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Genome Medicine

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https://www.readbyqxmd.com/read/29776422/beating-the-odds-programming-proliferation-in-the-mammalian-heart
#1
Rajan Jain, Andrey Poleshko, Jonathan A Epstein
The heart is one of the least regenerative organs in the human body; adult cardiac myocytes divide at extremely low frequency. Therefore, meaningful induction of cardiac regeneration requires in-depth understanding of myocyte cell-cycle control. Recent insights into how myocytes can be coaxed into duplicating in vivo might inform emerging therapeutics.
May 18, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29747675/correction-to-differential-analysis-between-somatic-mutation-and-germline-variation-profiles-reveals-cancer-related-genes
#2
Pawel F Przytycki, Mona Singh
Due to an error introduced during copyediting of this article [1], reference [8] incorrectly reads.
May 10, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29703216/simple-paired-heavy-and-light-chain-antibody-repertoire-sequencing-using-endoplasmic-reticulum-microsomes
#3
Praneeth Reddy Devulapally, Jörg Bürger, Thorsten Mielke, Zoltán Konthur, Hans Lehrach, Marie-Laure Yaspo, Jörn Glökler, Hans-Jörg Warnatz
Existing methods for paired antibody heavy- and light-chain repertoire sequencing rely on specialized equipment and are limited by their commercial availability and high costs. Here, we report a novel simple and cost-effective emulsion-based single-cell paired antibody repertoire sequencing method that employs only basic laboratory equipment. We performed a proof-of-concept using mixed mouse hybridoma cells and we also showed that our method can be used for discovery of novel antigen-specific monoclonal antibodies by sequencing human CD19+ B cell IgM and IgG repertoires isolated from peripheral whole blood before and seven days after Td (Tetanus toxoid/Diphtheria toxoid) booster immunization...
April 27, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29695279/mutationalpatterns-comprehensive-genome-wide-analysis-of-mutational-processes
#4
Francis Blokzijl, Roel Janssen, Ruben van Boxtel, Edwin Cuppen
BACKGROUND: Base substitution catalogues represent historical records of mutational processes that have been active in a cell. Such processes can be distinguished by various characteristics, like mutation type, sequence context, transcriptional and replicative strand bias, genomic distribution and association with (epi)-genomic features. RESULTS: We have created MutationalPatterns, an R/Bioconductor package that allows researchers to characterize a broad range of patterns in base substitution catalogues to dissect the underlying molecular mechanisms...
April 25, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29690921/pathogen-detection-in-the-crispr-cas-era
#5
Dipali G Sashital
CRISPR-Cas systems have provided revolutionary tools for genome editing. The discovery of Cas proteins with alternative activities has now enabled sensitive and robust tools for detecting nucleic acids. Recent reports harnessing these new CRISPR-Cas technologies display their potential for providing low-cost and practical diagnostic tools for pathogen and disease detection.
April 24, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29673390/enabling-multiplexed-testing-of-pooled-donor-cells-through-whole-genome-sequencing
#6
Yingleong Chan, Ying Kai Chan, Daniel B Goodman, Xiaoge Guo, Alejandro Chavez, Elaine T Lim, George M Church
We describe a method that enables the multiplex screening of a pool of many different donor cell lines. Our method accurately predicts each donor proportion from the pool without requiring the use of unique DNA barcodes as markers of donor identity. Instead, we take advantage of common single nucleotide polymorphisms, whole-genome sequencing, and an algorithm to calculate the proportions from the sequencing data. By testing using simulated and real data, we showed that our method robustly predicts the individual proportions from a mixed-pool of numerous donors, thus enabling the multiplexed testing of diverse donor cells en masse...
April 19, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29665865/integrative-analysis-reveals-functional-and-regulatory-roles-of-h3k79me2-in-mediating-alternative-splicing
#7
Tianbao Li, Qi Liu, Nick Garza, Steven Kornblau, Victor X Jin
BACKGROUND: Accumulating evidence suggests alternative splicing (AS) is a co-transcriptional splicing process not only controlled by RNA-binding splicing factors, but also mediated by epigenetic regulators, such as chromatin structure, nucleosome density, and histone modification. Aberrant AS plays an important role in regulating various diseases, including cancers. METHODS: In this study, we integrated AS events derived from RNA-seq with H3K79me2 ChIP-seq data across 34 different normal and cancer cell types and found the higher enrichment of H3K79me2 in two AS types, skipping exon (SE) and alternative 3' splice site (A3SS)...
April 17, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29661213/sensitivity-to-sequencing-depth-in-single-cell-cancer-genomics
#8
João M Alves, David Posada
BACKGROUND: Querying cancer genomes at single-cell resolution is expected to provide a powerful framework to understand in detail the dynamics of cancer evolution. However, given the high costs currently associated with single-cell sequencing, together with the inevitable technical noise arising from single-cell genome amplification, cost-effective strategies that maximize the quality of single-cell data are critically needed. Taking advantage of previously published single-cell whole-genome and whole-exome cancer datasets, we studied the impact of sequencing depth and sampling effort towards single-cell variant detection...
April 16, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29653584/exposure-to-the-gut-microbiota-drives-distinct-methylome-and-transcriptome-changes-in-intestinal-epithelial-cells-during-postnatal-development
#9
Wei-Hung Pan, Felix Sommer, Maren Falk-Paulsen, Thomas Ulas, Philipp Best, Antonella Fazio, Priyadarshini Kachroo, Anne Luzius, Marlene Jentzsch, Ateequr Rehman, Fabian Müller, Thomas Lengauer, Jörn Walter, Sven Künzel, John F Baines, Stefan Schreiber, Andre Franke, Joachim L Schultze, Fredrik Bäckhed, Philip Rosenstiel
BACKGROUND: The interplay of epigenetic processes and the intestinal microbiota may play an important role in intestinal development and homeostasis. Previous studies have established that the microbiota regulates a large proportion of the intestinal epithelial transcriptome in the adult host, but microbial effects on DNA methylation and gene expression during early postnatal development are still poorly understood. Here, we sought to investigate the microbial effects on DNA methylation and the transcriptome of intestinal epithelial cells (IECs) during postnatal development...
April 13, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29653583/new-additions-to-the-cancer-precision-medicine-toolkit
#10
Elaine R Mardis
New computational and database-driven tools are emerging to aid in the interpretation of cancer genomic data as its use becomes more common in clinical evidence-based cancer medicine. Two such open source tools, published recently in Genome Medicine, provide important advances to address the clinical cancer genomics data interpretation bottleneck.
April 13, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29598827/integrated-biology-approach-reveals-molecular-and-pathological-interactions-among-alzheimer-s-a%C3%AE-42-tau-trem2-and-tyrobp-in-drosophila-models
#11
Michiko Sekiya, Minghui Wang, Naoki Fujisaki, Yasufumi Sakakibara, Xiuming Quan, Michelle E Ehrlich, Philip L De Jager, David A Bennett, Eric E Schadt, Sam Gandy, Kanae Ando, Bin Zhang, Koichi M Iijima
BACKGROUND: Cerebral amyloidosis, neuroinflammation, and tauopathy are key features of Alzheimer's disease (AD), but interactions among these features remain poorly understood. Our previous multiscale molecular network models of AD revealed TYROBP as a key driver of an immune- and microglia-specific network that was robustly associated with AD pathophysiology. Recent genetic studies of AD further identified pathogenic mutations in both TREM2 and TYROBP. METHODS: In this study, we systematically examined molecular and pathological interactions among Aβ, tau, TREM2, and TYROBP by integrating signatures from transgenic Drosophila models of AD and transcriptome-wide gene co-expression networks from two human AD cohorts...
March 29, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29592813/cancer-genome-interpreter-annotates-the-biological-and-clinical-relevance-of-tumor-alterations
#12
David Tamborero, Carlota Rubio-Perez, Jordi Deu-Pons, Michael P Schroeder, Ana Vivancos, Ana Rovira, Ignasi Tusquets, Joan Albanell, Jordi Rodon, Josep Tabernero, Carmen de Torres, Rodrigo Dienstmann, Abel Gonzalez-Perez, Nuria Lopez-Bigas
While tumor genome sequencing has become widely available in clinical and research settings, the interpretation of tumor somatic variants remains an important bottleneck. Here we present the Cancer Genome Interpreter, a versatile platform that automates the interpretation of newly sequenced cancer genomes, annotating the potential of alterations detected in tumors to act as drivers and their possible effect on treatment response. The results are organized in different levels of evidence according to current knowledge, which we envision can support a broad range of oncology use cases...
March 28, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29587883/elevated-polygenic-burden-for-autism-is-associated-with-differential-dna-methylation-at-birth
#13
Eilis Hannon, Diana Schendel, Christine Ladd-Acosta, Jakob Grove, Christine Søholm Hansen, Shan V Andrews, David Michael Hougaard, Michaeline Bresnahan, Ole Mors, Mads Vilhelm Hollegaard, Marie Bækvad-Hansen, Mady Hornig, Preben Bo Mortensen, Anders D Børglum, Thomas Werge, Marianne Giørtz Pedersen, Merete Nordentoft, Joseph Buxbaum, M Daniele Fallin, Jonas Bybjerg-Grauholm, Abraham Reichenberg, Jonathan Mill
BACKGROUND: Autism spectrum disorder (ASD) is a severe neurodevelopmental disorder characterized by deficits in social communication and restricted, repetitive behaviors, interests, or activities. The etiology of ASD involves both inherited and environmental risk factors, with epigenetic processes hypothesized as one mechanism by which both genetic and non-genetic variation influence gene regulation and pathogenesis. The aim of this study was to identify DNA methylation biomarkers of ASD detectable at birth...
March 28, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29580275/the-emerging-roles-of-exosomes-in-the-modulation-of-immune-responses-in-cancer
#14
Paul Kurywchak, Jena Tavormina, Raghu Kalluri
Exosomes are promising tools for improving cancer care, but conversely may also contribute to tumor progression. Here, we highlight recently discovered roles of exosomes in modulating immune responses in cancer, with emphasis on exosomal surface proteins and on RNA and DNA content. We also discuss how exosomes could be exploited as biomarkers and delivery vehicles in cancer therapy.
March 26, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29580271/local-adaptation-in-european-populations-affected-the-genetics-of-psychiatric-disorders-and-behavioral-traits
#15
Renato Polimanti, Manfred H Kayser, Joel Gelernter
BACKGROUND: Recent studies have used genome-wide data to investigate evolutionary mechanisms related to behavioral phenotypes, identifying widespread signals of positive selection. Here, we conducted a genome-wide investigation to study whether the molecular mechanisms involved in these traits were affected by local adaptation. METHODS: We performed a polygenic risk score analysis in a sample of 2455 individuals from 23 European populations with respect to variables related to geo-climate diversity, pathogen diversity, and language phonological complexity...
March 26, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29580258/detection-of-creutzfeldt-jakob-disease-prions-in-skin-implications-for-healthcare
#16
Akin Nihat, Simon Mead
Evidence has recently been reported of prion seeding activity in skin tissue from patients with sporadic Creutzfeldt-Jakob disease (sCJD). This is relevant information for infection control measures during surgery. The work uses very sensitive prion assays now available for medical research, and may soon be adapted to related neurodegenerative disorders.
March 26, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29558971/advances-in-liquid-biopsy-approaches-for-early-detection-and-monitoring-of-cancer
#17
Anna Babayan, Klaus Pantel
Progress in sensitive analytical approaches has opened new avenues for the detection of cells or products such as circulating cell-free DNA released by tumors. These 'liquid biopsies' are being explored in clinical trials for early cancer detection, prediction of recurrent disease, and assessment of therapeutic resistance mechanisms.
March 20, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29558968/baldr-a-computational-pipeline-for-paired-heavy-and-light-chain-immunoglobulin-reconstruction-in-single-cell-rna-seq-data
#18
Amit A Upadhyay, Robert C Kauffman, Amber N Wolabaugh, Alice Cho, Nirav B Patel, Samantha M Reiss, Colin Havenar-Daughton, Reem A Dawoud, Gregory K Tharp, Iñaki Sanz, Bali Pulendran, Shane Crotty, F Eun-Hyung Lee, Jens Wrammert, Steven E Bosinger
B cells play a critical role in the immune response by producing antibodies, which display remarkable diversity. Here we describe a bioinformatic pipeline, BALDR (BCR Assignment of Lineage using De novo Reconstruction) that accurately reconstructs the paired heavy and light chain immunoglobulin gene sequences from Illumina single-cell RNA-seq data. BALDR was accurate for clonotype identification in human and rhesus macaque influenza vaccine and simian immunodeficiency virus vaccine induced vaccine-induced plasmablasts and naïve and antigen-specific memory B cells...
March 20, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29544535/from-somatic-variants-towards-precision-oncology-evidence-driven-reporting-of-treatment-options-in-molecular-tumor-boards
#19
Júlia Perera-Bel, Barbara Hutter, Christoph Heining, Annalen Bleckmann, Martina Fröhlich, Stefan Fröhling, Hanno Glimm, Benedikt Brors, Tim Beißbarth
BACKGROUND: A comprehensive understanding of cancer has been furthered with technological improvements and decreasing costs of next-generation sequencing (NGS). However, the complexity of interpreting genomic data is hindering the implementation of high-throughput technologies in the clinical context: increasing evidence on gene-drug interactions complicates the task of assigning clinical significance to genomic variants. METHODS: Here we present a method that automatically matches patient-specific genomic alterations to treatment options...
March 15, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29486792/nsaid-use-and-somatic-exomic-mutations-in-barrett-s-esophagus
#20
Patricia C Galipeau, Kenji M Oman, Thomas G Paulson, Carissa A Sanchez, Qing Zhang, Jerry A Marty, Jeffrey J Delrow, Mary K Kuhner, Thomas L Vaughan, Brian J Reid, Xiaohong Li
BACKGROUND: Use of aspirin and other non-steroidal anti-inflammatory drugs (NSAIDs) has been shown to protect against tetraploidy, aneuploidy, and chromosomal alterations in the metaplastic condition Barrett's esophagus (BE) and to lower the incidence and mortality of esophageal adenocarcinoma (EA). The esophagus is exposed to both intrinsic and extrinsic mutagens resulting from gastric reflux, chronic inflammation, and exposure to environmental carcinogens such as those found in cigarettes...
February 27, 2018: Genome Medicine
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