present in pre-invasive lesions. These assumptions need to be tested with the increasing focus on both personalised cancer treatments and early detection methodologies. METHODS: We examined genomic copy number changes in 256 pre-invasive and invasive samples from 69 oral cancer patients...
June 7, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28592290/dna-methylation-based-chromatin-compartments-and-chip-seq-profiles-reveal-transcriptional-drivers-of-prostate-carcinogenesis
#18
Poppy Simmonds, Erick Loomis, Edward Curry
BACKGROUND: Profiles of DNA methylation of many tissues relevant in human disease have been obtained from microarrays and are publicly available. These can be used to generate maps of chromatin compartmentalization, demarcating open and closed chromatin across the genome. Additionally, large sets of genome-wide transcription factor binding profiles have been made available thanks to ChIP-seq technology. METHODS: We have identified genomic regions with altered chromatin compartmentalization in prostate adenocarcinoma tissue relative to normal prostate tissue, using DNA methylation microarray data from The Cancer Genome Atlas...
June 7, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28587651/erratum-to-pancreatic-%C3%AE-cell-regeneration-advances-in-understanding-the-genes-and-signaling-pathways-involved
#19
Solomon Afelik, Meritxell Rovira
No abstract text is available yet for this article.
June 6, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28569207/seed-effect-modeling-improves-the-consistency-of-genome-wide-loss-of-function-screens-and-identifies-synthetic-lethal-vulnerabilities-in-cancer-cells
#20
Alok Jaiswal, Gopal Peddinti, Yevhen Akimov, Krister Wennerberg, Sergey Kuznetsov, Jing Tang, Tero Aittokallio
BACKGROUND: Genome-wide loss-of-function profiling is widely used for systematic identification of genetic dependencies in cancer cells; however, the poor reproducibility of RNA interference (RNAi) screens has been a major concern due to frequent off-target effects. Currently, a detailed understanding of the key factors contributing to the sub-optimal consistency is still a lacking, especially on how to improve the reliability of future RNAi screens by controlling for factors that determine their off-target propensity...
June 1, 2017: Genome Medicine
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