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American Journal of Human Genetics

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https://www.readbyqxmd.com/read/28625504/mutations-in-armc9-which-encodes-a-basal-body-protein-cause-joubert-syndrome-in-humans-and-ciliopathy-phenotypes-in-zebrafish
#1
Julie C Van De Weghe, Tamara D S Rusterholz, Brooke Latour, Megan E Grout, Kimberly A Aldinger, Ranad Shaheen, Jennifer C Dempsey, Sateesh Maddirevula, Yong-Han H Cheng, Ian G Phelps, Matthias Gesemann, Himanshu Goel, Ohad S Birk, Talal Alanzi, Rifaat Rawashdeh, Arif O Khan, Michael J Bamshad, Deborah A Nickerson, Stephan C F Neuhauss, William B Dobyns, Fowzan S Alkuraya, Ronald Roepman, Ruxandra Bachmann-Gagescu, Dan Doherty
Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by hypotonia, ataxia, abnormal eye movements, and variable cognitive impairment. It is defined by a distinctive brain malformation known as the "molar tooth sign" on axial MRI. Subsets of affected individuals have malformations such as coloboma, polydactyly, and encephalocele, as well as progressive retinal dystrophy, fibrocystic kidney disease, and liver fibrosis. More than 35 genes have been associated with JS, but in a subset of families the genetic cause remains unknown...
June 14, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28602422/loss-of-function-variants-in-mylk-cause-recessive-megacystis-microcolon-intestinal-hypoperistalsis-syndrome
#2
Danny Halim, Erwin Brosens, Françoise Muller, Michael F Wangler, Arthur L Beaudet, James R Lupski, Zeynep H Coban Akdemir, Michael Doukas, Hans J Stoop, Bianca M de Graaf, Rutger W W Brouwer, Wilfred F J van Ijcken, Jean-François Oury, Jonathan Rosenblatt, Alan J Burns, Dick Tibboel, Robert M W Hofstra, Maria M Alves
Megacystis microcolon intestinal hypoperistalsis syndrome (MMIHS) is a congenital disorder characterized by loss of smooth muscle contraction in the bladder and intestine. To date, three genes are known to be involved in MMIHS pathogenesis: ACTG2, MYH11, and LMOD1. However, for approximately 10% of affected individuals, the genetic cause of the disease is unknown, suggesting that other loci are most likely involved. Here, we report on three MMIHS-affected subjects from two consanguineous families with no variants in the known MMIHS-associated genes...
June 7, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28602423/a-fast-and-accurate-algorithm-to-test-for-binary-phenotypes-and-its-application-to-phewas
#3
Rounak Dey, Ellen M Schmidt, Goncalo R Abecasis, Seunggeun Lee
The availability of electronic health record (EHR)-based phenotypes allows for genome-wide association analyses in thousands of traits and has great potential to enable identification of genetic variants associated with clinical phenotypes. We can interpret the phenome-wide association study (PheWAS) result for a single genetic variant by observing its association across a landscape of phenotypes. Because a PheWAS can test thousands of binary phenotypes, and most of them have unbalanced or often extremely unbalanced case-control ratios (1:10 or 1:600, respectively), existing methods cannot provide an accurate and scalable way to test for associations...
June 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575653/dynamic-role-of-trans-regulation-of-gene-expression-in-relation-to-complex-traits
#4
Chen Yao, Roby Joehanes, Andrew D Johnson, Tianxiao Huan, Chunyu Liu, Jane E Freedman, Peter J Munson, David E Hill, Marc Vidal, Daniel Levy
No abstract text is available yet for this article.
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575652/mutations-in-kdsr-cause-recessive-progressive-symmetric-erythrokeratoderma
#5
Lynn M Boyden, Nicholas G Vincent, Jing Zhou, Ronghua Hu, Brittany G Craiglow, Susan J Bayliss, Ilana S Rosman, Anne W Lucky, Luis A Diaz, Lowell A Goldsmith, Amy S Paller, Richard P Lifton, Susan J Baserga, Keith A Choate
The discovery of new genetic determinants of inherited skin disorders has been instrumental to the understanding of epidermal function, differentiation, and renewal. Here, we show that mutations in KDSR (3-ketodihydrosphingosine reductase), encoding an enzyme in the ceramide synthesis pathway, lead to a previously undescribed recessive Mendelian disorder in the progressive symmetric erythrokeratoderma spectrum. This disorder is characterized by severe lesions of thick scaly skin on the face and genitals and thickened, red, and scaly skin on the hands and feet...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575651/mutations-in-nkx6-2-cause-progressive-spastic-ataxia-and-hypomyelination
#6
Viorica Chelban, Nisha Patel, Jana Vandrovcova, M Natalia Zanetti, David S Lynch, Mina Ryten, Juan A Botía, Oscar Bello, Eloise Tribollet, Stephanie Efthymiou, Indran Davagnanam, Fahad A Bashiri, Nicholas W Wood, James E Rothman, Fowzan S Alkuraya, Henry Houlden
Progressive limb spasticity and cerebellar ataxia are frequently found together in clinical practice and form a heterogeneous group of degenerative disorders that are classified either as pure spastic ataxia or as complex spastic ataxia with additional neurological signs. Inheritance is either autosomal dominant or autosomal recessive. Hypomyelinating features on MRI are sometimes seen with spastic ataxia, but this is usually mild in adults and severe and life limiting in children. We report seven individuals with an early-onset spastic-ataxia phenotype...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575650/defects-in-the-cell-signaling-mediator-%C3%AE-catenin-cause-the-retinal-vascular-condition-fevr
#7
Evangelia S Panagiotou, Carla Sanjurjo Soriano, James A Poulter, Emma C Lord, Denisa Dzulova, Hiroyuki Kondo, Atsushi Hiyoshi, Brian Hon-Yin Chung, Yoyo Wing-Yiu Chu, Connie H Y Lai, Mark E Tafoya, Dyah Karjosukarso, Rob W J Collin, Joanne Topping, Louise M Downey, Manir Ali, Chris F Inglehearn, Carmel Toomes
Familial exudative vitreoretinopathy (FEVR) is an inherited blinding disorder characterized by the abnormal development of the retinal vasculature. The majority of mutations identified in FEVR are found within four genes that encode the receptor complex (FZD4, LRP5, and TSPAN12) and ligand (NDP) of a molecular pathway that controls angiogenesis, the Norrin-β-catenin signaling pathway. However, half of all FEVR-affected case subjects do not harbor mutations in these genes, indicating that further mutated genes remain to be identified...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575649/genetic-variation-driven-gene-expression-changes-highlight-genes-with-important-functions-for-kidney-disease
#8
Yi-An Ko, Huiguang Yi, Chengxiang Qiu, Shizheng Huang, Jihwan Park, Nora Ledo, Anna Köttgen, Hongzhe Li, Daniel J Rader, Michael A Pack, Christopher D Brown, Katalin Susztak
Chronic kidney disease (CKD) is a complex gene-environmental disease affecting close to 10% of the US population. Genome-wide association studies (GWASs) have identified sequence variants, localized to non-coding genomic regions, associated with kidney function. Despite these robust observations, the mechanism by which variants lead to CKD remains a critical unanswered question. Expression quantitative trait loci (eQTL) analysis is a method to identify genetic variation associated with gene expression changes in specific tissue types...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575648/mutations-in-sult2b1-cause-autosomal-recessive-congenital-ichthyosis-in-humans
#9
Lisa Heinz, Gwang-Jin Kim, Slaheddine Marrakchi, Julie Christiansen, Hamida Turki, Marc-Alexander Rauschendorf, Mark Lathrop, Ingrid Hausser, Andreas D Zimmer, Judith Fischer
Ichthyoses are a clinically and genetically heterogeneous group of genodermatoses associated with abnormal scaling of the skin over the whole body. Mutations in nine genes are known to cause non-syndromic forms of autosomal-recessive congenital ichthyosis (ARCI). However, not all genetic causes for ARCI have been discovered to date. Using whole-exome sequencing (WES) and multigene panel screening, we identified 6 ARCI-affected individuals from three unrelated families with mutations in Sulfotransferase family 2B member 1 (SULT2B1), showing their causative association with ARCI...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28575647/yy1-haploinsufficiency-causes-an-intellectual-disability-syndrome-featuring-transcriptional-and-chromatin-dysfunction
#10
Michele Gabriele, Anneke T Vulto-van Silfhout, Pierre-Luc Germain, Alessandro Vitriolo, Raman Kumar, Evelyn Douglas, Eric Haan, Kenjiro Kosaki, Toshiki Takenouchi, Anita Rauch, Katharina Steindl, Eirik Frengen, Doriana Misceo, Christeen Ramane J Pedurupillay, Petter Stromme, Jill A Rosenfeld, Yunru Shao, William J Craigen, Christian P Schaaf, David Rodriguez-Buritica, Laura Farach, Jennifer Friedman, Perla Thulin, Scott D McLean, Kimberly M Nugent, Jenny Morton, Jillian Nicholl, Joris Andrieux, Asbjørg Stray-Pedersen, Pascal Chambon, Sophie Patrier, Sally A Lynch, Susanne Kjaergaard, Pernille M Tørring, Charlotte Brasch-Andersen, Anne Ronan, Arie van Haeringen, Peter J Anderson, Zöe Powis, Han G Brunner, Rolph Pfundt, Janneke H M Schuurs-Hoeijmakers, Bregje W M van Bon, Stefan Lelieveld, Christian Gilissen, Willy M Nillesen, Lisenka E L M Vissers, Jozef Gecz, David A Koolen, Giuseppe Testa, Bert B A de Vries
Yin and yang 1 (YY1) is a well-known zinc-finger transcription factor with crucial roles in normal development and malignancy. YY1 acts both as a repressor and as an activator of gene expression. We have identified 23 individuals with de novo mutations or deletions of YY1 and phenotypic features that define a syndrome of cognitive impairment, behavioral alterations, intrauterine growth restriction, feeding problems, and various congenital malformations. Our combined clinical and molecular data define "YY1 syndrome" as a haploinsufficiency syndrome...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28552198/evaluating-the-clinical-validity-of-gene-disease-associations-an-evidence-based-framework-developed-by-the-clinical-genome-resource
#11
Natasha T Strande, Erin Rooney Riggs, Adam H Buchanan, Ozge Ceyhan-Birsoy, Marina DiStefano, Selina S Dwight, Jenny Goldstein, Rajarshi Ghosh, Bryce A Seifert, Tam P Sneddon, Matt W Wright, Laura V Milko, J Michael Cherry, Monica A Giovanni, Michael F Murray, Julianne M O'Daniel, Erin M Ramos, Avni B Santani, Alan F Scott, Sharon E Plon, Heidi L Rehm, Christa L Martin, Jonathan S Berg
With advances in genomic sequencing technology, the number of reported gene-disease relationships has rapidly expanded. However, the evidence supporting these claims varies widely, confounding accurate evaluation of genomic variation in a clinical setting. Despite the critical need to differentiate clinically valid relationships from less well-substantiated relationships, standard guidelines for such evaluation do not currently exist. The NIH-funded Clinical Genome Resource (ClinGen) has developed a framework to define and evaluate the clinical validity of gene-disease pairs across a variety of Mendelian disorders...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28552197/large-scale-identification-of-common-trait-and-disease-variants-affecting-gene-expression
#12
Mads Engel Hauberg, Wen Zhang, Claudia Giambartolomei, Oscar Franzén, David L Morris, Timothy J Vyse, Arno Ruusalepp, Pamela Sklar, Eric E Schadt, Johan L M Björkegren, Panos Roussos
Genome-wide association studies (GWASs) have identified a multitude of genetic loci involved with traits and diseases. However, it is often unclear which genes are affected in such loci and whether the associated genetic variants lead to increased or decreased gene function. To mitigate this, we integrated associations of common genetic variants in 57 GWASs with 24 studies of expression quantitative trait loci (eQTLs) from a broad range of tissues by using a Mendelian randomization approach. We discovered a total of 3,484 instances of gene-trait-associated changes in expression at a false-discovery rate < 0...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28552196/whole-genome-sequencing-coupled-to-imputation-discovers-genetic-signals-for-anthropometric-traits
#13
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
https://www.readbyqxmd.com/read/28552195/biallelic-mutations-in-cfap43-and-cfap44-cause-male-infertility-with-multiple-morphological-abnormalities-of-the-sperm-flagella
#14
Shuyan Tang, Xiong Wang, Weiyu Li, Xiaoyu Yang, Zheng Li, Wangjie Liu, Caihua Li, Zijue Zhu, Lingxiang Wang, Jiaxiong Wang, Ling Zhang, Xiaoling Sun, Erlei Zhi, Hongyan Wang, Hong Li, Li Jin, Yang Luo, Jian Wang, Shenmin Yang, Feng Zhang
Sperm motility is vital to human reproduction. Malformations of sperm flagella can cause male infertility. Men with multiple morphological abnormalities of the flagella (MMAF) have abnormal spermatozoa with absent, short, coiled, bent, and/or irregular-caliber flagella, which impair sperm motility. The known human MMAF-associated genes, such as DNAH1, only account for fewer than 45% of affected individuals. Pathogenic mechanisms in the genetically unexplained MMAF remain to be elucidated. Here, we conducted genetic analyses by using whole-exome sequencing and genome-wide comparative genomic hybridization microarrays in a multi-center cohort of 30 Han Chinese men affected by MMAF...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28528868/pleiotropic-effects-of-trait-associated-genetic-variation-on-dna-methylation-utility-for-refining-gwas-loci
#15
Eilis Hannon, Mike Weedon, Nicholas Bray, Michael O'Donovan, Jonathan Mill
Most genetic variants identified in genome-wide association studies (GWASs) of complex traits are thought to act by affecting gene regulation rather than directly altering the protein product. As a consequence, the actual genes involved in disease are not necessarily the most proximal to the associated variants. By integrating data from GWAS analyses with those from genetic studies of regulatory variation, it is possible to identify variants pleiotropically associated with both a complex trait and measures of gene regulation...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28502612/marrvel-integration-of-human-and-model-organism-genetic-resources-to-facilitate-functional-annotation-of-the-human-genome
#16
Julia Wang, Rami Al-Ouran, Yanhui Hu, Seon-Young Kim, Ying-Wooi Wan, Michael F Wangler, Shinya Yamamoto, Hsiao-Tuan Chao, Aram Comjean, Stephanie E Mohr, Norbert Perrimon, Zhandong Liu, Hugo J Bellen
One major challenge encountered with interpreting human genetic variants is the limited understanding of the functional impact of genetic alterations on biological processes. Furthermore, there remains an unmet demand for an efficient survey of the wealth of information on human homologs in model organisms across numerous databases. To efficiently assess the large volume of publically available information, it is important to provide a concise summary of the most relevant information in a rapid user-friendly format...
June 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28475864/retraction-notice-to-a-bloc-1-mutation-screen-reveals-that-pldn-is-mutated-in-hermansky-pudlak-syndrome-type-9
#17
Andrew R Cullinane, James A Curry, Carmelo Carmona-Rivera, C Gail Summers, Carla Ciccone, Nicholas D Cardillo, Heidi Dorward, Richard A Hess, James G White, David Adams, Marjan Huizing, William A Gahl
No abstract text is available yet for this article.
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28475863/gzf1-mutations-expand-the-genetic-heterogeneity-of-larsen-syndrome
#18
Nisha Patel, Hanan E Shamseldin, Nadia Sakati, Arif O Khan, Ameen Softa, Fatima M Al-Fadhli, Mais Hashem, Firdous M Abdulwahab, Tarfa Alshidi, Rana Alomar, Eman Alobeid, Salma M Wakil, Dilek Colak, Fowzan S Alkuraya
Larsen syndrome is characterized by the dislocation of large joints and other less consistent clinical findings. Heterozygous FLNB mutations account for the majority of Larsen syndrome cases, but biallelic mutations in CHST3 and B4GALT7 have been more recently described, thus confirming the existence of recessive forms of the disease. In a multiplex consanguineous Saudi family affected by severe and recurrent large joint dislocation and severe myopia, we identified a homozygous truncating variant in GZF1 through a combined autozygome and exome approach...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28475862/high-resolution-genetic-maps-identify-multiple-type-2-diabetes-loci-at-regulatory-hotspots-in-african-americans-and-europeans
#19
Winston Lau, Toby Andrew, Nikolas Maniatis
Interpretation of results from genome-wide association studies for T2D is challenging. Only very few loci have been replicated in African ancestry populations and the identification of the implicated functional genes remain largely undefined. We used genetic maps that capture detailed linkage disequilibrium information in European and African Americans and applied these to large T2D case-control samples in order to estimate locations for putative functional variants in both populations. Replicated T2D locations were tested for evidence of being regulatory hotspots using adipose expression...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28475861/widespread-allelic-heterogeneity-in-complex-traits
#20
Farhad Hormozdiari, Anthony Zhu, Gleb Kichaev, Chelsea J-T Ju, Ayellet V Segrè, Jong Wha J Joo, Hyejung Won, Sriram Sankararaman, Bogdan Pasaniuc, Sagiv Shifman, Eleazar Eskin
Recent successes in genome-wide association studies (GWASs) make it possible to address important questions about the genetic architecture of complex traits, such as allele frequency and effect size. One lesser-known aspect of complex traits is the extent of allelic heterogeneity (AH) arising from multiple causal variants at a locus. We developed a computational method to infer the probability of AH and applied it to three GWASs and four expression quantitative trait loci (eQTL) datasets. We identified a total of 4,152 loci with strong evidence of AH...
May 4, 2017: American Journal of Human Genetics
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