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Human Mutation

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https://www.readbyqxmd.com/read/28730625/fgf9-mutation-causes-craniosynostosis-along-with-multiple-synostoses
#1
Maria Rodriguez-Zabala, Miriam Aza-Carmona, Carlos I Rivera-Pedroza, Alberta Belinchón, Isabel Guerrero-Zapata, Jimena Barraza-García, Elena Vallespin, Min Lu, Angela Del Pozo, Marc J Glucksman, Fernando Santos-Simarro, Karen E Heath
Craniosynostosis is commonly caused by mutations in fibroblast growth factor receptors, highlighting the essential role of FGF-mediated signalling in skeletal development. We set out to identify the molecular defect in a family referred for craniosynostosis and in whom no mutation was previously detected. Using Next-generation sequencing, we identified a novel missense mutation in FGF9. Modelling based upon the crystal structure and functional studies confirmed its pathogenicity showing that it impaired homodimerization and FGFR3 binding...
July 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/28726266/survival-among-children-with-lethal-congenital-contracture-syndrome-11-caused-by-novel-mutations-in-the-gliomedin-gene-gldn
#2
Jennifer A Wambach, Georg M Stettner, Tobias B Haack, Karin Writzl, Andreja Škofljanec, Aleš Maver, Francina Munell, Stephan Ossowski, Mattia Bosio, Daniel J Wegner, Marwan Shinawi, Dustin Baldridge, Bader Alhaddad, Tim M Strom, Dorothy K Grange, Ekkehard Wilichowski, Robin Troxell, James Collins, Barbara B Warner, Robert E Schmidt, Alan Pestronk, F Sessions Cole, Robert Steinfeld
Biallelic GLDN mutations have recently been identified among infants with lethal congenital contracture syndrome 11 (LCCS11). GLDN encodes gliomedin, a protein required for the formation of the nodes of Ranvier and development of the human peripheral nervous system. We report 6 infants and children from 4 unrelated families with biallelic GLDN mutations, 4 of whom survived beyond the neonatal period into infancy, childhood, and late adolescence with intensive care and chronic respiratory and nutritional support...
July 20, 2017: Human Mutation
https://www.readbyqxmd.com/read/28722338/hdr-del-a-tool-based-on-hamming-distance-for-prioritizing-pathogenic-chromosomal-deletions-in-exome-sequencing
#3
Atsuko Imai, Masakazu Kohda, Kaori Kobayashi, Tomoko Hirata, Yasushi Sakata, Kei Murayama, Akira Ohtake, Yasushi Okazaki, Akihiro Nakaya, Jurg Ott
High-density oligonucleotide arrays have been widely used to detect pathogenic chromosomal deletions. In addition to high-density oligonucleotide arrays, programs using whole exome sequencing have become available for estimating copy number variations using depth of coverage. Here we propose a new statistical method, HDR-del, to prioritize pathogenic chromosomal deletions based on Hamming distance in exome sequencing. In vcf (Variant Call Format) files generated from exome sequencing, hemizygous chromosomal deletion regions lack heterozygous variants and lead to apparent long runs of homozygosity (ROH)...
July 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28722276/identification-and-functional-analysis-of-an-adamtsl1-variant-associated-with-a-complex-phenotype-including-congenital-glaucoma-craniofacial-and-other-systemic-features-in-a-three-generation-human-pedigree
#4
Kathryn Hendee, Lauren Weiping Wang, Linda M Reis, Gregory M Rice, Suneel S Apte, Elena V Semina
Developmental glaucoma can occur as an isolated or syndromic condition and is genetically heterogeneous. We describe a three-generation family affected with developmental glaucoma, myopia, and/or retinal defects associated with variable craniofacial/dental, auditory, brain, renal, and limb anomalies. Whole exome sequencing identified a heterozygous c.124T> C, p.(Trp42Arg) allele in ADAMTSL1; co-segregation analysis confirmed the presence of this allele in four affected family members. The mutation affects a highly conserved residue and is strongly predicted to have a deleterious effect on protein function...
July 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28714244/the-role-of-de-novo-mutations-in-the-development-of-amyotrophic-lateral-sclerosis
#5
Perry Tc van Doormaal, Nicola Ticozzi, Jochen H Weishaupt, Kevin Kenna, Frank P Diekstra, Federico Verde, Peter M Andersen, Annelot M Dekker, Cinzia Tiloca, Nicolai Marroquin, Daniel J Overste, Viviana Pensato, Peter Nürnberg, Sara L Pulit, Raymond D Schellevis, Daniela Calini, Janine Altmüller, Laurent C Francioli, Bernard Muller, Barbara Castellotti, Susanne Motameny, Antonia Ratti, Joachim Wolf, Cinzia Gellera, Albert C Ludolph, Leonard H van den Berg, Christian Kubisch, John E Landers, Jan H Veldink, Vincenzo Silani, Alexander E Volk
The genetic basis combined with the sporadic occurrence of amyotrophic lateral sclerosis (ALS) suggests a role of de novo mutations in disease pathogenesis. Previous studies provided some evidence for this hypothesis, however results were conflicting: no genes with recurrent occurring de novo mutations were identified and different pathways were postulated. In this study we analyzed whole-exome data from 82 new patient-parents trios and combined it with the datasets of all previously published amyotrophic lateral sclerosis trios (173 trios in total)...
July 17, 2017: Human Mutation
https://www.readbyqxmd.com/read/28714225/leveraging-splice-affecting-variant-predictors-and-a-minigene-validation-system-to-identify-mendelian-disease-causing-variants-amongst-exon-captured-variants-of-uncertain-significance
#6
Zachry T Soens, Justin Branch, Shijing Wu, Zhisheng Yuan, Yumei Li, Hui Li, Keqing Wang, Mingchu Xu, Lavan Rajan, Fabiana L Motta, Renata T Simões, Irma Lopez-Solache, Radwan Ajlan, David G Birch, Peiquan Zhao, Fernanda B Porto, Juliana Sallum, Robert K Koenekoop, Ruifang Sui, Rui Chen
The genetic heterogeneity of Mendelian disorders results in a significant proportion of patients that are unable to be assigned a confident molecular diagnosis after conventional exon sequencing and variant interpretation. Here we evaluated how many patients with an inherited retinal disease (IRD) have variants of uncertain significance (VUS's) that are disrupting splicing in a known IRD gene by means other than affecting the canonical dinucleotide splice site. Three in silico splice-affecting variant predictors were leveraged to annotate and prioritize variants for splicing functional validation...
July 17, 2017: Human Mutation
https://www.readbyqxmd.com/read/28714182/rare-coding-variants-in-mapk7-predispose-to-adolescent-idiopathic-scoliosis
#7
Wenjie Gao, Chong Chen, Taifeng Zhou, Shulan Yang, Bo Gao, Hang Zhou, Chengjie Lian, Zizhao Wu, Xianjian Qiu, Xiaoming Yang, Esam Alattar, Wentao Liu, Deying Su, Silong Sun, Yulan Chen, Kenneth M C Cheung, Youqiang Song, Keith K D Luk, Danny Chan, Pak Chung Sham, Chao Xing, Chiea Chuen Khor, Gabriel Liu, Junlin Yang, Yubin Deng, Dingjun Hao, Dongsheng Huang, Quan-Zhen Li, Caixia Xu, Peiqiang Su
Adolescent idiopathic scoliosis (AIS) is a complex genetic disorder characterized by three-dimensional spinal curvatures, affecting 2-3% of school age children, yet the causes underlying AIS are not well understood. Here, we firstly conducted a whole-exome sequencing and linkage analysis on a three-generation Chinese family with autosomal dominant (AD) AIS, then performed targeted sequencing in a discovery cohort comprising 20 AD-AIS families and 86 simplex patients, and finally identified three disease-associated missense variants (c...
July 17, 2017: Human Mutation
https://www.readbyqxmd.com/read/28703315/using-whole-exome-sequencing-to-investigate-the-genetic-bases-of-lysosomal-storage-diseases-of-unknown-etiology
#8
Nan Wang, Yeting Zhang, Erika Gedvilaite, Jui Wan Loh, Timothy Lin, Xiuping Liu, Chang-Gong Liu, Dibyendu Kumar, Robert Donnelly, Kimiyo Raymond, Edward H Schuchman, David E Sleat, Peter Lobel, Jinchuan Xing
Lysosomes are membrane-bound, acidic eukaryotic cellular organelles that play important roles in the degradation of macromolecules. Mutations that cause the loss of lysosomal protein function can lead to a group of disorders categorized as the lysosomal storage diseases (LSDs). Suspicion of LSD is frequently based on clinical and pathologic findings, but in some cases, the underlying genetic and biochemical defects remain unknown. Here, we performed whole exome sequencing (WES) on 14 suspected LSD cases to evaluate the feasibility of using WES for identifying causal mutations...
July 12, 2017: Human Mutation
https://www.readbyqxmd.com/read/28681398/analysis-of-large-scale-sequencing-cohorts-does-not-support-the-role-of-variants-in-ucp2-as-a-cause-of-hyperinsulinaemic-hypoglycaemia
#9
LETTER
Thomas W Laver, Michael N Weedon, Richard Caswell, Khalid Hussain, Sian Ellard, Sarah E Flanagan
No abstract text is available yet for this article.
July 5, 2017: Human Mutation
https://www.readbyqxmd.com/read/28677295/boc-is-a-modifier-gene-in-holoprosencephaly
#10
Mingi Hong, Kshitij Srivastava, Sungjin Kim, Benjamin L Allen, Daniel J Leahy, Ping Hu, Erich Roessler, Robert S Krauss, Maximilian Muenke
Holoprosencephaly (HPE), a common developmental defect of the forebrain and midface, has a complex etiology. Heterozygous, loss-of-function mutations in the Sonic hedgehog (SHH) pathway are associated with HPE. However, mutation carriers display highly variable clinical presentation, leading to an "autosomal dominant with modifier" model, in which the penetrance and expressivity of a predisposing mutation is graded by genetic or environmental modifiers. Such modifiers have not been identified. Boc encodes a SHH co-receptor and is a silent HPE modifier gene in mice...
July 4, 2017: Human Mutation
https://www.readbyqxmd.com/read/28677221/characterization-of-cryptic-splicing-in-germline-pten-intronic-variants-in-cowden-syndrome
#11
Hannah Jinlian Chen, Todd Romigh, Kaitlin Sesock, Charis Eng
Germline mutations in the tumor suppressor gene PTEN predispose to subsets of Cowden syndrome, Bannayan-Riley-Ruvalcaba syndrome and autism. Evidence-based classification of PTEN variants as either deleterious or benign is urgently needed for accurate molecular diagnosis and gene-informed genetic counseling. We studied 34 different germline PTEN intronic variants from 61 Cowden syndrome patients, characterized their PTEN mRNA processing and analyzed PTEN expression and downstream readouts of P-AKT and P-ERK1/2...
July 4, 2017: Human Mutation
https://www.readbyqxmd.com/read/28677207/new-role-of-lrp5-associated-with-non-syndromic-autosomal-recessive-hereditary-hearing-loss
#12
Wenjun Xia, Jiongjiong Hu, Fei Liu, Jing Ma, Shaoyang Sun, Jin Zhang, Kaiyue Jin, Jianbo Huang, Nan Jiang, Xu Wang, Wenwen Li, Zhaoxin Ma, Duan Ma
Human hearing loss is a common neurosensory disorder about which many basic research and clinically relevant questions are unresolved. And at least 50% of hearing loss are due to a genetic etiology. Although hundreds of genes have been reported, there were still hundreds of related deafness genes to be found. Clinical, genetic, and functional investigations were performed to identify the causative mutation in a distinctive Chinese family with post-lingual non-syndromic sensorineural hearing loss. Whole-exome sequencing identified lipoprotein receptor-related protein 5 (LRP5), a member of the low-density lipoprotein receptor family, as the causative gene in this family...
July 4, 2017: Human Mutation
https://www.readbyqxmd.com/read/28675565/compound-heterozygosity-for-loss-of-function-gars-variants-results-in-a-multisystem-developmental-syndrome-that-includes-severe-growth-retardation
#13
Stephanie N Oprescu, Xenia Chepa-Lotrea, Ryuichi Takase, Gretchen Golas, Thomas C Markello, David R Adams, Camilo Toro, Andrea L Gropman, Ya-Ming Hou, May Christine V Malicdan, William A Gahl, Cynthia J Tifft, Anthony Antonellis
Aminoacyl-tRNA synthetases (ARSs) are ubiquitously expressed enzymes that ligate amino acids onto tRNA molecules. Genes encoding ARSs have been implicated in myriad dominant and recessive disease phenotypes. Glycyl-tRNA synthetase (GARS) is a bifunctional ARS that charges tRNA(Gly) in the cytoplasm and mitochondria. GARS variants have been associated with dominant Charcot-Marie-Tooth disease but have not been convincingly implicated in recessive phenotypes. Here, we describe a patient from the NIH Undiagnosed Diseases Program with a multisystem, developmental phenotype...
July 4, 2017: Human Mutation
https://www.readbyqxmd.com/read/28649782/heterozygous-variants-in-actl6a-encoding-a-component-of-the-baf-complex-are-associated-with-intellectual-disability
#14
Ronit Marom, Mahim Jain, Lindsay C Burrage, I-Wen Song, Brett H Graham, Chester W Brown, Servi J C Stevens, Alexander P A Stegmann, Andrew T Gunter, Julie D Kaplan, Ralitza H Gavrilova, Marwan Shinawi, Jill A Rosenfeld, Yangjin Bae, Alyssa A Tran, Yuqing Chen, James T Lu, Richard A Gibbs, Christine Eng, Yaping Yang, Justine Rousseau, Bert B A de Vries, Philippe M Campeau, Brendan Lee
Pathogenic variants in genes encoding components of the BAF chromatin remodeling complex have been associated with intellectual disability syndromes. We identified heterozygous, novel variants in ACTL6A, a gene encoding a component of the BAF complex, in three subjects with varying degrees of intellectual disability. Two subjects have missense variants affecting highly conserved amino acid residues within the actin-like domain. Missense mutations in the homologous region in yeast actin were previously reported to be dominant lethal and were associated with impaired binding of the human ACTL6A to β-actin and BRG1...
June 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28649752/investigating-dna-rna-and-protein-based-features-as-a-means-to-discriminate-pathogenic-synonymous-variants
#15
Mark Livingstone, Lukas Folkman, Yuedong Yang, Ping Zhang, Matthew Mort, David N Cooper, Yunlong Liu, Bela Stantic, Yaoqi Zhou
Synonymous single nucleotide variants (SNVs), although they do not alter the encoded protein sequences, have been implicated in many genetic diseases. Experimental studies indicate that synonymous SNVs can lead to changes in the secondary and tertiary structures of DNA and RNA, thereby impacting translational efficiency, co-translational protein folding as well as the binding of DNA/RNA-binding proteins. However, the importance of these various features in disease phenotypes is not clearly understood. Here we have built a support vector machine model (termed DDIG-SN) as a means to discriminate disease-causing synonymous variants...
June 25, 2017: Human Mutation
https://www.readbyqxmd.com/read/28639312/quantification-of-transmission-risk-in-a-male-patient-with-a-flnb-mosaic-mutation-causing-larsen-syndrome-implications-for-genetic-counselling-in-post-zygotic-mosaicism-cases
#16
Marie Bernkopf, David Hunt, Nils Koelling, Tim Morgan, Amanda L Collins, Joanna Fairhurst, Stephen P Robertson, Andrew G L Douglas, Anne Goriely
We report the case of a male patient with Larsen syndrome found to be mosaic for a novel point mutation in FLNB in whom it was possible to provide evidence-based personalised counselling on transmission risk to future offspring. Using dideoxy-sequencing, a low-level FLNB c.698A>G, encoding p.(Tyr233Cys) mutation was detected in buccal mucosa and fibroblast DNA. Mutation quantification was performed by deep Next-Generation sequencing (NGS) of DNA extracted from three somatic tissues (blood, fibroblasts, saliva) and a sperm sample...
June 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/28634997/working-toward-precision-medicine-predicting-phenotypes-from-exomes-in-the-critical-assessment-of-genome-interpretation-cagi-challenges
#17
Roxana Daneshjou, Yanran Wang, Yana Bromberg, Samuele Bovo, Pier L Martelli, Giulia Babbi, Pietro Di Lena, Rita Casadio, Matthew Edwards, David Gifford, David T Jones, Laksshman Sundaram, Rajendra Bhat, Xiaolin Li, Lipika R Pal, Kunal Kundu, Yizhou Yin, John Moult, Yuxiang Jiang, Vikas Pejaver, Kymberleigh A Pagel, Biao Li, Sean D Mooney, Predrag Radivojac, Sohela Shah, Marco Carraro, Alessandra Gasparini, Emanuela Leonardi, Manuel Giollo, Carlo Ferrari, Silvio C E Tosatto, Eran Bachar, Johnathan R Azaria, Yanay Ofran, Ron Unger, Abhishek Niroula, Mauno Vihinen, Billy Chang, Maggie H Wang, Andre Franke, Britt-Sabina Petersen, Mehdi Pirooznia, Peter Zandi, Richard McCombie, James B Potash, Russ B Altman, Teri E Klein, Roger A Hoskins, Susanna Repo, Steven E Brenner, Alexander A Morgan
Precision medicine aims to predict a patient's disease risk and best therapeutic options by using that individual's genetic sequencing data. The Critical Assessment of Genome Interpretation (CAGI) is a community experiment consisting of genotype-phenotype prediction challenges; participants build models, undergo assessment, and share key findings. For CAGI 4, three challenges involved using exome-sequencing data: Crohn's disease, bipolar disorder, and warfarin dosing. Previous CAGI challenges included prior versions of the Crohn's disease challenge...
June 21, 2017: Human Mutation
https://www.readbyqxmd.com/read/28699299/-matching-consent-to-purpose-the-example-of-the-matchmaker-exchange
#18
Stephanie O M Dyke, Bartha M Knoppers, Ada Hamosh, Helen V Firth, Matthew Hurles, Michael Brudno, Kym M Boycott, Anthony A Philippakis, Heidi L Rehm
The Matchmaker Exchange (MME) connects rare disease clinicians and researchers to facilitate the sharing of data from undiagnosed patients for the purpose of novel gene discovery. Such sharing raises the odds that two or more similar patients with candidate genes in common may be found, thereby allowing their condition to be more readily studied and understood. Consent considerations for data sharing in MME included both the ethical and legal differences between clinical and research settings and the level of privacy risk involved in sharing varying amounts of rare disease patient data to enable patient matches...
June 14, 2017: Human Mutation
https://www.readbyqxmd.com/read/28608363/misynpat-an-integrated-knowledge-base-linking-clinical-genetic-and-structural-data-for-disease-causing-mutations-in-human-mitochondrial-aminoacyl-trna-synthetases
#19
Luc Moulinier, Raymond Ripp, Gaston Castillo, Olivier Poch, Marie Sissler
Numerous mutations in each of the mitochondrial aminoacyl-tRNA synthetases have been implicated in human diseases. The mutations are autosomal and recessive and lead mainly to neurological disorders, although with pleiotropic effects. The processes and interactions that drive the etiology of the disorders associated with mitochondrial aminoacyl-tRNA synthetases are far from understood. The complexity of the clinical, genetic and structural data requires concerted, interdisciplinary efforts to understand the molecular biology of these disorders...
June 12, 2017: Human Mutation
https://www.readbyqxmd.com/read/28603918/cftr-france-a-national-relational-patient-database-for-sharing-genetic-and-phenotypic-data-associated-with-rare-cftr-variants-a
#20
Mireille Claustres, Corinne Theze, Marie des Georges, David Baux, Emmanuelle Girodon, Thierry Bienvenu, Marie-Pierre Audrezet, Ingrid Dugueperoux, Claude Ferec, Guy Lalau, Adrien Pagin, Alain Kitzis, Vincent Thoreau, Véronique Gaston, Eric Bieth, Marie-Claire Malinge, Marie-Pierre Reboul, Patricia Fergelot, Lydie Lemonnier, Chadia Mekki, Pascale Fanen, Anne Bergougnoux, Souphatta Sasorith, Caroline Raynal, Corinne Bareil
Most of 2,000 variants identified in the CFTR (cystic fibrosis transmembrane regulator) gene are rare or private. Their interpretation is hampered by the lack of available data and resources, making patient care and genetic counseling challenging. We developed a patient-based database dedicated to the annotations of rare CFTR variants in the context of their cis- and trans-allelic combinations. Based on almost 30 years' experience of CFTR testing, CFTR-France (https://cftr.iurc.montp.inserm.fr/cftr) currently compiles 16,819 variant records from 4,615 individuals with cystic fibrosis (CF) or CFTR-RD (related disorders), fetuses with ultrasound bowel anomalies, newborns awaiting clinical diagnosis and asymptomatic compound heterozygotes...
June 12, 2017: Human Mutation
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