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Genome Medicine

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https://www.readbyqxmd.com/read/28340599/dna-methylation-changes-at-infertility-genes-in-newborn-twins-conceived-by-in-vitro-fertilisation
#1
Juan E Castillo-Fernandez, Yuk Jing Loke, Sebastian Bass-Stringer, Fei Gao, Yudong Xia, Honglong Wu, Hanlin Lu, Yuan Liu, Jun Wang, Tim D Spector, Richard Saffery, Jeffrey M Craig, Jordana T Bell
BACKGROUND: The association of in vitro fertilisation (IVF) and DNA methylation has been studied predominantly at regulatory regions of imprinted genes and at just thousands of the ~28 million CpG sites in the human genome. METHODS: We investigated the links between IVF and DNA methylation patterns in whole cord blood cells (n = 98) and cord blood mononuclear cells (n = 82) from newborn twins using genome-wide methylated DNA immunoprecipitation coupled with deep sequencing...
March 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28330499/a-novel-multi-network-approach-reveals-tissue-specific-cellular-modulators-of-fibrosis-in-systemic-sclerosis
#2
Jaclyn N Taroni, Casey S Greene, Viktor Martyanov, Tammara A Wood, Romy B Christmann, Harrison W Farber, Robert A Lafyatis, Christopher P Denton, Monique E Hinchcliff, Patricia A Pioli, J Matthew Mahoney, Michael L Whitfield
BACKGROUND: Systemic sclerosis (SSc) is a multi-organ autoimmune disease characterized by skin fibrosis. Internal organ involvement is heterogeneous. It is unknown whether disease mechanisms are common across all involved affected tissues or if each manifestation has a distinct underlying pathology. METHODS: We used consensus clustering to compare gene expression profiles of biopsies from four SSc-affected tissues (skin, lung, esophagus, and peripheral blood) from patients with SSc, and the related conditions pulmonary fibrosis (PF) and pulmonary arterial hypertension, and derived a consensus disease-associate signature across all tissues...
March 23, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28327206/lessons-learned-from-additional-research-analyses-of-unsolved-clinical-exome-cases
#3
Mohammad K Eldomery, Zeynep Coban-Akdemir, Tamar Harel, Jill A Rosenfeld, Tomasz Gambin, Asbjørg Stray-Pedersen, Sébastien Küry, Sandra Mercier, Davor Lessel, Jonas Denecke, Wojciech Wiszniewski, Samantha Penney, Pengfei Liu, Weimin Bi, Seema R Lalani, Christian P Schaaf, Michael F Wangler, Carlos A Bacino, Richard Alan Lewis, Lorraine Potocki, Brett H Graham, John W Belmont, Fernando Scaglia, Jordan S Orange, Shalini N Jhangiani, Theodore Chiang, Harsha Doddapaneni, Jianhong Hu, Donna M Muzny, Fan Xia, Arthur L Beaudet, Eric Boerwinkle, Christine M Eng, Sharon E Plon, V Reid Sutton, Richard A Gibbs, Jennifer E Posey, Yaping Yang, James R Lupski
BACKGROUND: Given the rarity of most single-gene Mendelian disorders, concerted efforts of data exchange between clinical and scientific communities are critical to optimize molecular diagnosis and novel disease gene discovery. METHODS: We designed and implemented protocols for the study of cases for which a plausible molecular diagnosis was not achieved in a clinical genomics diagnostic laboratory (i.e. unsolved clinical exomes). Such cases were recruited to a research laboratory for further analyses, in order to potentially: (1) accelerate novel disease gene discovery; (2) increase the molecular diagnostic yield of whole exome sequencing (WES); and (3) gain insight into the genetic mechanisms of disease...
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28327175/schizophrenia-and-substance-use-comorbidity-a-genome-wide-perspective
#4
Renato Polimanti, Arpana Agrawal, Joel Gelernter
Dual diagnosis with substance use disorders (SUDs) consistently contributes to the premature mortality and increased disability observed in schizophrenia. Large genome-wide association studies are providing the information needed to investigate the genetic architecture of psychiatric disorders. Here, we discuss recent genetic investigations of dual diagnosis (i.e., schizophrenia plus a SUD) and how these findings can inform public health messages.
March 21, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28279190/imiquimod-has-strain-dependent-effects-in-mice-and-does-not-uniquely-model-human-psoriasis
#5
William R Swindell, Kellie A Michaels, Andrew J Sutter, Doina Diaconu, Yi Fritz, Xianying Xing, Mrinal K Sarkar, Yun Liang, Alex Tsoi, Johann E Gudjonsson, Nicole L Ward
BACKGROUND: Imiquimod (IMQ) produces a cutaneous phenotype in mice frequently studied as an acute model of human psoriasis. Whether this phenotype depends on strain or sex has never been systematically investigated on a large scale. Such effects, however, could lead to conflicts among studies, while further impacting study outcomes and efforts to translate research findings. METHODS: RNA-seq was used to evaluate the psoriasiform phenotype elicited by 6 days of Aldara (5% IMQ) treatment in both sexes of seven mouse strains (C57BL/6 J (B6), BALB/cJ, CD1, DBA/1 J, FVB/NJ, 129X1/SvJ, and MOLF/EiJ)...
March 9, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28270201/exploration-of-haplotype-research-consortium-imputation-for-genome-wide-association-studies-in-20-032-generation-scotland-participants
#6
Reka Nagy, Thibaud S Boutin, Jonathan Marten, Jennifer E Huffman, Shona M Kerr, Archie Campbell, Louise Evenden, Jude Gibson, Carmen Amador, David M Howard, Pau Navarro, Andrew Morris, Ian J Deary, Lynne J Hocking, Sandosh Padmanabhan, Blair H Smith, Peter Joshi, James F Wilson, Nicholas D Hastie, Alan F Wright, Andrew M McIntosh, David J Porteous, Chris S Haley, Veronique Vitart, Caroline Hayward
BACKGROUND: The Generation Scotland: Scottish Family Health Study (GS:SFHS) is a family-based population cohort with DNA, biological samples, socio-demographic, psychological and clinical data from approximately 24,000 adult volunteers across Scotland. Although data collection was cross-sectional, GS:SFHS became a prospective cohort due to of the ability to link to routine Electronic Health Record (EHR) data. Over 20,000 participants were selected for genotyping using a large genome-wide array...
March 7, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28253899/schizophrenia-and-the-dynamic-genome
#7
Patrick F Sullivan
No abstract text is available yet for this article.
March 2, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28245856/characterization-of-oral-and-gut-microbiome-temporal-variability-in-hospitalized-cancer-patients
#8
Jessica R Galloway-Peña, Daniel P Smith, Pranoti Sahasrabhojane, W Duncan Wadsworth, Bryan M Fellman, Nadim J Ajami, Elizabeth J Shpall, Naval Daver, Michele Guindani, Joseph F Petrosino, Dimitrios P Kontoyiannis, Samuel A Shelburne
BACKGROUND: Understanding longitudinal variability of the microbiome in ill patients is critical to moving microbiome-based measurements and therapeutics into clinical practice. However, the vast majority of data regarding microbiome stability are derived from healthy subjects. Herein, we sought to determine intra-patient temporal microbiota variability, the factors driving such variability, and its clinical impact in an extensive longitudinal cohort of hospitalized cancer patients during chemotherapy...
February 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28241858/machine-learning-identifies-a-compact-gene-set-for-monitoring-the-circadian-clock-in-human-blood
#9
Jacob J Hughey
BACKGROUND: The circadian clock and the daily rhythms it produces are crucial for human health, but are often disrupted by the modern environment. At the same time, circadian rhythms may influence the efficacy and toxicity of therapeutics and the metabolic response to food intake. Developing treatments for circadian dysfunction, as well as optimizing the daily timing of treatments for other health conditions, will require a simple and accurate method to monitor the molecular state of the circadian clock...
February 28, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28231819/genomic-analysis-of-63-220-tumors-reveals-insights-into-tumor-uniqueness-and-targeted-cancer-immunotherapy-strategies
#10
Ryan J Hartmaier, Jehad Charo, David Fabrizio, Michael E Goldberg, Lee A Albacker, William Pao, Juliann Chmielecki
BACKGROUND: The integration of genomics with immunotherapy has potential value for cancer vaccine development. Given the clinical successes of immune checkpoint modulators, interest in cancer vaccines as therapeutic options has been revived. Current data suggest that each tumor contains a unique set of mutations (mutanome), thus requiring the creation of individualized cancer vaccines. However, rigorous analysis of non-individualized cancer immunotherapy approaches across multiple cancer types and in the context of known driver alterations has yet to be reported...
February 24, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28228157/genetics-and-genomics-of-dilated-cardiomyopathy-and-systolic-heart-failure
#11
REVIEW
Upasana Tayal, Sanjay Prasad, Stuart A Cook
Heart failure is a major health burden, affecting 40 million people globally. One of the main causes of systolic heart failure is dilated cardiomyopathy (DCM), the leading global indication for heart transplantation. Our understanding of the genetic basis of both DCM and systolic heart failure has improved in recent years with the application of next-generation sequencing and genome-wide association studies (GWAS). This has enabled rapid sequencing at scale, leading to the discovery of many novel rare variants in DCM and of common variants in both systolic heart failure and DCM...
February 22, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28219444/a-functional-snp-associated-with-atopic-dermatitis-controls-cell-type-specific-methylation-of-the-vstm1-gene-locus
#12
Dilip Kumar, Kia Joo Puan, Anand Kumar Andiappan, Bernett Lee, Geertje H A Westerlaken, Doreen Haase, Rossella Melchiotti, Zhuang Li, Nurhashikin Yusof, Josephine Lum, Geraldine Koh, Shihui Foo, Joe Yeong, Alexessander Couto Alves, Juha Pekkanen, Liang Dan Sun, Astrid Irwanto, Benjamin P Fairfax, Vivek Naranbhai, John E A Common, Mark Tang, Chin Keh Chuang, Marjo-Riitta Jarvelin, Julian C Knight, Xuejun Zhang, Fook Tim Chew, Shyam Prabhakar, Liu Jianjun, De Yun Wang, Francesca Zolezzi, Michael Poidinger, E Birgitte Lane, Linde Meyaard, Olaf Rötzschke
BACKGROUND: Expression quantitative trait loci (eQTL) databases represent a valuable resource to link disease-associated SNPs to specific candidate genes whose gene expression is significantly modulated by the SNP under investigation. We previously identified signal inhibitory receptor on leukocytes-1 (SIRL-1) as a powerful regulator of human innate immune cell function. While it is constitutively high expressed on neutrophils, on monocytes the SIRL-1 surface expression varies strongly between individuals...
February 20, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28212680/mecp2-mutations-progress-towards-understanding-and-treating-rett-syndrome
#13
Ruth R Shah, Adrian P Bird
Rett syndrome is a profound neurological disorder caused by mutations in the MECP2 gene, but preclinical research has indicated that it is potentially treatable. Progress towards this goal depends on the development of increasingly relevant model systems and on our improving knowledge of MeCP2 function in the brain.
February 17, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28187790/retinoic-acid-and-tgf-%C3%AE-signalling-cooperate-to-overcome-mycn-induced-retinoid-resistance
#14
David J Duffy, Aleksandar Krstic, Melinda Halasz, Thomas Schwarzl, Anja Konietzny, Kristiina Iljin, Desmond G Higgins, Walter Kolch
BACKGROUND: Retinoid therapy is widely employed in clinical oncology to differentiate malignant cells into their more benign counterparts. However, certain high-risk cohorts, such as patients with MYCN-amplified neuroblastoma, are innately resistant to retinoid therapy. Therefore, we employed a precision medicine approach to globally profile the retinoid signalling response and to determine how an excess of cellular MYCN antagonises these signalling events to prevent differentiation and confer resistance...
February 10, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28173873/microbiomic-differences-in-tumor-and-paired-normal-tissue-in-head-and-neck-squamous-cell-carcinomas
#15
Hannah Wang, Pauline Funchain, Gurkan Bebek, Jessica Altemus, Huan Zhang, Farshad Niazi, Charissa Peterson, Walter T Lee, Brian B Burkey, Charis Eng
BACKGROUND: While the role of the gut microbiome in inflammation and colorectal cancers has received much recent attention, there are few data to support an association between the oral microbiome and head and neck squamous cell carcinomas. Prior investigations have been limited to comparisons of microbiota obtained from surface swabs of the oral cavity. This study aims to identify microbiomic differences in paired tumor and non-tumor tissue samples in a large group of 121 patients with head and neck squamous cell carcinomas and correlate these differences with clinical-pathologic features...
February 7, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28166811/pathogenic-variant-burden-in-the-exac-database-an-empirical-approach-to-evaluating-population-data-for-clinical-variant-interpretation
#16
Yuya Kobayashi, Shan Yang, Keith Nykamp, John Garcia, Stephen E Lincoln, Scott E Topper
BACKGROUND: The frequency of a variant in the general population is a key criterion used in the clinical interpretation of sequence variants. With certain exceptions, such as founder mutations, the rarity of a variant is a prerequisite for pathogenicity. However, defining the threshold at which a variant should be considered "too common" is challenging and therefore diagnostic laboratories have typically set conservative allele frequency thresholds. METHODS: Recent publications of large population sequencing data, such as the Exome Aggregation Consortium (ExAC) database, provide an opportunity to characterize with accuracy and precision the frequency distributions of very rare disease-causing alleles...
February 6, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28153049/longitudinal-analysis-of-treatment-induced-genomic-alterations-in-gliomas
#17
E Zeynep Erson-Omay, Octavian Henegariu, S Bülent Omay, Akdes Serin Harmancı, Mark W Youngblood, Ketu Mishra-Gorur, Jie Li, Koray Özduman, Geneive Carrión-Grant, Victoria E Clark, Caner Çağlar, Mehmet Bakırcıoğlu, M Necmettin Pamir, Viviane Tabar, Alexander O Vortmeyer, Kaya Bilguvar, Katsuhito Yasuno, Lisa M DeAngelis, Joachim M Baehring, Jennifer Moliterno, Murat Günel
BACKGROUND: Glioblastoma multiforme (GBM) constitutes nearly half of all malignant brain tumors and has a median survival of 15 months. The standard treatment for these lesions includes maximal resection, radiotherapy, and chemotherapy; however, individual tumors display immense variability in their response to these approaches. Genomic techniques such as whole-exome sequencing (WES) provide an opportunity to understand the molecular basis of this variability. METHODS: Here, we report WES-guided treatment of a patient with a primary GBM and two subsequent recurrences, demonstrating the dynamic nature of treatment-induced molecular changes and their implications for clinical decision-making...
February 2, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28137280/high-dimensional-assessment-of-b-cell-responses-to-quadrivalent-meningococcal-conjugate-and-plain-polysaccharide-vaccine
#18
Daniel O'Connor, Elizabeth A Clutterbuck, Amber J Thompson, Matthew D Snape, Maheshi N Ramasamy, Dominic F Kelly, Andrew J Pollard
BACKGROUND: Neisseria meningitidis is a globally important cause of meningitis and septicaemia. Twelve capsular groups of meningococci are known, and quadrivalent vaccines against four of these (A, C, W and Y) are available as plain-polysaccharide and protein-polysaccharide conjugate vaccines. Here we apply contemporary methods to describe B-cell responses to meningococcal polysaccharide and conjugate vaccines. METHODS: Twenty adults were randomly assigned to receive either a meningococcal plain-polysaccharide or conjugate vaccine; one month later all received the conjugate vaccine...
January 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28129791/new-strategies-for-cancer-immunotherapy-targeting-regulatory-t-cells
#19
Francesca Finotello, Zlatko Trajanoski
The immunosuppressive action of regulatory T (Treg) cells is one mechanism attributed to the limited success of cancer immunotherapies with checkpoint blockers. Two recent studies report distinct transcriptional profiles of tumor-infiltrating Treg cells and expression of specific molecules, suggesting novel strategies to overcome resistance to cancer immunotherapy.
January 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28126037/molecular-dissection-of-germline-chromothripsis-in-a-developmental-context-using-patient-derived-ips-cells
#20
Sjors Middelkamp, Sebastiaan van Heesch, A Koen Braat, Joep de Ligt, Maarten van Iterson, Marieke Simonis, Markus J van Roosmalen, Martijn J E Kelder, Evelien Kruisselbrink, Ron Hochstenbach, Nienke E Verbeek, Elly F Ippel, Youri Adolfs, R Jeroen Pasterkamp, Wigard P Kloosterman, Ewart W Kuijk, Edwin Cuppen
BACKGROUND: Germline chromothripsis causes complex genomic rearrangements that are likely to affect multiple genes and their regulatory contexts. The contribution of individual rearrangements and affected genes to the phenotypes of patients with complex germline genomic rearrangements is generally unknown. METHODS: To dissect the impact of germline chromothripsis in a relevant developmental context, we performed trio-based RNA expression analysis on blood cells, induced pluripotent stem cells (iPSCs), and iPSC-derived neuronal cells from a patient with de novo germline chromothripsis and both healthy parents...
January 26, 2017: Genome Medicine
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