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JOURNAL ARTICLE
Hakan Cangul, Xiao-Hui Liao, Erik Schoenmakers, Jukka Kero, Sharon Barone, Panudda Srichomkwun, Hideyuki Iwayama, Eva G Serra, Halil Saglam, Erdal Eren, Omer Tarim, Adeline K Nicholas, Ilona Zvetkova, Carl A Anderson, Fiona E Karet Frankl, Kristien Boelaert, Marja Ojaniemi, Jarmo Jääskeläinen, Konrad Patyra, Christoffer Löf, E Dillwyn Williams, Manoocher Soleimani, Timothy Barrett, Eamonn R Maher, V Krishna Chatterjee, Samuel Refetoff, Nadia Schoenmakers
Defects in genes mediating thyroid hormone biosynthesis result in dyshormonogenic congenital hypothyroidism (CH). Here, we report homozygous truncating mutations in SLC26A7 in 6 unrelated families with goitrous CH and show that goitrous hypothyroidism also occurs in Slc26a7-null mice. In both species, the gene is expressed predominantly in the thyroid gland, and loss of function is associated with impaired availability of iodine for thyroid hormone synthesis, partially corrected in mice by iodine supplementation...
October 18, 2018: JCI Insight
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JOURNAL ARTICLE
Gianina Ravenscroft, Irina T Zaharieva, Carlo A Bortolotti, Matteo Lambrughi, Marcello Pignataro, Marco Borsari, Caroline A Sewry, Rahul Phadke, Goknur Haliloglu, Royston Ong, Hayley Goullée, Tamieka Whyte, Uk K Consortium, Adnan Manzur, Beril Talim, Ulkuhan Kaya, Daniel P S Osborn, Alistair R R Forrest, Nigel G Laing, Francesco Muntoni
Congenital myopathies are typically characterised by early onset hypotonia, weakness and hallmark features on biopsy. Despite the rapid pace of gene discovery, ∼50% of patients with a congenital myopathy remain without a genetic diagnosis following screening of known disease genes. We performed exome sequencing on two consanguineous probands diagnosed with a congenital myopathy and muscle biopsy showing selective atrophy/hypotrophy or absence of type II myofibres. We identified variants in the gene (MYL1) encoding the skeletal muscle fast-twitch specific myosin essential light chain (ELC) in both probands...
December 15, 2018: Human Molecular Genetics
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S Riazuddin, M Hussain, A Razzaq, Z Iqbal, M Shahzad, D L Polla, Y Song, E van Beusekom, A A Khan, L Tomas-Roca, M Rashid, M Y Zahoor, W M Wissink-Lindhout, M A R Basra, M Ansar, Z Agha, K van Heeswijk, F Rasheed, M Van de Vorst, J A Veltman, C Gilissen, J Akram, T Kleefstra, M Z Assir, D Grozeva, K Carss, F L Raymond, T D O'Connor, S A Riazuddin, S N Khan, Z M Ahmed, A P M de Brouwer, H van Bokhoven, S Riazuddin
This Article was originally published under a CC BY-NC-SA 4.0 license, but has now been made available under a CC BY 4.0 license. The PDF and HTML versions of the Article have been modified accordingly.
November 2020: Molecular Psychiatry
#24
JOURNAL ARTICLE
Urielle Ullmann, Luigi D'Argenzio, Shrey Mathur, Tamieka Whyte, Ros Quinlivan, Cheryl Longman, Maria Elena Farrugia, Adnan Manzur, Tracey Willis, Heinz Jungbluth, Matthew Pitt, Sebahattin Cirak, Lucy Feng, William Stewart, Rachael Mein, Rahul Phadke, Caroline Sewry, Anna Sarkozy, Francesco Muntoni
Autosomal recessive mutations in the ECEL1 gene have recently been associated with a wide phenotypic spectrum including severe congenital contractural syndromes and distal arthrogryposis type 5D (DA5D). Here, we describe four novel families with ECEL1 gene mutations, reporting 15 years of follow-up for four patients and detailed muscle pathological description for three individuals. In particular, we observed mild myopathic features, prominent core-like areas in one individual, and presence of nCAM positive fibres in three patients from 2 unrelated families suggesting a possible problem with innervation...
September 2018: Neuromuscular Disorders: NMD
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JOURNAL ARTICLE
Elizabeth B Claus, Alex J Cornish, Peter Broderick, Joellen M Schildkraut, Sara E Dobbins, Amy Holroyd, Lisa Calvocoressi, Lingeng Lu, Helen M Hansen, Ivan Smirnov, Kyle M Walsh, Johannes Schramm, Per Hoffmann, Markus M Nöthen, Karl-Heinz Jöckel, Anthony Swerdlow, Signe Benzon Larsen, Christoffer Johansen, Matthias Simon, Melissa Bondy, Margaret Wrensch, Richard S Houlston, Joseph L Wiemels
Background: Meningiomas are adult brain tumors originating in the meningeal coverings of the brain and spinal cord, with significant heritable basis. Genome-wide association studies (GWAS) have previously identified only a single risk locus for meningioma, at 10p12.31. Methods: To identify a susceptibility locus for meningioma, we conducted a meta-analysis of 2 GWAS, imputed using a merged reference panel from the 1000 Genomes Project and UK10K data, with validation in 2 independent sample series totaling 2138 cases and 12081 controls...
October 9, 2018: Neuro-oncology
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JOURNAL ARTICLE
N L O'Brien, A Fiorentino, D Curtis, C Rayner, C Petrosellini, M Al Eissa, N J Bass, A McQuillin, S I Sharp
Recent results imply that rare variants contribute to the risk of schizophrenia. Exome sequence data from the UK10K project was used to identify three rare, amino acid changing variants in the ITGB4 gene which segregated with schizophrenia in two families: rs750367954, rs147480547 and rs145976111. Association analysis was carried out in the exome-sequenced Swedish schizophrenia study and in UCL schizophrenia and bipolar cases and controls genotyped for these variants. A gene-wise weighted burden test was performed on a trio sample of schizophrenia cases and their parents...
September 2018: Schizophrenia Research
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JOURNAL ARTICLE
Jianping Sun, Karim Oualkacha, Vincenzo Forgetta, Hou-Feng Zheng, J Brent Richards, Daniel S Evans, Eric Orwoll, Celia M T Greenwood
Performance of a recently developed test for association between multivariate phenotypes and sets of genetic variants (MURAT) is demonstrated using measures of bone mineral density (BMD). By combining individual-level whole genome sequenced data from the UK10K study, and imputed genome-wide genetic data on individuals from the Study of Osteoporotic Fractures (SOF) and the Osteoporotic Fractures in Men Study (MrOS), a data set of 8810 individuals was assembled; tests of association were performed between autosomal gene-sets of genetic variants and BMD measured at lumbar spine and femoral neck...
January 9, 2018: Scientific Reports
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JOURNAL ARTICLE
Venu Pullabhatla, Amy L Roberts, Myles J Lewis, Daniele Mauro, David L Morris, Christopher A Odhams, Philip Tombleson, Ulrika Liljedahl, Simon Vyse, Michael A Simpson, Sascha Sauer, Emanuele de Rinaldis, Ann-Christine Syvänen, Timothy J Vyse
The omnigenic model of complex disease stipulates that the majority of the heritability will be explained by the effects of common variation on genes in the periphery of core disease pathways. Rare variant associations, expected to explain far less of the heritability, may be enriched in core disease genes and thus will be instrumental in the understanding of complex disease pathogenesis and their potential therapeutic targets. Here, using complementary whole-exome sequencing, high-density imputation, and in vitro cellular assays, we identify candidate core genes in the pathogenesis of systemic lupus erythematosus (SLE)...
February 1, 2018: Human Molecular Genetics
#29
JOURNAL ARTICLE
Ruoyu Zhang, Yiqin Wang, Kaixiong Ye, Martin Picard, Zhenglong Gu
BACKGROUND: The accumulation of mitochondrial DNA (mtDNA) mutations, and the reduction of mtDNA copy number, both disrupt mitochondrial energetics, and may contribute to aging and age-associated phenotypes. However, there are few genetic and epidemiological studies on the spectra of blood mtDNA heteroplasmies, and the distribution of mtDNA copy numbers in different age groups and their impact on age-related phenotypes. In this work, we used whole-genome sequencing data of isolated peripheral blood mononuclear cells (PBMCs) from the UK10K project to investigate in parallel mtDNA heteroplasmy and copy number in 1511 women, between 17 and 85 years old, recruited in the TwinsUK cohorts...
November 21, 2017: BMC Genomics
#30
JOURNAL ARTICLE
Mariam M Al Eissa, Alessia Fiorentino, Sally I Sharp, Niamh L O'Brien, Kate Wolfe, Giovanni Giaroli, David Curtis, Nicholas J Bass, Andrew McQuillin
Schizophrenia (SCZ) is a severe, highly heritable psychiatric disorder. Elucidation of the genetic architecture of the disorder will facilitate greater understanding of the altered underlying neurobiological mechanisms. The aim of this study was to identify likely aetiological variants in subjects affected with SCZ. Exome sequence data from a SCZ cas-control sample from Sweden was analysed for likely aetiological variants using a weighted burden test. Suggestive evidence implicated the UNC-51-like kinase (ULK1) gene, and it was observed that four rare variants that were more common in the Swedish SCZ cases were also more common in UK10K SCZ cases, as compared to obesity cases...
March 2018: Annals of Human Genetics
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JOURNAL ARTICLE
Lee Moir, Elena G Bochukova, Rebecca Dumbell, Gareth Banks, Rasneer S Bains, Patrick M Nolan, Cheryl Scudamore, Michelle Simon, Kimberly A Watson, Julia Keogh, Elana Henning, Audrey Hendricks, Stephen O'Rahilly, Inês Barroso, Adrienne E Sullivan, David C Bersten, Murray L Whitelaw, Susan Kirsch, Elizabeth Bentley, I Sadaf Farooqi, Roger D Cox
OBJECTIVE: Genetic studies in obese rodents and humans can provide novel insights into the mechanisms involved in energy homeostasis. METHODS: In this study, we genetically mapped the chromosomal region underlying the development of severe obesity in a mouse line identified as part of a dominant N-ethyl-N-nitrosourea (ENU) mutagenesis screen. We characterized the metabolic and behavioral phenotype of obese mutant mice and examined changes in hypothalamic gene expression...
November 2017: Molecular Metabolism
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JOURNAL ARTICLE
Jeroen G J van Rooij, Mila Jhamai, Pascal P Arp, Stephan C A Nouwens, Marijn Verkerk, Albert Hofman, M Arfan Ikram, Annemieke J Verkerk, Joyce B J van Meurs, Fernando Rivadeneira, André G Uitterlinden, Robert Kraaij
We have generated a next-generation whole-exome sequencing data set of 2628 participants of the population-based Rotterdam Study cohort, comprising 669 737 single-nucleotide variants and 24 019 short insertions and deletions. Because of broad and deep longitudinal phenotyping of the Rotterdam Study, this data set permits extensive interpretation of genetic variants on a range of clinically relevant outcomes, and is accessible as a control data set. We show that next-generation sequencing data sets yield a large degree of population-specific variants, which are not captured by other available large sequencing efforts, being ExAC, ESP, 1000G, UK10K, GoNL and DECODE...
October 2017: European Journal of Human Genetics: EJHG
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JOURNAL ARTICLE
Bram P Prins, Karoline B Kuchenbaecker, Yanchun Bao, Melissa Smart, Delilah Zabaneh, Ghazaleh Fatemifar, Jian'an Luan, Nick J Wareham, Robert A Scott, John R B Perry, Claudia Langenberg, Michaela Benzeval, Meena Kumari, Eleftheria Zeggini
Serum biomarker levels are associated with the risk of complex diseases. Here, we aimed to gain insights into the genetic architecture of biomarker traits which can reflect health status. We performed genome-wide association analyses for twenty serum biomarkers involved in organ function and reproductive health. 9,961 individuals from the UK Household Longitudinal Study were genotyped using the Illumina HumanCoreExome array and variants imputed to the 1000 Genomes Project and UK10K haplotypes. We establish a polygenic heritability for all biomarkers, confirm associations of fifty-four established loci, and identify five novel, replicating associations at genome-wide significance...
September 8, 2017: Scientific Reports
#34
JOURNAL ARTICLE
Despoina Manousaki, Tom Dudding, Simon Haworth, Yi-Hsiang Hsu, Ching-Ti Liu, Carolina Medina-Gómez, Trudy Voortman, Nathalie van der Velde, Håkan Melhus, Cassianne Robinson-Cohen, Diana L Cousminer, Maria Nethander, Liesbeth Vandenput, Raymond Noordam, Vincenzo Forgetta, Celia M T Greenwood, Mary L Biggs, Bruce M Psaty, Jerome I Rotter, Babette S Zemel, Jonathan A Mitchell, Bruce Taylor, Mattias Lorentzon, Magnus Karlsson, Vincent V W Jaddoe, Henning Tiemeier, Natalia Campos-Obando, Oscar H Franco, Andre G Utterlinden, Linda Broer, Natasja M van Schoor, Annelies C Ham, M Arfan Ikram, David Karasik, Renée de Mutsert, Frits R Rosendaal, Martin den Heijer, Thomas J Wang, Lars Lind, Eric S Orwoll, Dennis O Mook-Kanamori, Karl Michaëlsson, Bryan Kestenbaum, Claes Ohlsson, Dan Mellström, Lisette C P G M de Groot, Struan F A Grant, Douglas P Kiel, M Carola Zillikens, Fernando Rivadeneira, Stephen Sawcer, Nicholas J Timpson, J Brent Richards
Vitamin D insufficiency is common, correctable, and influenced by genetic factors, and it has been associated with risk of several diseases. We sought to identify low-frequency genetic variants that strongly increase the risk of vitamin D insufficiency and tested their effect on risk of multiple sclerosis, a disease influenced by low vitamin D concentrations. We used whole-genome sequencing data from 2,619 individuals through the UK10K program and deep-imputation data from 39,655 individuals genotyped genome-wide...
August 3, 2017: American Journal of Human Genetics
#35
JOURNAL ARTICLE
Di Zhang, Linhai Zhao, Biao Li, Zongxiao He, Gao T Wang, Dajiang J Liu, Suzanne M Leal
Massively parallel sequencing technologies provide great opportunities for discovering rare susceptibility variants involved in complex disease etiology via large-scale imputation and exome and whole-genome sequence-based association studies. Due to modest effect sizes, large sample sizes of tens to hundreds of thousands of individuals are required for adequately powered studies. Current analytical tools are obsolete when it comes to handling these large datasets. To facilitate the analysis of large-scale sequence-based studies, we developed SEQSpark which implements parallel processing based on Spark to increase the speed and efficiency of performing data quality control, annotation, and association analysis...
July 6, 2017: American Journal of Human Genetics
#36
JOURNAL ARTICLE
Audrey E Hendricks, Elena G Bochukova, Gaëlle Marenne, Julia M Keogh, Neli Atanassova, Rebecca Bounds, Eleanor Wheeler, Vanisha Mistry, Elana Henning, Antje Körner, Dawn Muddyman, Shane McCarthy, Anke Hinney, Johannes Hebebrand, Robert A Scott, Claudia Langenberg, Nick J Wareham, Praveen Surendran, Joanna M Howson, Adam S Butterworth, John Danesh, Børge G Nordestgaard, Sune F Nielsen, Shoaib Afzal, Sofia Papadia, Sofie Ashford, Sumedha Garg, Glenn L Millhauser, Rafael I Palomino, Alexandra Kwasniewska, Ioanna Tachmazidou, Stephen O'Rahilly, Eleftheria Zeggini, Inês Barroso, I Sadaf Farooqi
Obesity is a genetically heterogeneous disorder. Using targeted and whole-exome sequencing, we studied 32 human and 87 rodent obesity genes in 2,548 severely obese children and 1,117 controls. We identified 52 variants contributing to obesity in 2% of cases including multiple novel variants in GNAS, which were sometimes found with accelerated growth rather than short stature as described previously. Nominally significant associations were found for rare functional variants in BBS1, BBS9, GNAS, MKKS, CLOCK and ANGPTL6...
June 29, 2017: Scientific Reports
#37
JOURNAL ARTICLE
Tarjinder Singh, James T R Walters, Mandy Johnstone, David Curtis, Jaana Suvisaari, Minna Torniainen, Elliott Rees, Conrad Iyegbe, Douglas Blackwood, Andrew M McIntosh, Georg Kirov, Daniel Geschwind, Robin M Murray, Marta Di Forti, Elvira Bramon, Michael Gandal, Christina M Hultman, Pamela Sklar, Aarno Palotie, Patrick F Sullivan, Michael C O'Donovan, Michael J Owen, Jeffrey C Barrett
By performing a meta-analysis of rare coding variants in whole-exome sequences from 4,133 schizophrenia cases and 9,274 controls, de novo mutations in 1,077 family trios, and copy number variants from 6,882 cases and 11,255 controls, we show that individuals with schizophrenia carry a significant burden of rare, damaging variants in 3,488 genes previously identified as having a near-complete depletion of loss-of-function variants. In patients with schizophrenia who also have intellectual disability, this burden is concentrated in risk genes associated with neurodevelopmental disorders...
August 2017: Nature Genetics
#38
JOURNAL ARTICLE
Yali Xue, Massimo Mezzavilla, Marc Haber, Shane McCarthy, Yuan Chen, Vagheesh Narasimhan, Arthur Gilly, Qasim Ayub, Vincenza Colonna, Lorraine Southam, Christopher Finan, Andrea Massaia, Himanshu Chheda, Priit Palta, Graham Ritchie, Jennifer Asimit, George Dedoussis, Paolo Gasparini, Aarno Palotie, Samuli Ripatti, Nicole Soranzo, Daniela Toniolo, James F Wilson, Richard Durbin, Chris Tyler-Smith, Eleftheria Zeggini
The genetic features of isolated populations can boost power in complex-trait association studies, and an in-depth understanding of how their genetic variation has been shaped by their demographic history can help leverage these advantageous characteristics. Here, we perform a comprehensive investigation using 3,059 newly generated low-depth whole-genome sequences from eight European isolates and two matched general populations, together with published data from the 1000 Genomes Project and UK10K. Sequencing data give deeper and richer insights into population demography and genetic characteristics than genotype-chip data, distinguishing related populations more effectively and allowing their functional variants to be studied more fully...
June 23, 2017: Nature Communications
#39
JOURNAL ARTICLE
Peizhou Liao, Glen A Satten, Yi-Juan Hu
A fundamental challenge in analyzing next-generation sequencing (NGS) data is to determine an individual's genotype accurately, as the accuracy of the inferred genotype is essential to downstream analyses. Correctly estimating the base-calling error rate is critical to accurate genotype calls. Phred scores that accompany each call can be used to decide which calls are reliable. Some genotype callers, such as GATK and SAMtools, directly calculate the base-calling error rates from phred scores or recalibrated base quality scores...
July 2017: Genetic Epidemiology
#40
JOURNAL ARTICLE
Ioanna Tachmazidou, Dániel Süveges, Josine L Min, Graham R S Ritchie, Julia Steinberg, Klaudia Walter, Valentina Iotchkova, Jeremy Schwartzentruber, Jie Huang, Yasin Memari, Shane McCarthy, Andrew A Crawford, Cristina Bombieri, Massimiliano Cocca, Aliki-Eleni Farmaki, Tom R Gaunt, Pekka Jousilahti, Marjolein N Kooijman, Benjamin Lehne, Giovanni Malerba, Satu Männistö, Angela Matchan, Carolina Medina-Gomez, Sarah J Metrustry, Abhishek Nag, Ioanna Ntalla, Lavinia Paternoster, Nigel W Rayner, Cinzia Sala, William R Scott, Hashem A Shihab, Lorraine Southam, Beate St Pourcain, Michela Traglia, Katerina Trajanoska, Gialuigi Zaza, Weihua Zhang, María S Artigas, Narinder Bansal, Marianne Benn, Zhongsheng Chen, Petr Danecek, Wei-Yu Lin, Adam Locke, Jian'an Luan, Alisa K Manning, Antonella Mulas, Carlo Sidore, Anne Tybjaerg-Hansen, Anette Varbo, Magdalena Zoledziewska, Chris Finan, Konstantinos Hatzikotoulas, Audrey E Hendricks, John P Kemp, Alireza Moayyeri, Kalliope Panoutsopoulou, Michal Szpak, Scott G Wilson, Michael Boehnke, Francesco Cucca, Emanuele Di Angelantonio, Claudia Langenberg, Cecilia Lindgren, Mark I McCarthy, Andrew P Morris, Børge G Nordestgaard, Robert A Scott, Martin D Tobin, Nicholas J Wareham, Paul Burton, John C Chambers, George Davey Smith, George Dedoussis, Janine F Felix, Oscar H Franco, Giovanni Gambaro, Paolo Gasparini, Christopher J Hammond, Albert Hofman, Vincent W V Jaddoe, Marcus Kleber, Jaspal S Kooner, Markus Perola, Caroline Relton, Susan M Ring, Fernando Rivadeneira, Veikko Salomaa, Timothy D Spector, Oliver Stegle, Daniela Toniolo, André G Uitterlinden, Inês Barroso, Celia M T Greenwood, John R B Perry, Brian R Walker, Adam S Butterworth, Yali Xue, Richard Durbin, Kerrin S Small, Nicole Soranzo, Nicholas J Timpson, Eleftheria Zeggini
Deep sequence-based imputation can enhance the discovery power of genome-wide association studies by assessing previously unexplored variation across the common- and low-frequency spectra. We applied a hybrid whole-genome sequencing (WGS) and deep imputation approach to examine the broader allelic architecture of 12 anthropometric traits associated with height, body mass, and fat distribution in up to 267,616 individuals. We report 106 genome-wide significant signals that have not been previously identified, including 9 low-frequency variants pointing to functional candidates...
June 1, 2017: American Journal of Human Genetics
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