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https://www.readbyqxmd.com/read/27917292/deep-resequencing-of-cftr-in-762-f508del-homozygotes-reveals-clusters-of-non-coding-variants-associated-with-cystic-fibrosis-disease-traits
#1
Briana Vecchio-Pagán, Scott M Blackman, Melissa Lee, Melis Atalar, Matthew J Pellicore, Rhonda G Pace, Arianna L Franca, Karen S Raraigh, Neeraj Sharma, Michael R Knowles, Garry R Cutting
Extensive phenotypic variability is commonly observed in individuals with Mendelian disorders, even among those with identical genotypes in the disease-causing gene. To determine whether variants within and surrounding CFTR contribute to phenotypic variability in cystic fibrosis (CF), we performed deep sequencing of CFTR in 762 patients homozygous for the common CF-causing variant, F508del. In phase 1, ~200 kb encompassing CFTR and extending 10 kb 5' and 5 kb 3' of the gene was sequenced in 486 F508del homozygotes selected from the extremes of sweat chloride concentration...
2016: Human Genome Variation
https://www.readbyqxmd.com/read/27914500/effect-of-l-arginine-asymmetric-dimethylarginine-and-symmetric-dimethylarginine-on-ischemic-heart-disease-risk-a-mendelian-randomization-study
#2
Shiu Lun Au Yeung, Shi Lin Lin, Hung San Hugh Simon Lam, Catherine Mary Schooling
BACKGROUND: l-arginine is a commonly consumed dietary conditional essential amino acid found in food items and supplements, which is closely related to asymmetric dimethylarginine (ADMA) and symmetric dimethylarginine (SDMA). l-arginine is thought to increase nitric oxide and be cardioprotective, whereas ADMA and SDMA may inhibit nitric oxide synthesis and increase cardiovascular disease risk. Unexpectedly, l-arginine increased mortality in a small trial. To clarify the effects of these potential targets of intervention, we assessed the risk of ischemic heart disease (IHD) by genetically determined l-arginine, ADMA, and SDMA...
December 2016: American Heart Journal
https://www.readbyqxmd.com/read/27913672/first-model-of-dimeric-lrrk2-the-challenge-of-unrevealing-the-structure-of-a-multidomain-parkinson-s-associated-protein
#3
REVIEW
Giambattista Guaitoli, Bernd K Gilsbach, Francesco Raimondi, Christian Johannes Gloeckner
Mutations within the leucine-rich repeat kinase 2 (LRRK2) gene represent the most common cause of Mendelian forms of Parkinson's disease, among autosomal dominant cases. Its gene product, LRRK2, is a large multidomain protein that belongs to the Roco protein family exhibiting GTPase and kinase activity, with the latter activity increased by pathogenic mutations. To allow rational drug design against LRRK2 and to understand the cross-regulation of the G- and the kinase domain at a molecular level, it is key to solve the three-dimensional structure of the protein...
December 15, 2016: Biochemical Society Transactions
https://www.readbyqxmd.com/read/27913149/mutations-at-protein-protein-interfaces-small-changes-over-big-surfaces-have-large-impacts-on-human-health
#4
REVIEW
Harry C Jubb, Arun P Pandurangan, Meghan A Turner, Bernardo Ochoa-Montaño, Tom L Blundell, David B Ascher
Many essential biological processes including cell regulation and signalling are mediated through the assembly of protein complexes. Changes to protein-protein interaction (PPI) interfaces can affect the formation of multiprotein complexes, and consequently lead to disruptions in interconnected networks of PPIs within and between cells, further leading to phenotypic changes as functional interactions are created or disrupted. Mutations altering PPIs have been linked to the development of genetic diseases including cancer and rare Mendelian diseases, and to the development of drug resistance...
November 29, 2016: Progress in Biophysics and Molecular Biology
https://www.readbyqxmd.com/read/27908689/pcsk9-genetic-variants-and-risk-of-type-2-diabetes-a-mendelian-randomisation-study
#5
Amand F Schmidt, Daniel I Swerdlow, Michael V Holmes, Riyaz S Patel, Zammy Fairhurst-Hunter, Donald M Lyall, Fernando Pires Hartwig, Bernardo Lessa Horta, Elina Hyppönen, Christine Power, Max Moldovan, Erik van Iperen, G Kees Hovingh, Ilja Demuth, Kristina Norman, Elisabeth Steinhagen-Thiessen, Juri Demuth, Lars Bertram, Tian Liu, Stefan Coassin, Johann Willeit, Stefan Kiechl, Karin Willeit, Dan Mason, John Wright, Richard Morris, Goya Wanamethee, Peter Whincup, Yoav Ben-Shlomo, Stela McLachlan, Jackie F Price, Mika Kivimaki, Catherine Welch, Adelaida Sanchez-Galvez, Pedro Marques-Vidal, Andrew Nicolaides, Andrie G Panayiotou, N Charlotte Onland-Moret, Yvonne T van der Schouw, Giuseppe Matullo, Giovanni Fiorito, Simonetta Guarrera, Carlotta Sacerdote, Nicholas J Wareham, Claudia Langenberg, Robert Scott, Jian'an Luan, Martin Bobak, Sofia Malyutina, Andrzej Pająk, Ruzena Kubinova, Abdonas Tamosiunas, Hynek Pikhart, Lise Lotte Nystrup Husemoen, Niels Grarup, Oluf Pedersen, Torben Hansen, Allan Linneberg, Kenneth Starup Simonsen, Jackie Cooper, Steve E Humphries, Murray Brilliant, Terrie Kitchner, Hakon Hakonarson, David S Carrell, Catherine A McCarty, H Lester Kirchner, Eric B Larson, David R Crosslin, Mariza de Andrade, Dan M Roden, Joshua C Denny, Cara Carty, Stephen Hancock, John Attia, Elizabeth Holliday, Martin O' Donnell, Salim Yusuf, Michael Chong, Guillaume Pare, Pim van der Harst, M Abdullah Said, Ruben N Eppinga, Niek Verweij, Harold Snieder, Tim Christen, Dennis O Mook-Kanamori, Stefan Gustafsson, Lars Lind, Erik Ingelsson, Raha Pazoki, Oscar Franco, Albert Hofman, Andre Uitterlinden, Abbas Dehghan, Alexander Teumer, Sebastian Baumeister, Marcus Dörr, Markus M Lerch, Uwe Völker, Henry Völzke, Joey Ward, Jill P Pell, Daniel J Smith, Tom Meade, Anke H Maitland-van der Zee, Ekaterina V Baranova, Robin Young, Ian Ford, Archie Campbell, Sandosh Padmanabhan, Michiel L Bots, Diederick E Grobbee, Philippe Froguel, Dorothée Thuillier, Beverley Balkau, Amélie Bonnefond, Bertrand Cariou, Melissa Smart, Yanchun Bao, Meena Kumari, Anubha Mahajan, Paul M Ridker, Daniel I Chasman, Alex P Reiner, Leslie A Lange, Marylyn D Ritchie, Folkert W Asselbergs, Juan-Pablo Casas, Brendan J Keating, David Preiss, Aroon D Hingorani, Naveed Sattar
BACKGROUND: Statin treatment and variants in the gene encoding HMG-CoA reductase are associated with reductions in both the concentration of LDL cholesterol and the risk of coronary heart disease, but also with modest hyperglycaemia, increased bodyweight, and modestly increased risk of type 2 diabetes, which in no way offsets their substantial benefits. We sought to investigate the associations of LDL cholesterol-lowering PCSK9 variants with type 2 diabetes and related biomarkers to gauge the likely effects of PCSK9 inhibitors on diabetes risk...
November 28, 2016: Lancet Diabetes & Endocrinology
https://www.readbyqxmd.com/read/27906690/the-long-road-to-leptin
#6
Jeffrey Friedman
Leptin is an adipose tissue hormone that functions as an afferent signal in a negative feedback loop that maintains homeostatic control of adipose tissue mass. This endocrine system thus serves a critical evolutionary function by protecting individuals from the risks associated with being too thin (starvation) or too obese (predation and temperature dysregulation). Mutations in leptin or its receptor cause massive obesity in mice and humans, and leptin can effectively treat obesity in leptin-deficient patients...
December 1, 2016: Journal of Clinical Investigation
https://www.readbyqxmd.com/read/27902751/exploration-of-a-polygenic-risk-score-for-alcohol-consumption-a-longitudinal-analysis-from-the-alspac-cohort
#7
Michelle Taylor, Andrew J Simpkin, Philip C Haycock, Frank Dudbridge, Luisa Zuccolo
BACKGROUND: Uncertainty remains about the true extent by which alcohol consumption causes a number of health outcomes. Genetic variants, or combinations of variants built into a polygenic risk score (PGRS), can be used in an instrumental variable framework to assess causality between a phenotype and disease outcome of interest, a method known as Mendelian randomisation (MR). We aimed to identify genetic variants involved in the aetiology of alcohol consumption, and develop a PGRS for alcohol...
2016: PloS One
https://www.readbyqxmd.com/read/27901035/homocysteine-reducing-b-vitamins-and-ischemic-heart-disease-a-separate-sample-mendelian-randomization-analysis
#8
J V Zhao, C M Schooling
BACKGROUND/OBJECTIVES: Observationally, homocysteine is positively associated with ischemic heart disease (IHD) and unhealthy lipids; folate and vitamin B12, which reduce homocysteine, are associated with lower IHD risk and healthy lipids. Randomized controlled trials have shown no benefits of folate and vitamin B12 for IHD. To clarify the role of these potential targets of intervention in IHD we assessed how genetically determined homocysteine, folate and vitamin-B12-affected IHD and lipids...
November 30, 2016: European Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/27898412/the-rise-and-rise-of-exome-sequencing
#9
Chee-Seng Ku, David N Cooper, George P Patrinos
Beginning in 2009, the advent of exome sequencing has contributed significantly towards new discoveries of heritable germline mutations and de novo mutations for rare Mendelian disorders with hitherto unknown genetic aetiologies. Exome sequencing is an efficient tool to identify disease mutations without the need of a multi-generational pedigree. Sequencing a single proband or multiple affected individuals has been shown to be successful in identifying disease mutations, but parents would be required in the case of de novo mutations...
November 30, 2016: Public Health Genomics
https://www.readbyqxmd.com/read/27896999/identify-cancer-driver-genes-through-shared-mendelian-disease-pathogenic-variants-and-cancer-somatic-mutations
#10
Meng Ma, Changchang Wang, Benjamin S Glicksberg, Eric E Schadt, Shuyu D Li, Rong Chen
Genomic sequencing studies in the past several years have yielded a large number of cancer somatic mutations. There remains a major challenge in delineating a small fraction of somatic mutations that are oncogenic drivers from a background of predominantly passenger mutations. Although computational tools have been developed to predict the functional impact of mutations, their utility is limited. In this study, we applied an alternative approach to identify potentially novel cancer drivers as those somatic mutations that overlap with known pathogenic mutations in Mendelian diseases...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896429/copy-number-variability-in-parkinson-s-disease-assembling-the-puzzle-through-a-systems-biology-approach
#11
REVIEW
Valentina La Cognata, Giovanna Morello, Velia D'Agata, Sebastiano Cavallaro
Parkinson's disease (PD), the second most common progressive neurodegenerative disorder of aging, was long believed to be a non-genetic sporadic origin syndrome. The proof that several genetic loci are responsible for rare Mendelian forms has represented a revolutionary breakthrough, enabling to reveal molecular mechanisms underlying this debilitating still incurable condition. While single nucleotide polymorphisms (SNPs) and small indels constitute the most commonly investigated DNA variations accounting for only a limited number of PD cases, larger genomic molecular rearrangements have emerged as significant PD-causing mutations, including submicroscopic Copy Number Variations (CNVs)...
November 28, 2016: Human Genetics
https://www.readbyqxmd.com/read/27894351/characterizing-the-morbid-genome-of-ciliopathies
#12
Ranad Shaheen, Katarzyna Szymanska, Basudha Basu, Nisha Patel, Nour Ewida, Eissa Faqeih, Amal Al Hashem, Nada Derar, Hadeel Alsharif, Mohammed A Aldahmesh, Anas M Alazami, Mais Hashem, Niema Ibrahim, Firdous M Abdulwahab, Rawda Sonbul, Hisham Alkuraya, Maha Alnemer, Saeed Al Tala, Muneera Al-Husain, Heba Morsy, Mohammed Zain Seidahmed, Neama Meriki, Mohammed Al-Owain, Saad AlShahwan, Brahim Tabarki, Mustafa A Salih, Tariq Faquih, Mohamed El-Kalioby, Marius Ueffing, Karsten Boldt, Clare V Logan, David A Parry, Nada Al Tassan, Dorota Monies, Andre Megarbane, Mohamed Abouelhoda, Anason Halees, Colin A Johnson, Fowzan S Alkuraya
BACKGROUND: Ciliopathies are clinically diverse disorders of the primary cilium. Remarkable progress has been made in understanding the molecular basis of these genetically heterogeneous conditions; however, our knowledge of their morbid genome, pleiotropy, and variable expressivity remains incomplete. RESULTS: We applied genomic approaches on a large patient cohort of 371 affected individuals from 265 families, with phenotypes that span the entire ciliopathy spectrum...
November 28, 2016: Genome Biology
https://www.readbyqxmd.com/read/27884205/whole-genome-sequence-analysis-of-serum-amino-acid-levels
#13
Bing Yu, Paul S de Vries, Ginger A Metcalf, Zhe Wang, Elena V Feofanova, Xiaoming Liu, Donna Marie Muzny, Lynne E Wagenknecht, Richard A Gibbs, Alanna C Morrison, Eric Boerwinkle
BACKGROUND: Blood levels of amino acids are important biomarkers of disease and are influenced by synthesis, protein degradation, and gene-environment interactions. Whole genome sequence analysis of amino acid levels may establish a paradigm for analyzing quantitative risk factors. RESULTS: In a discovery cohort of 1872 African Americans and a replication cohort of 1552 European Americans we sequenced exons and whole genomes and measured serum levels of 70 amino acids...
November 24, 2016: Genome Biology
https://www.readbyqxmd.com/read/27884173/revisiting-the-morbid-genome-of-mendelian-disorders
#14
Mohamed Abouelhoda, Tariq Faquih, Mohamed El-Kalioby, Fowzan S Alkuraya
BACKGROUND: The pathogenicity of many Mendelian variants has been challenged by large-scale sequencing efforts. However, many rare and benign "disease mutations" are difficult to analyze due to their rarity. The Saudi Arabian variome is enriched for homozygosity due to inbreeding, a key advantage that can be exploited for the critical examination of previously published variants. RESULTS: We collated all "disease-related mutations" listed in the Human Gene Mutation Database (HGMD) and ClinVar, including "variants of uncertain significance" (VOUS)...
November 24, 2016: Genome Biology
https://www.readbyqxmd.com/read/27882376/plasma-levels-of-the-anti-coagulation-protein-c-and-the-risk-of-ischaemic-heart-disease-a-mendelian-randomisation-study
#15
C Mary Schooling, Yi Zhong
Protein C is an environmentally modifiable anticoagulant, which protects against venous thrombosis, whether it also protects against ischaemic heart disease is unclear, based on observational studies and relatively small genetic studies. It was our study aim to clarify the role of protein C in ischaemic heart disease the risk of coronary artery disease/myocardial infarction (CAD/MI) was assessed according to genetically predicted protein C in very large studies. Associations with lipids and diabetes were similarly assessed to rule out effects via traditional cardiovascular disease risk factors...
November 24, 2016: Thrombosis and Haemostasis
https://www.readbyqxmd.com/read/27879323/issues-and-challenges-in-diagnostic-sequencing-for-inherited-cardiac-conditions
#16
REVIEW
Roddy Walsh, Stuart A Cook
BACKGROUND: Inherited cardiac conditions are a relatively common group of Mendelian diseases associated with ill health and death, often in the young. Research into the genetic causes of these conditions has enabled confirmatory and predictive diagnostic sequencing to become an integral part of the clinical management of inherited cardiomyopathies, arrhythmias, aortopathies, and dyslipidemias. CONTENT: Currently, the principle benefit of clinical genetic testing is the cascade screening of family members of patients with a pathogenic variant, enabling targeted follow up of presymptomatic genotype-positive individuals and discharge of genotype-negative individuals to health...
November 22, 2016: Clinical Chemistry
https://www.readbyqxmd.com/read/27868075/novel-mutation-of-interferon-%C3%AE-receptor-1-gene-presenting-as-early-life-mycobacterial-bronchial-disease
#17
Maria J Gutierrez, Neelu Kalra, Alexandra Horwitz, Gustavo Nino
Mendelian susceptibility to mycobacterial diseases (MSMD) are a spectrum of inherited disorders characterized by localized or disseminated infections caused by atypical mycobacteria. Interferon-γ receptor 1 (IFNGR1) deficiency was the first identified genetic disorder recognized as MSMD. Mutations in the genes encoding IFNGR1 can be recessive or dominant and cause complete or partial receptor deficiency. We present the case of a 2½-year-old boy with a history of recurrent wheezing, diagnosed with endobronchial mycobacterial infection...
October 2016: Journal of Investigative Medicine High Impact Case Reports
https://www.readbyqxmd.com/read/27864007/six-generations-of-epidermolytic-palmoplantar-keratoderma-associated-with-a-krt9-r163w-mutation
#18
Peng Wang, Xiao-Jing Kang, Xiao-Hui Tang, Jian-Yong Liu, Wen-Zheng Li, Wei-Jia Wang, Sheng-Nan Liang, Yan-Yan Feng, Yuan Ding, Wen-Jing Chen
Epidermolytic palmoplantar keratoderma (EPPK) is a rare autosomal dominant skin disorder characterized by diffuse hyperkeratosis on the palms and soles. Whole-exome sequencing (WES) has become a powerful tool for the detection of rare causal variants of Mendelian disorders. However, no causal gene for EPPK in the Uygur population has been identified until now, and no treatment exists than can address the underlying pathology.WES analysis was undertaken on two individuals from a large Uygur EPPK pedigree whose disease locus mapped to 17q21...
November 2016: Cancer Genetics
https://www.readbyqxmd.com/read/27863359/is-hyperhomocysteinemia-a-causal-factor-for-heart-failure-the-impact-of-the-functional-variants-of-mthfr-and-pon1-on-ischemic-and-non-ischemic-etiology
#19
Ewa Strauss, Wieslaw Supinski, Artur Radziemski, Grzegorz Oszkinis, Andrzej Leon Pawlak, Jerzy Gluszek
BACKGROUND: Hyperhomocysteinemia was found to be uniformly associated with the development of heart failure (HF) and HF mortality; however, it is uncertain whether this relation is causative or not. We used Mendelian randomization to examine the associations of the methylene tetrahydrofolate gene (MTHFR) and paraoxonase 1 gene (PON1) variants as a proxy for lifelong exposure to high Hcy and Hcy-thiolactone concentrations with the development of HF in men aged ≤60years and the occurrence of adverse effects at one-year follow-up...
November 9, 2016: International Journal of Cardiology
https://www.readbyqxmd.com/read/27863252/the-allelic-landscape-of-human-blood-cell-trait-variation-and-links-to-common-complex-disease
#20
William J Astle, Heather Elding, Tao Jiang, Dave Allen, Dace Ruklisa, Alice L Mann, Daniel Mead, Heleen Bouman, Fernando Riveros-Mckay, Myrto A Kostadima, John J Lambourne, Suthesh Sivapalaratnam, Kate Downes, Kousik Kundu, Lorenzo Bomba, Kim Berentsen, John R Bradley, Louise C Daugherty, Olivier Delaneau, Kathleen Freson, Stephen F Garner, Luigi Grassi, Jose Guerrero, Matthias Haimel, Eva M Janssen-Megens, Anita Kaan, Mihir Kamat, Bowon Kim, Amit Mandoli, Jonathan Marchini, Joost H A Martens, Stuart Meacham, Karyn Megy, Jared O'Connell, Romina Petersen, Nilofar Sharifi, Simon M Sheard, James R Staley, Salih Tuna, Martijn van der Ent, Klaudia Walter, Shuang-Yin Wang, Eleanor Wheeler, Steven P Wilder, Valentina Iotchkova, Carmel Moore, Jennifer Sambrook, Hendrik G Stunnenberg, Emanuele Di Angelantonio, Stephen Kaptoge, Taco W Kuijpers, Enrique Carrillo-de-Santa-Pau, David Juan, Daniel Rico, Alfonso Valencia, Lu Chen, Bing Ge, Louella Vasquez, Tony Kwan, Diego Garrido-Martín, Stephen Watt, Ying Yang, Roderic Guigo, Stephan Beck, Dirk S Paul, Tomi Pastinen, David Bujold, Guillaume Bourque, Mattia Frontini, John Danesh, David J Roberts, Willem H Ouwehand, Adam S Butterworth, Nicole Soranzo
Many common variants have been associated with hematological traits, but identification of causal genes and pathways has proven challenging. We performed a genome-wide association analysis in the UK Biobank and INTERVAL studies, testing 29.5 million genetic variants for association with 36 red cell, white cell, and platelet properties in 173,480 European-ancestry participants. This effort yielded hundreds of low frequency (<5%) and rare (<1%) variants with a strong impact on blood cell phenotypes. Our data highlight general properties of the allelic architecture of complex traits, including the proportion of the heritable component of each blood trait explained by the polygenic signal across different genome regulatory domains...
November 17, 2016: Cell
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