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Genome Medicine

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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
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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
https://www.readbyqxmd.com/read/28569182/a-pharmacogenetic-signature-of-high-response-to-copaxone-in-late-phase-clinical-trial-cohorts-of-multiple-sclerosis
#9
Colin J Ross, Fadi Towfic, Jyoti Shankar, Daphna Laifenfeld, Mathis Thoma, Matthew Davis, Brian Weiner, Rebecca Kusko, Ben Zeskind, Volker Knappertz, Iris Grossman, Michael R Hayden
BACKGROUND: Copaxone is an efficacious and safe therapy that has demonstrated clinical benefit for over two decades in patients with relapsing forms of multiple sclerosis (MS). On an individual level, patients show variability in their response to Copaxone, with some achieving significantly higher response levels. The involvement of genes (e.g., HLA-DRB1*1501) with high inter-individual variability in Copaxone's mechanism of action (MoA) suggests the potential contribution of genetics to treatment response...
May 31, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28558813/genome-annotation-for-clinical-genomic-diagnostics-strengths-and-weaknesses
#10
REVIEW
Charles A Steward, Alasdair P J Parker, Berge A Minassian, Sanjay M Sisodiya, Adam Frankish, Jennifer Harrow
The Human Genome Project and advances in DNA sequencing technologies have revolutionized the identification of genetic disorders through the use of clinical exome sequencing. However, in a considerable number of patients, the genetic basis remains unclear. As clinicians begin to consider whole-genome sequencing, an understanding of the processes and tools involved and the factors to consider in the annotation of the structure and function of genomic elements that might influence variant identification is crucial...
May 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28554332/genomic-diagnosis-for-children-with-intellectual-disability-and-or-developmental-delay
#11
Kevin M Bowling, Michelle L Thompson, Michelle D Amaral, Candice R Finnila, Susan M Hiatt, Krysta L Engel, J Nicholas Cochran, Kyle B Brothers, Kelly M East, David E Gray, Whitley V Kelley, Neil E Lamb, Edward J Lose, Carla A Rich, Shirley Simmons, Jana S Whittle, Benjamin T Weaver, Amy S Nesmith, Richard M Myers, Gregory S Barsh, E Martina Bebin, Gregory M Cooper
BACKGROUND: Developmental disabilities have diverse genetic causes that must be identified to facilitate precise diagnoses. We describe genomic data from 371 affected individuals, 309 of which were sequenced as proband-parent trios. METHODS: Whole-exome sequences (WES) were generated for 365 individuals (127 affected) and whole-genome sequences (WGS) were generated for 612 individuals (244 affected). RESULTS: Pathogenic or likely pathogenic variants were found in 100 individuals (27%), with variants of uncertain significance in an additional 42 (11...
May 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28549478/gladiator-a-global-approach-for-elucidating-disease-modules
#12
Yael Silberberg, Martin Kupiec, Roded Sharan
BACKGROUND: Understanding the genetic basis of disease is an important challenge in biology and medicine. The observation that disease-related proteins often interact with one another has motivated numerous network-based approaches for deciphering disease mechanisms. In particular, protein-protein interaction networks were successfully used to illuminate disease modules, i.e., interacting proteins working in concert to drive a disease. The identification of these modules can further our understanding of disease mechanisms...
May 26, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28545587/type-2-diabetes-and-obesity-induce-similar-transcriptional-reprogramming-in-human-myocytes
#13
Leif Väremo, Tora Ida Henriksen, Camilla Scheele, Christa Broholm, Maria Pedersen, Mathias Uhlén, Bente Klarlund Pedersen, Jens Nielsen
BACKGROUND: Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). The close association between obesity and T2D makes it difficult to isolate specific effects attributed to the disease alone. Therefore, here we set out to identify and characterize intrinsic properties of myocytes, associated independently with T2D or obesity. METHODS: We generated and analyzed RNA-seq data from primary differentiated myotubes from 24 human subjects, using a factorial design (healthy/T2D and non-obese/obese), to determine the influence of each specific factor on genome-wide transcription...
May 25, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28539127/dissecting-microsatellite-instability-in-colorectal-cancer-one-size-does-not-fit-all
#14
Robert M Samstein, Timothy A Chan
Microsatellite instability (MSI) marks distinct subsets of tumors in many cancer types and is caused by mutations in genes required for mismatch repair. A recent report analyses the molecular foundations of MSI-positive colorectal cancers and reveals substantial molecular heterogeneity, which might have consequences for the potential use of immunotherapy in MSI-positive cancers.See related research by Sveen et al. 10.1186/s13073-017-0434-0.
May 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28539123/multilevel-genomics-of-colorectal-cancers-with-microsatellite-instability-clinical-impact-of-jak1-mutations-and-consensus-molecular-subtype-1
#15
Anita Sveen, Bjarne Johannessen, Torstein Tengs, Stine A Danielsen, Ina A Eilertsen, Guro E Lind, Kaja C G Berg, Edward Leithe, Leonardo A Meza-Zepeda, Enric Domingo, Ola Myklebost, David Kerr, Ian Tomlinson, Arild Nesbakken, Rolf I Skotheim, Ragnhild A Lothe
BACKGROUND: Approximately 15% of primary colorectal cancers have DNA mismatch repair deficiency, causing a complex genome with thousands of small mutations-the microsatellite instability (MSI) phenotype. We investigated molecular heterogeneity and tumor immunogenicity in relation to clinical endpoints within this distinct subtype of colorectal cancers. METHODS: A total of 333 primary MSI+ colorectal tumors from multiple cohorts were analyzed by multilevel genomics and computational modeling-including mutation profiling, clonality modeling, and neoantigen prediction in a subset of the tumors, as well as gene expression profiling for consensus molecular subtypes (CMS) and immune cell infiltration...
May 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28539110/novel-insights-into-the-hla-class-i-immunopeptidome-and-t-cell-immunosurveillance
#16
Cornelis J M Melief, Jan H Kessler
Advances in mass spectrometry have allowed the high-throughput quantitative identification of human leukocyte antigen (HLA) class I ligands, and recent studies have reported on the breadth and diversity of the HLA class I immunopeptidome. These findings have far-reaching implications for immunosurveillance by T cells and translational value for immunotherapy.
May 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28511717/pancreatic-%C3%AE-cell-regeneration-advances-in-understanding-the-genes-and-signaling-pathways-involved
#17
Solomon Afelik, Meritxell Rovira
Recent advances in β-cell regeneration in vivo are providing insights into the mechanisms involved in the conversion of distinct pancreatic cell lineages into β cells. These mechanisms mostly involve reactivation of the gene encoding the pancreatic endocrine cell-specifying transcription factor neurogenin-3.
May 16, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28454591/lost-in-translation-returning-germline-genetic-results-in-genome-scale-cancer-research
#18
Amber L Johns, Skye H McKay, Jeremy L Humphris, Mark Pinese, Lorraine A Chantrill, R Scott Mead, Katherine Tucker, Lesley Andrews, Annabel Goodwin, Conrad Leonard, Hilda A High, Katia Nones, Ann-Marie Patch, Neil D Merrett, Nick Pavlakis, Karin S Kassahn, Jaswinder S Samra, David K Miller, David K Chang, Marina Pajic, John V Pearson, Sean M Grimmond, Nicola Waddell, Nikolajs Zeps, Anthony J Gill, Andrew V Biankin
BACKGROUND: The return of research results (RoR) remains a complex and well-debated issue. Despite the debate, actual data related to the experience of giving individual results back, and the impact these results may have on clinical care and health outcomes, is sorely lacking. Through the work of the Australian Pancreatic Cancer Genome Initiative (APGI) we: (1) delineate the pathway back to the patient where actionable research data were identified; and (2) report the clinical utilisation of individual results returned...
April 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28449715/functional-implications-of-microbial-and-viral-gut-metagenome-changes-in-early-stage-l-dopa-na%C3%A3-ve-parkinson-s-disease-patients
#19
J R Bedarf, F Hildebrand, L P Coelho, S Sunagawa, M Bahram, F Goeser, P Bork, U Wüllner
BACKGROUND: Parkinson's disease (PD) presently is conceptualized as a protein aggregation disease in which pathology involves both the enteric and the central nervous system, possibly spreading from one to another via the vagus nerves. As gastrointestinal dysfunction often precedes or parallels motor symptoms, the enteric system with its vast diversity of microorganisms may be involved in PD pathogenesis. Alterations in the enteric microbial taxonomic level of L-DOPA-naïve PD patients might also serve as a biomarker...
April 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28446242/activity-of-distinct-growth-factor-receptor-network-components-in-breast-tumors-uncovers-two-biologically-relevant-subtypes
#20
Mumtahena Rahman, Shelley M MacNeil, David F Jenkins, Gajendra Shrestha, Sydney R Wyatt, Jasmine A McQuerry, Stephen R Piccolo, Laura M Heiser, Joe W Gray, W Evan Johnson, Andrea H Bild
BACKGROUND: The growth factor receptor network (GFRN) plays a significant role in driving key oncogenic processes. However, assessment of global GFRN activity is challenging due to complex crosstalk among GFRN components, or pathways, and the inability to study complex signaling networks in patient tumors. Here, pathway-specific genomic signatures were used to interrogate GFRN activity in breast tumors and the consequent phenotypic impact of GRFN activity patterns. METHODS: Novel pathway signatures were generated in human primary mammary epithelial cells by overexpressing key genes from GFRN pathways (HER2, IGF1R, AKT1, EGFR, KRAS (G12V), RAF1, BAD)...
April 26, 2017: Genome Medicine
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