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American Journal of Human Genetics

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https://www.readbyqxmd.com/read/28502612/marrvel-integration-of-human-and-model-organism-genetic-resources-to-facilitate-functional-annotation-of-the-human-genome
#1
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...
May 3, 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
#2
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
#3
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
#4
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
#5
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
https://www.readbyqxmd.com/read/28475860/charge-and-kabuki-syndromes-gene-specific-dna-methylation-signatures-identify-epigenetic-mechanisms-linking-these-clinically-overlapping-conditions
#6
Darci T Butcher, Cheryl Cytrynbaum, Andrei L Turinsky, Michelle T Siu, Michal Inbar-Feigenberg, Roberto Mendoza-Londono, David Chitayat, Susan Walker, Jerry Machado, Oana Caluseriu, Lucie Dupuis, Daria Grafodatskaya, William Reardon, Brigitte Gilbert-Dussardier, Alain Verloes, Frederic Bilan, Jeff M Milunsky, Raveen Basran, Blake Papsin, Tracy L Stockley, Stephen W Scherer, Sanaa Choufani, Michael Brudno, Rosanna Weksberg
Epigenetic dysregulation has emerged as a recurring mechanism in the etiology of neurodevelopmental disorders. Two such disorders, CHARGE and Kabuki syndromes, result from loss of function mutations in chromodomain helicase DNA-binding protein 7 (CHD7(LOF)) and lysine (K) methyltransferase 2D (KMT2D(LOF)), respectively. Although these two syndromes are clinically distinct, there is significant phenotypic overlap. We therefore expected that epigenetically driven developmental pathways regulated by CHD7 and KMT2D would overlap and that DNA methylation (DNAm) alterations downstream of the mutations in these genes would identify common target genes, elucidating a mechanistic link between these two conditions, as well as specific target genes for each disorder...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28475859/inferring-human-demographic-histories-of-non-african-populations-from-patterns-of-allele-sharing
#7
Jeffrey D Wall
Recent human-genetics studies have come to different conclusions regarding how and when modern humans spread out of Africa and into the rest of the world. I present here a simple parsimony-based analysis that suggests that East Asians and Melanesians are sister groups, and I discuss what implications this has for recent claims made about the demographic histories of non-African populations.
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28475858/systematic-computational-identification-of-variants-that-activate-exonic-and-intronic-cryptic-splice-sites
#8
Melissa Lee, Patrick Roos, Neeraj Sharma, Melis Atalar, Taylor A Evans, Matthew J Pellicore, Emily Davis, Anh-Thu N Lam, Susan E Stanley, Sara E Khalil, George M Solomon, Doug Walker, Karen S Raraigh, Briana Vecchio-Pagan, Mary Armanios, Garry R Cutting
We developed a variant-annotation method that combines sequence-based machine-learning classification with a context-dependent algorithm for selecting splice variants. Our approach is distinctive in that it compares the splice potential of a sequence bearing a variant with the splice potential of the reference sequence. After training, classification accurately identified 168 of 180 (93.3%) canonical splice sites of five genes. The combined method, CryptSplice, identified and correctly predicted the effect of 18 of 21 (86%) known splice-altering variants in CFTR, a well-studied gene whose loss-of-function variants cause cystic fibrosis (CF)...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28475857/mutations-in-epigenetic-regulation-genes-are-a-major-cause-of-overgrowth-with-intellectual-disability
#9
Katrina Tatton-Brown, Chey Loveday, Shawn Yost, Matthew Clarke, Emma Ramsay, Anna Zachariou, Anna Elliott, Harriet Wylie, Anna Ardissone, Olaf Rittinger, Fiona Stewart, I Karen Temple, Trevor Cole, Shazia Mahamdallie, Sheila Seal, Elise Ruark, Nazneen Rahman
To explore the genetic architecture of human overgrowth syndromes and human growth control, we performed experimental and bioinformatic analyses of 710 individuals with overgrowth (height and/or head circumference ≥+2 SD) and intellectual disability (OGID). We identified a causal mutation in 1 of 14 genes in 50% (353/710). This includes HIST1H1E, encoding histone H1.4, which has not been associated with a developmental disorder previously. The pathogenic HIST1H1E mutations are predicted to result in a product that is less effective in neutralizing negatively charged linker DNA because it has a reduced net charge, and in DNA binding and protein-protein interactions because key residues are truncated...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28475856/international-cooperation-to-enable-the-diagnosis-of-all-rare-genetic-diseases
#10
Kym M Boycott, Ana Rath, Jessica X Chong, Taila Hartley, Fowzan S Alkuraya, Gareth Baynam, Anthony J Brookes, Michael Brudno, Angel Carracedo, Johan T den Dunnen, Stephanie O M Dyke, Xavier Estivill, Jack Goldblatt, Catherine Gonthier, Stephen C Groft, Ivo Gut, Ada Hamosh, Philip Hieter, Sophie Höhn, Matthew E Hurles, Petra Kaufmann, Bartha M Knoppers, Jeffrey P Krischer, Milan Macek, Gert Matthijs, Annie Olry, Samantha Parker, Justin Paschall, Anthony A Philippakis, Heidi L Rehm, Peter N Robinson, Pak-Chung Sham, Rumen Stefanov, Domenica Taruscio, Divya Unni, Megan R Vanstone, Feng Zhang, Han Brunner, Michael J Bamshad, Hanns Lochmüller
Provision of a molecularly confirmed diagnosis in a timely manner for children and adults with rare genetic diseases shortens their "diagnostic odyssey," improves disease management, and fosters genetic counseling with respect to recurrence risks while assuring reproductive choices. In a general clinical genetics setting, the current diagnostic rate is approximately 50%, but for those who do not receive a molecular diagnosis after the initial genetics evaluation, that rate is much lower. Diagnostic success for these more challenging affected individuals depends to a large extent on progress in the discovery of genes associated with, and mechanisms underlying, rare diseases...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28457472/duplicated-enhancer-region-increases-expression-of-ctsb-and-segregates-with-keratolytic-winter-erythema-in-south-african-and-norwegian-families
#11
Thandiswa Ngcungcu, Martin Oti, Jan C Sitek, Bjørn I Haukanes, Bolan Linghu, Robert Bruccoleri, Tomasz Stokowy, Edward J Oakeley, Fan Yang, Jiang Zhu, Marc Sultan, Joost Schalkwijk, Ivonne M J J van Vlijmen-Willems, Charlotte von der Lippe, Han G Brunner, Kari M Ersland, Wayne Grayson, Stine Buechmann-Moller, Olav Sundnes, Nanguneri Nirmala, Thomas M Morgan, Hans van Bokhoven, Vidar M Steen, Peter R Hull, Joseph Szustakowski, Frank Staedtler, Huiqing Zhou, Torunn Fiskerstrand, Michele Ramsay
Keratolytic winter erythema (KWE) is a rare autosomal-dominant skin disorder characterized by recurrent episodes of palmoplantar erythema and epidermal peeling. KWE was previously mapped to 8p23.1-p22 (KWE critical region) in South African families. Using targeted resequencing of the KWE critical region in five South African families and SNP array and whole-genome sequencing in two Norwegian families, we identified two overlapping tandem duplications of 7.67 kb (South Africans) and 15.93 kb (Norwegians). The duplications segregated with the disease and were located upstream of CTSB, a gene encoding cathepsin B, a cysteine protease involved in keratinocyte homeostasis...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28434495/dysfunction-of-the-cerebral-glucose-transporter-slc45a1-in-individuals-with-intellectual-disability-and-epilepsy
#12
Myriam Srour, Noriaki Shimokawa, Fadi F Hamdan, Christina Nassif, Chantal Poulin, Lihadh Al Gazali, Jill A Rosenfeld, Noriyuki Koibuchi, Guy A Rouleau, Aisha Al Shamsi, Jacques L Michaud
Glucose transport across the blood brain barrier and into neural cells is critical for normal cerebral physiologic function. Dysfunction of the cerebral glucose transporter GLUT1 (encoded by SLC2A1) is known to result in epilepsy, intellectual disability (ID), and movement disorder. Using whole-exome sequencing, we identified rare homozygous missense variants (c.526C>T [p.Arg176Trp] and c.629C>T [p.Ala210Val]) in SLC45A1, encoding another cerebral glucose transporter, in two consanguineous multiplex families with moderate to severe ID, epilepsy, and variable neuropsychiatric features...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28413019/germline-mutations-in-cdh23-encoding-cadherin-related-23-are-associated-with-both-familial-and-sporadic-pituitary-adenomas
#13
Qilin Zhang, Cheng Peng, Jianping Song, Yichao Zhang, Jianhua Chen, Zhijian Song, Xuefei Shou, Zengyi Ma, Hong Peng, Xuemin Jian, Wenqiang He, Zhao Ye, Zhiqiang Li, Yongfei Wang, Hongying Ye, Zhaoyun Zhang, Ming Shen, Feng Tang, Hong Chen, Zhifeng Shi, Chunjui Chen, Zhengyuan Chen, Yue Shen, Ye Wang, Shaoyong Lu, Jian Zhang, Yiming Li, Shiqi Li, Ying Mao, Liangfu Zhou, Hai Yan, Yongyong Shi, Chuanxin Huang, Yao Zhao
Pituitary adenoma (PA) is one of the most common intracranial neoplasms. Several genetic predisposing factors for PA have been identified, but they account for a small portion of cases. In this study, we sought to identify the PA genetic risk factors by focusing on causative mutations for PAs. Among the 4 affected and 17 asymptomatic members from one family with familial PA, whole-exome sequencing identified cosegregation of the PA phenotype with the heterozygous missense mutation c.4136G>T (p.Arg1379Leu) in cadherin-related 23 (CDH23)...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28413018/plaa-mutations-cause-a-lethal-infantile-epileptic-encephalopathy-by-disrupting-ubiquitin-mediated-endolysosomal-degradation-of-synaptic-proteins
#14
Emma A Hall, Michael S Nahorski, Lyndsay M Murray, Ranad Shaheen, Emma Perkins, Kosala N Dissanayake, Yosua Kristaryanto, Ross A Jones, Julie Vogt, Manon Rivagorda, Mark T Handley, Girish R Mali, Tooba Quidwai, Dinesh C Soares, Margaret A Keighren, Lisa McKie, Richard L Mort, Noor Gammoh, Amaya Garcia-Munoz, Tracey Davey, Matthieu Vermeren, Diana Walsh, Peter Budd, Irene A Aligianis, Eissa Faqeih, Alan J Quigley, Ian J Jackson, Yogesh Kulathu, Mandy Jackson, Richard R Ribchester, Alex von Kriegsheim, Fowzan S Alkuraya, C Geoffrey Woods, Eamonn R Maher, Pleasantine Mill
During neurotransmission, synaptic vesicles undergo multiple rounds of exo-endocytosis, involving recycling and/or degradation of synaptic proteins. While ubiquitin signaling at synapses is essential for neural function, it has been assumed that synaptic proteostasis requires the ubiquitin-proteasome system (UPS). We demonstrate here that turnover of synaptic membrane proteins via the endolysosomal pathway is essential for synaptic function. In both human and mouse, hypomorphic mutations in the ubiquitin adaptor protein PLAA cause an infantile-lethal neurodysfunction syndrome with seizures...
May 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28388435/de-novo-disruption-of-the-proteasome-regulatory-subunit-psmd12-causes-a-syndromic-neurodevelopmental-disorder
#15
Sébastien Küry, Thomas Besnard, Frédéric Ebstein, Tahir N Khan, Tomasz Gambin, Jessica Douglas, Carlos A Bacino, William J Craigen, Stephan J Sanders, Andrea Lehmann, Xénia Latypova, Kamal Khan, Mathilde Pacault, Stephanie Sacharow, Kimberly Glaser, Eric Bieth, Laurence Perrin-Sabourin, Marie-Line Jacquemont, Megan T Cho, Elizabeth Roeder, Anne-Sophie Denommé-Pichon, Kristin G Monaghan, Bo Yuan, Fan Xia, Sylvain Simon, Dominique Bonneau, Philippe Parent, Brigitte Gilbert-Dussardier, Sylvie Odent, Annick Toutain, Laurent Pasquier, Deborah Barbouth, Chad A Shaw, Ankita Patel, Janice L Smith, Weimin Bi, Sébastien Schmitt, Wallid Deb, Mathilde Nizon, Sandra Mercier, Marie Vincent, Caroline Rooryck, Valérie Malan, Ignacio Briceño, Alberto Gómez, Kimberly M Nugent, James B Gibson, Benjamin Cogné, James R Lupski, Holly A F Stessman, Evan E Eichler, Kyle Retterer, Yaping Yang, Richard Redon, Nicholas Katsanis, Jill A Rosenfeld, Peter-Michael Kloetzel, Christelle Golzio, Stéphane Bézieau, Paweł Stankiewicz, Bertrand Isidor
No abstract text is available yet for this article.
April 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28366443/modeling-the-mutational-and-phenotypic-landscapes-of-pelizaeus-merzbacher-disease-with-human-ipsc-derived-oligodendrocytes
#16
Zachary S Nevin, Daniel C Factor, Robert T Karl, Panagiotis Douvaras, Jeremy Laukka, Martha S Windrem, Steven A Goldman, Valentina Fossati, Grace M Hobson, Paul J Tesar
Pelizaeus-Merzbacher disease (PMD) is a pediatric disease of myelin in the central nervous system and manifests with a wide spectrum of clinical severities. Although PMD is a rare monogenic disease, hundreds of mutations in the X-linked myelin gene proteolipid protein 1 (PLP1) have been identified in humans. Attempts to identify a common pathogenic process underlying PMD have been complicated by an incomplete understanding of PLP1 dysfunction and limited access to primary human oligodendrocytes. To address this, we generated panels of human induced pluripotent stem cells (hiPSCs) and hiPSC-derived oligodendrocytes from 12 individuals with mutations spanning the genetic and clinical diversity of PMD-including point mutations and duplication, triplication, and deletion of PLP1-and developed an in vitro platform for molecular and cellular characterization of all 12 mutations simultaneously...
April 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28366442/human-demographic-history-impacts-genetic-risk-prediction-across-diverse-populations
#17
Alicia R Martin, Christopher R Gignoux, Raymond K Walters, Genevieve L Wojcik, Benjamin M Neale, Simon Gravel, Mark J Daly, Carlos D Bustamante, Eimear E Kenny
The vast majority of genome-wide association studies (GWASs) are performed in Europeans, and their transferability to other populations is dependent on many factors (e.g., linkage disequilibrium, allele frequencies, genetic architecture). As medical genomics studies become increasingly large and diverse, gaining insights into population history and consequently the transferability of disease risk measurement is critical. Here, we disentangle recent population history in the widely used 1000 Genomes Project reference panel, with an emphasis on populations underrepresented in medical studies...
April 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28343630/de-novo-truncating-mutations-in-the-last-and-penultimate-exons-of-ppm1d-cause-an-intellectual-disability-syndrome
#18
Sandra Jansen, Sinje Geuer, Rolph Pfundt, Rachel Brough, Priyanka Ghongane, Johanna C Herkert, Elysa J Marco, Marjolein H Willemsen, Tjitske Kleefstra, Mark Hannibal, Joseph T Shieh, Sally Ann Lynch, Frances Flinter, David R FitzPatrick, Alice Gardham, Birgitta Bernhard, Nicola Ragge, Ruth Newbury-Ecob, Raphael Bernier, Malin Kvarnung, E A Helena Magnusson, Marja W Wessels, Marjon A van Slegtenhorst, Kristin G Monaghan, Petra de Vries, Joris A Veltman, Christopher J Lord, Lisenka E L M Vissers, Bert B A de Vries
Intellectual disability (ID) is a highly heterogeneous disorder involving at least 600 genes, yet a genetic diagnosis remains elusive in ∼35%-40% of individuals with moderate to severe ID. Recent meta-analyses statistically analyzing de novo mutations in >7,000 individuals with neurodevelopmental disorders highlighted mutations in PPM1D as a possible cause of ID. PPM1D is a type 2C phosphatase that functions as a negative regulator of cellular stress-response pathways by mediating a feedback loop of p38-p53 signaling, thereby contributing to growth inhibition and suppression of stress-induced apoptosis...
April 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28343629/biallelic-variants-in-otud6b-cause-an-intellectual-disability-syndrome-associated-with-seizures-and-dysmorphic-features
#19
Teresa Santiago-Sim, Lindsay C Burrage, Frédéric Ebstein, Mari J Tokita, Marcus Miller, Weimin Bi, Alicia A Braxton, Jill A Rosenfeld, Maher Shahrour, Andrea Lehmann, Benjamin Cogné, Sébastien Küry, Thomas Besnard, Bertrand Isidor, Stéphane Bézieau, Isabelle Hazart, Honey Nagakura, LaDonna L Immken, Rebecca O Littlejohn, Elizabeth Roeder, Bulent Kara, Katia Hardies, Sarah Weckhuysen, Patrick May, Johannes R Lemke, Orly Elpeleg, Bassam Abu-Libdeh, Kiely N James, Jennifer L Silhavy, Mahmoud Y Issa, Maha S Zaki, Joseph G Gleeson, John R Seavitt, Mary E Dickinson, M Cecilia Ljungberg, Sara Wells, Sara J Johnson, Lydia Teboul, Christine M Eng, Yaping Yang, Peter-Michael Kloetzel, Jason D Heaney, Magdalena A Walkiewicz
Ubiquitination is a posttranslational modification that regulates many cellular processes including protein degradation, intracellular trafficking, cell signaling, and protein-protein interactions. Deubiquitinating enzymes (DUBs), which reverse the process of ubiquitination, are important regulators of the ubiquitin system. OTUD6B encodes a member of the ovarian tumor domain (OTU)-containing subfamily of deubiquitinating enzymes. Herein, we report biallelic pathogenic variants in OTUD6B in 12 individuals from 6 independent families with an intellectual disability syndrome associated with seizures and dysmorphic features...
April 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28343628/functional-architectures-of-local-and-distal-regulation-of-gene-expression-in-multiple-human-tissues
#20
Xuanyao Liu, Hilary K Finucane, Alexander Gusev, Gaurav Bhatia, Steven Gazal, Luke O'Connor, Brendan Bulik-Sullivan, Fred A Wright, Patrick F Sullivan, Benjamin M Neale, Alkes L Price
Genetic variants that modulate gene expression levels play an important role in the etiology of human diseases and complex traits. Although large-scale eQTL mapping studies routinely identify many local eQTLs, the molecular mechanisms by which genetic variants regulate expression remain unclear, particularly for distal eQTLs, which these studies are not well powered to detect. Here, we leveraged all variants (not just those that pass stringent significance thresholds) to analyze the functional architecture of local and distal regulation of gene expression in 15 human tissues by employing an extension of stratified LD-score regression that produces robust results in simulations...
April 6, 2017: American Journal of Human Genetics
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