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Genome Medicine

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https://www.readbyqxmd.com/read/29329552/correction-to-linkage-whole-genome-sequence-and-biological-data-implicate-variants-in-rab10-in-alzheimer-s-disease-resilience
#1
Perry G Ridge, Celeste M Karch, Simon Hsu, Ivan Arano, Craig C Teerlink, Mark T W Ebbert, Josue D Gonzalez Murcia, James M Farnham, Anna R Damato, Mariet Allen, Xue Wang, Oscar Harari, Victoria M Fernandez, Rita Guerreiro, Jose Bras, John Hardy, Ronald Munger, Maria Norton, Celeste Sassi, Andrew Singleton, Steven G Younkin, Dennis W Dickson, Todd E Golde, Nathan D Price, Nilüfer Ertekin-Taner, Carlos Cruchaga, Alison M Goate, Christopher Corcoran, JoAnn Tschanz, Lisa A Cannon-Albright, John S K Kauwe
The original version of this article [1] unfortunately contained a typographical error. The 'Alzheimer's Disease Neuroimaging Initiative' was erroneously included as 'Alzheimer's Disease Neuroimaging Initative' in the author list of the article.
January 12, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29310717/characterization-of-glycosylphosphatidylinositol-biosynthesis-defects-by-clinical-features-flow-cytometry-and-automated-image-analysis
#2
Alexej Knaus, Jean Tori Pantel, Manuela Pendziwiat, Nurulhuda Hajjir, Max Zhao, Tzung-Chien Hsieh, Max Schubach, Yaron Gurovich, Nicole Fleischer, Marten Jäger, Sebastian Köhler, Hiltrud Muhle, Christian Korff, Rikke S Møller, Allan Bayat, Patrick Calvas, Nicolas Chassaing, Hannah Warren, Steven Skinner, Raymond Louie, Christina Evers, Marc Bohn, Hans-Jürgen Christen, Myrthe van den Born, Ewa Obersztyn, Agnieszka Charzewska, Milda Endziniene, Fanny Kortüm, Natasha Brown, Peter N Robinson, Helenius J Schelhaas, Yvonne Weber, Ingo Helbig, Stefan Mundlos, Denise Horn, Peter M Krawitz
BACKGROUND: Glycosylphosphatidylinositol biosynthesis defects (GPIBDs) cause a group of phenotypically overlapping recessive syndromes with intellectual disability, for which pathogenic mutations have been described in 16 genes of the corresponding molecular pathway. An elevated serum activity of alkaline phosphatase (AP), a GPI-linked enzyme, has been used to assign GPIBDs to the phenotypic series of hyperphosphatasia with mental retardation syndrome (HPMRS) and to distinguish them from another subset of GPIBDs, termed multiple congenital anomalies hypotonia seizures syndrome (MCAHS)...
January 9, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29301589/linking-foxo3-ncoa3-and-tcf7l2-to-ras-pathway-phenotypes-through-a-genome-wide-forward-genetic-screen-in-human-colorectal-cancer-cells
#3
Snehangshu Kundu, Muhammad Akhtar Ali, Niklas Handin, Narendra Padhan, Jimmy Larsson, Maria Karoutsou, Kenneth Ban, Jacek R Wiśniewski, Per Artursson, Liqun He, Mats Hellström, Tobias Sjöblom
BACKGROUND: The Ras pathway genes KRAS, BRAF, or ERBBs have somatic mutations in ~ 60% of human colorectal carcinomas. At present, it is unknown whether the remaining cases lack mutations activating the Ras pathway or whether they have acquired mutations in genes hitherto unknown to belong to the pathway. METHODS: To address the second possibility and extend the compendium of Ras pathway genes, we used genome-wide transposon mutagenesis of two human colorectal cancer cell systems deprived of their activating KRAS or BRAF allele to identify genes enabling growth in low glucose, a Ras pathway phenotype, when targeted...
January 4, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29301565/modeling-psychiatric-disorders-using-patient-stem-cell-derived-neurons-a-way-forward
#4
Krishna C Vadodaria, Debha N Amatya, Maria C Marchetto, Fred H Gage
Our understanding of the neurobiology of psychiatric disorders remains limited, and biomarker-based clinical management is yet to be developed. Induced pluripotent stem cell (iPSC) technology has revolutionized our capacity to generate patient-derived neurons to model psychiatric disorders. Here, we highlight advantages and caveats of iPSC disease modeling and outline strategies for addressing current challenges.
January 4, 2018: Genome Medicine
https://www.readbyqxmd.com/read/29282103/within-host-evolution-of-enterococcus-faecium-during-longitudinal-carriage-and-transition-to-bloodstream-infection-in-immunocompromised-patients
#5
Danesh Moradigaravand, Theodore Gouliouris, Beth Blane, Plamena Naydenova, Catherine Ludden, Charles Crawley, Nicholas M Brown, M Estée Török, Julian Parkhill, Sharon J Peacock
BACKGROUND: Enterococcus faecium is a leading cause of hospital-acquired infection, particularly in the immunocompromised. Here, we use whole genome sequencing of E. faecium to study within-host evolution and the transition from gut carriage to invasive disease. METHODS: We isolated and sequenced 180 E. faecium from four immunocompromised patients who developed bloodstream infection during longitudinal surveillance of E. faecium in stool and their immediate environment...
December 27, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29273096/genetic-variation-in-human-drug-related-genes
#6
Charlotta Pauline Irmgard Schärfe, Roman Tremmel, Matthias Schwab, Oliver Kohlbacher, Debora Susan Marks
BACKGROUND: Variability in drug efficacy and adverse effects are observed in clinical practice. While the extent of genetic variability in classic pharmacokinetic genes is rather well understood, the role of genetic variation in drug targets is typically less studied. METHODS: Based on 60,706 human exomes from the ExAC dataset, we performed an in-depth computational analysis of the prevalence of functional variants in 806 drug-related genes, including 628 known drug targets...
December 22, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29273094/b3galnt2-mutations-associated-with-non-syndromic-autosomal-recessive-intellectual-disability-reveal-a-lack-of-genotype-phenotype-associations-in-the-muscular-dystrophy-dystroglycanopathies
#7
Reza Maroofian, Moniek Riemersma, Lucas T Jae, Narges Zhianabed, Marjolein H Willemsen, Willemijn M Wissink-Lindhout, Michèl A Willemsen, Arjan P M de Brouwer, Mohammad Yahya Vahidi Mehrjardi, Mahmoud Reza Ashrafi, Benno Kusters, Tjitske Kleefstra, Yalda Jamshidi, Mojila Nasseri, Rolph Pfundt, Thijn R Brummelkamp, Mohammad Reza Abbaszadegan, Dirk J Lefeber, Hans van Bokhoven
BACKGROUND: The phenotypic severity of congenital muscular dystrophy-dystroglycanopathy (MDDG) syndromes associated with aberrant glycosylation of α-dystroglycan ranges from the severe Walker-Warburg syndrome or muscle-eye-brain disease to mild, late-onset, isolated limb-girdle muscular dystrophy without neural involvement. However, muscular dystrophy is invariably found across the spectrum of MDDG patients. METHODS: Using linkage mapping and whole-exome sequencing in two families with an unexplained neurodevelopmental disorder, we have identified homozygous and compound heterozygous mutations in B3GALNT2...
December 22, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29268796/the-potential-of-circulating-tumor-dna-methylation-analysis-for-the-early-detection-and-management-of-ovarian-cancer
#8
Martin Widschwendter, Michal Zikan, Benjamin Wahl, Harri Lempiäinen, Tobias Paprotka, Iona Evans, Allison Jones, Shohreh Ghazali, Daniel Reisel, Johannes Eichner, Tamas Rujan, Zhen Yang, Andrew E Teschendorff, Andy Ryan, David Cibula, Usha Menon, Timo Wittenberger
BACKGROUND: Despite a myriad of attempts in the last three decades to diagnose ovarian cancer (OC) earlier, this clinical aim still remains a significant challenge. Aberrant methylation patterns of linked CpGs analyzed in DNA fragments shed by cancers into the bloodstream (i.e. cell-free DNA) can provide highly specific signals indicating cancer presence. METHODS: We analyzed 699 cancerous and non-cancerous tissues using a methylation array or reduced representation bisulfite sequencing to discover the most specific OC methylation patterns...
December 22, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29268762/methylation-patterns-in-serum-dna-for-early-identification-of-disseminated-breast-cancer
#9
Martin Widschwendter, Iona Evans, Allison Jones, Shohreh Ghazali, Daniel Reisel, Andy Ryan, Aleksandra Gentry-Maharaj, Michal Zikan, David Cibula, Johannes Eichner, Marianna Alunni-Fabbroni, Julian Koch, Wolfgang J Janni, Tobias Paprotka, Timo Wittenberger, Usha Menon, Benjamin Wahl, Brigitte Rack, Harri Lempiäinen
BACKGROUND: Monitoring treatment and early detection of fatal breast cancer (BC) remains a major unmet need. Aberrant circulating DNA methylation (DNAme) patterns are likely to provide a highly specific cancer signal. We hypothesized that cell-free DNAme markers could indicate disseminated breast cancer, even in the presence of substantial quantities of background DNA. METHODS: We used reduced representation bisulfite sequencing (RRBS) of 31 tissues and established serum assays based on ultra-high coverage bisulfite sequencing in two independent prospective serum sets (n = 110)...
December 22, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29262854/integrated-bayesian-analysis-of-rare-exonic-variants-to-identify-risk-genes-for-schizophrenia-and-neurodevelopmental-disorders
#10
Hoang T Nguyen, Julien Bryois, April Kim, Amanda Dobbyn, Laura M Huckins, Ana B Munoz-Manchado, Douglas M Ruderfer, Giulio Genovese, Menachem Fromer, Xinyi Xu, Dalila Pinto, Sten Linnarsson, Matthijs Verhage, August B Smit, Jens Hjerling-Leffler, Joseph D Buxbaum, Christina Hultman, Pamela Sklar, Shaun M Purcell, Kasper Lage, Xin He, Patrick F Sullivan, Eli A Stahl
BACKGROUND: Integrating rare variation from trio family and case-control studies has successfully implicated specific genes contributing to risk of neurodevelopmental disorders (NDDs) including autism spectrum disorders (ASD), intellectual disability (ID), developmental disorders (DDs), and epilepsy (EPI). For schizophrenia (SCZ), however, while sets of genes have been implicated through the study of rare variation, only two risk genes have been identified. METHODS: We used hierarchical Bayesian modeling of rare-variant genetic architecture to estimate mean effect sizes and risk-gene proportions, analyzing the largest available collection of whole exome sequence data for SCZ (1,077 trios, 6,699 cases, and 13,028 controls), and data for four NDDs (ASD, ID, DD, and EPI; total 10,792 trios, and 4,058 cases and controls)...
December 20, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29254502/clinical-implications-and-considerations-for-evaluation-of-in-silico-algorithms-for-use-with-acmg-amp-clinical-variant-interpretation-guidelines
#11
Lora J H Bean, Madhuri R Hegde
Clinical genetics laboratories have recently adopted guidelines for the interpretation of sequence variants set by the American College of Medical Genetics (ACMG) and Association for Molecular Pathology (AMP). The use of in silico algorithms to predict whether amino acid substitutions result in human disease is inconsistent across clinical laboratories. The clinical genetics community must carefully consider how in silico predictions can be incorporated into variant interpretation in clinical practice.Please see related Research article: https://doi...
December 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29254494/mapping-genetic-variations-to-three-dimensional-protein-structures-to-enhance-variant-interpretation-a-proposed-framework
#12
Gustavo Glusman, Peter W Rose, Andreas Prlić, Jennifer Dougherty, José M Duarte, Andrew S Hoffman, Geoffrey J Barton, Emøke Bendixen, Timothy Bergquist, Christian Bock, Elizabeth Brunk, Marija Buljan, Stephen K Burley, Binghuang Cai, Hannah Carter, JianJiong Gao, Adam Godzik, Michael Heuer, Michael Hicks, Thomas Hrabe, Rachel Karchin, Julia Koehler Leman, Lydie Lane, David L Masica, Sean D Mooney, John Moult, Gilbert S Omenn, Frances Pearl, Vikas Pejaver, Sheila M Reynolds, Ariel Rokem, Torsten Schwede, Sicheng Song, Hagen Tilgner, Yana Valasatava, Yang Zhang, Eric W Deutsch
The translation of personal genomics to precision medicine depends on the accurate interpretation of the multitude of genetic variants observed for each individual. However, even when genetic variants are predicted to modify a protein, their functional implications may be unclear. Many diseases are caused by genetic variants affecting important protein features, such as enzyme active sites or interaction interfaces. The scientific community has catalogued millions of genetic variants in genomic databases and thousands of protein structures in the Protein Data Bank...
December 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29254491/challenges-in-understanding-common-disease
#13
Peter M Visscher
Peter M. Visscher discusses advances in our understanding of complex disease, the challenges in applying this knowledge to functional follow-up, and the potential implications for therapeutic interventions.
December 18, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29241461/mapping-a-shared-genetic-basis-for-neurodevelopmental-disorders
#14
Matthew Jensen, Santhosh Girirajan
Distinct neurodevelopmental disorders have a common genetic etiology that explains the high degree of comorbidity among these disorders. A recent study sought to identify copy number variants across five neurodevelopmental disorders, and detected an enrichment for chromosome 9p24.3 duplication encompassing DOCK8 and KANK1 in affected individuals. Such large-scale studies will help uncover additional causative and modifier loci within common pathways, which will enable the development of therapeutic targets for the treatment of multiple disorders...
December 14, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29241446/narrowing-the-spectrum-the-new-frontier-of-precision-antimicrobials
#15
Alexandra E Paharik, Henry L Schreiber, Caitlin N Spaulding, Karen W Dodson, Scott J Hultgren
Antibiotics have become the standard of care for bacterial infections. However, rising rates of antibiotic-resistant infections are outpacing the development of new antimicrobials. Broad-spectrum antibiotics also harm beneficial microbial communities inhabiting humans. To combat antibiotic resistance and protect these communities, new precision antimicrobials must be engineered to target specific pathogens.
December 14, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29202807/granatum-a-graphical-single-cell-rna-seq-analysis-pipeline-for-genomics-scientists
#16
Xun Zhu, Thomas K Wolfgruber, Austin Tasato, Cédric Arisdakessian, David G Garmire, Lana X Garmire
BACKGROUND: Single-cell RNA sequencing (scRNA-Seq) is an increasingly popular platform to study heterogeneity at the single-cell level. Computational methods to process scRNA-Seq data are not very accessible to bench scientists as they require a significant amount of bioinformatic skills. RESULTS: We have developed Granatum, a web-based scRNA-Seq analysis pipeline to make analysis more broadly accessible to researchers. Without a single line of programming code, users can click through the pipeline, setting parameters and visualizing results via the interactive graphical interface...
December 5, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29202803/emerging-mechanisms-and-novel-targets-in-allergic-inflammation-and-asthma
#17
Scott T Weiss
Airway inflammation is key to the severity and persistence of asthma. Recent studies have revealed novel immune mechanisms that target dendritic cells, T helper 2 cytokines, regulatory T cells, and type 2 innate lymphoid cells in allergic inflammation, as well as novel approaches that target airway smooth muscle in asthma. These advances inform the development of new targeted treatments for allergic inflammation and asthma with the potential to provide therapeutic benefit.
December 4, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29191242/copy-number-variation-meta-analysis-reveals-a-novel-duplication-at-9p24-associated-with-multiple-neurodevelopmental-disorders
#18
Joseph T Glessner, Jin Li, Dai Wang, Michael March, Leandro Lima, Akshatha Desai, Dexter Hadley, Charlly Kao, Raquel E Gur, Nadine Cohen, Patrick M A Sleiman, Qingqin Li, Hakon Hakonarson
BACKGROUND: Neurodevelopmental and neuropsychiatric disorders represent a wide spectrum of heterogeneous yet inter-related disease conditions. The overlapping clinical presentations of these diseases suggest a shared genetic etiology. We aim to identify shared structural variants spanning the spectrum of five neuropsychiatric disorders. METHODS: We investigated copy number variations (CNVs) in five cohorts, including schizophrenia (SCZ), bipolar disease (BD), autism spectrum disorders (ASD), attention deficit hyperactivity disorder (ADHD), and depression, from 7849 cases and 10,799 controls...
November 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29187259/impact-of-iq-on-the-diagnostic-yield-of-chromosomal-microarray-in-a-community-sample-of-adults-with-schizophrenia
#19
Chelsea Lowther, Daniele Merico, Gregory Costain, Jack Waserman, Kerry Boyd, Abdul Noor, Marsha Speevak, Dimitri J Stavropoulos, John Wei, Anath C Lionel, Christian R Marshall, Stephen W Scherer, Anne S Bassett
BACKGROUND: Schizophrenia is a severe psychiatric disorder associated with IQ deficits. Rare copy number variations (CNVs) have been established to play an important role in the etiology of schizophrenia. Several of the large rare CNVs associated with schizophrenia have been shown to negatively affect IQ in population-based controls where no major neuropsychiatric disorder is reported. The aim of this study was to examine the diagnostic yield of microarray testing and the functional impact of genome-wide rare CNVs in a community ascertained cohort of adults with schizophrenia and low (< 85) or average (≥ 85) IQ...
November 30, 2017: Genome Medicine
https://www.readbyqxmd.com/read/29183403/linkage-whole-genome-sequence-and-biological-data-implicate-variants-in-rab10-in-alzheimer-s-disease-resilience
#20
Perry G Ridge, Celeste M Karch, Simon Hsu, Ivan Arano, Craig C Teerlink, Mark T W Ebbert, Josue D Gonzalez Murcia, James M Farnham, Anna R Damato, Mariet Allen, Xue Wang, Oscar Harari, Victoria M Fernandez, Rita Guerreiro, Jose Bras, John Hardy, Ronald Munger, Maria Norton, Celeste Sassi, Andrew Singleton, Steven G Younkin, Dennis W Dickson, Todd E Golde, Nathan D Price, Nilüfer Ertekin-Taner, Carlos Cruchaga, Alison M Goate, Christopher Corcoran, JoAnn Tschanz, Lisa A Cannon-Albright, John S K Kauwe
BACKGROUND: While age and the APOE ε4 allele are major risk factors for Alzheimer's disease (AD), a small percentage of individuals with these risk factors exhibit AD resilience by living well beyond 75 years of age without any clinical symptoms of cognitive decline. METHODS: We used over 200 "AD resilient" individuals and an innovative, pedigree-based approach to identify genetic variants that segregate with AD resilience. First, we performed linkage analyses in pedigrees with resilient individuals and a statistical excess of AD deaths...
November 29, 2017: Genome Medicine
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