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American Journal of Human Genetics

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https://www.readbyqxmd.com/read/28215400/somatic-mutations-in-tsc1-and-tsc2-cause-focal-cortical-dysplasia
#1
Jae Seok Lim, Ramu Gopalappa, Se Hoon Kim, Suresh Ramakrishna, Minji Lee, Woo-Il Kim, Junho Kim, Sang Min Park, Junehawk Lee, Jung-Hwa Oh, Heung Dong Kim, Chang-Hwan Park, Joon Soo Lee, Sangwoo Kim, Dong Seok Kim, Jung Min Han, Hoon-Chul Kang, Hyongbum Henry Kim, Jeong Ho Lee
Focal cortical dysplasia (FCD) is a major cause of the sporadic form of intractable focal epilepsies that require surgical treatment. It has recently been reported that brain somatic mutations in MTOR account for 15%-25% of FCD type II (FCDII), characterized by cortical dyslamination and dysmorphic neurons. However, the genetic etiologies of FCDII-affected individuals who lack the MTOR mutation remain unclear. Here, we performed deep hybrid capture and amplicon sequencing (read depth of 100×-20,012×) of five important mTOR pathway genes-PIK3CA, PIK3R2, AKT3, TSC1, and TSC2-by using paired brain and saliva samples from 40 FCDII individuals negative for MTOR mutations...
February 12, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28190456/mutations-in-inpp5k-encoding-a-phosphoinositide-5-phosphatase-cause-congenital-muscular-dystrophy-with-cataracts-and-mild-cognitive-impairment
#2
Manuela Wiessner, Andreas Roos, Christopher J Munn, Ranjith Viswanathan, Tamieka Whyte, Dan Cox, Benedikt Schoser, Caroline Sewry, Helen Roper, Rahul Phadke, Chiara Marini Bettolo, Rita Barresi, Richard Charlton, Carsten G Bönnemann, Osório Abath Neto, Umbertina C Reed, Edmar Zanoteli, Cristiane Araújo Martins Moreno, Birgit Ertl-Wagner, Rolf Stucka, Christian De Goede, Tamiris Borges da Silva, Denisa Hathazi, Margherita Dell'Aica, René P Zahedi, Simone Thiele, Juliane Müller, Helen Kingston, Susanna Müller, Elizabeth Curtis, Maggie C Walter, Tim M Strom, Volker Straub, Kate Bushby, Francesco Muntoni, Laura E Swan, Hanns Lochmüller, Jan Senderek
Phosphoinositides are small phospholipids that control diverse cellular downstream signaling events. Their spatial and temporal availability is tightly regulated by a set of specific lipid kinases and phosphatases. Congenital muscular dystrophies are hereditary disorders characterized by hypotonia and weakness from birth with variable eye and central nervous system involvement. In individuals exhibiting congenital muscular dystrophy, early-onset cataracts, and mild intellectual disability but normal cranial magnetic resonance imaging, we identified bi-allelic mutations in INPP5K, encoding inositol polyphosphate-5-phosphatase K...
February 8, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28190458/detection-of-imprinted-genes-by-single-cell-allele-specific-gene-expression
#3
Federico A Santoni, Georgios Stamoulis, Marco Garieri, Emilie Falconnet, Pascale Ribaux, Christelle Borel, Stylianos E Antonarakis
Genomic imprinting results in parental-specific gene expression. Imprinted genes are involved in the etiology of rare syndromes and have been associated with common diseases such as diabetes and cancer. Standard RNA bulk cell sequencing applied to whole-tissue samples has been used to detect imprinted genes in human and mouse models. However, lowly expressed genes cannot be detected by using RNA bulk approaches. Here, we report an original and robust method that combines single-cell RNA-seq and whole-genome sequencing into an optimized statistical framework to analyze genomic imprinting in specific cell types and in different individuals...
February 6, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28190457/public-attitudes-toward-consent-and-data-sharing-in-biobank-research-a-large-multi-site-experimental-survey-in-the-us
#4
Saskia C Sanderson, Kyle B Brothers, Nathaniel D Mercaldo, Ellen Wright Clayton, Armand H Matheny Antommaria, Sharon A Aufox, Murray H Brilliant, Diego Campos, David S Carrell, John Connolly, Pat Conway, Stephanie M Fullerton, Nanibaa' A Garrison, Carol R Horowitz, Gail P Jarvik, David Kaufman, Terrie E Kitchner, Rongling Li, Evette J Ludman, Catherine A McCarty, Jennifer B McCormick, Valerie D McManus, Melanie F Myers, Aaron Scrol, Janet L Williams, Martha J Shrubsole, Jonathan S Schildcrout, Maureen E Smith, Ingrid A Holm
Individuals participating in biobanks and other large research projects are increasingly asked to provide broad consent for open-ended research use and widespread sharing of their biosamples and data. We assessed willingness to participate in a biobank using different consent and data sharing models, hypothesizing that willingness would be higher under more restrictive scenarios. Perceived benefits, concerns, and information needs were also assessed. In this experimental survey, individuals from 11 US healthcare systems in the Electronic Medical Records and Genomics (eMERGE) Network were randomly allocated to one of three hypothetical scenarios: tiered consent and controlled data sharing; broad consent and controlled data sharing; or broad consent and open data sharing...
February 4, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28190459/mutations-in-inpp5k-cause-a-form-of-congenital-muscular-dystrophy-overlapping-marinesco-sj%C3%A3-gren-syndrome-and-dystroglycanopathy
#5
Daniel P S Osborn, Heather L Pond, Neda Mazaheri, Jeremy Dejardin, Christopher J Munn, Khaloob Mushref, Edmund S Cauley, Isabella Moroni, Maria Barbara Pasanisi, Elizabeth A Sellars, R Sean Hill, Jennifer N Partlow, Rebecca K Willaert, Jaipreet Bharj, Reza Azizi Malamiri, Hamid Galehdari, Gholamreza Shariati, Reza Maroofian, Marina Mora, Laura E Swan, Thomas Voit, Francesco J Conti, Yalda Jamshidi, M Chiara Manzini
Congenital muscular dystrophies display a wide phenotypic and genetic heterogeneity. The combination of clinical, biochemical, and molecular genetic findings must be considered to obtain the precise diagnosis and provide appropriate genetic counselling. Here we report five individuals from four families presenting with variable clinical features including muscular dystrophy with a reduction in dystroglycan glycosylation, short stature, intellectual disability, and cataracts, overlapping both the dystroglycanopathies and Marinesco-Sjögren syndrome...
February 1, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28190455/who-s-who-detecting-and-resolving-sample-anomalies-in-human-dna-sequencing-studies-with-peddy
#6
Brent S Pedersen, Aaron R Quinlan
The potential for genetic discovery in human DNA sequencing studies is greatly diminished if DNA samples from a cohort are mislabeled, swapped, or contaminated or if they include unintended individuals. Unfortunately, the potential for such errors is significant since DNA samples are often manipulated by several protocols, labs, or scientists in the process of sequencing. We have developed a software package, peddy, to identify and facilitate the remediation of such errors via interactive visualizations and reports comparing the stated sex, relatedness, and ancestry to what is inferred from the individual genotypes derived from whole-genome (WGS) or whole-exome (WES) sequencing...
January 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28190454/somatic-map2k1-mutations-are-associated-with-extracranial-arteriovenous-malformation
#7
Javier A Couto, August Y Huang, Dennis J Konczyk, Jeremy A Goss, Steven J Fishman, John B Mulliken, Matthew L Warman, Arin K Greene
Arteriovenous malformation (AVM) is a fast-flow, congenital vascular anomaly that may arise anywhere in the body. AVMs typically progress, causing destruction of surrounding tissue and, sometimes, cardiac overload. AVMs are difficult to control; they often re-expand after embolization or resection, and pharmacologic therapy is unavailable. We studied extracranial AVMs in order to identify their biological basis. We performed whole-exome sequencing (WES) and whole-genome sequencing (WGS) on AVM tissue from affected individuals...
January 30, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28157543/mutations-in-mapkbp1-cause-juvenile-or-late-onset-cilia-independent-nephronophthisis
#8
Maxence S Macia, Jan Halbritter, Marion Delous, Cecilie Bredrup, Arthur Gutter, Emilie Filhol, Anne E C Mellgren, Sabine Leh, Albane Bizet, Daniela A Braun, Heon Y Gee, Flora Silbermann, Charline Henry, Pauline Krug, Christine Bole-Feysot, Patrick Nitschké, Dominique Joly, Philippe Nicoud, André Paget, Heidi Haugland, Damien Brackmann, Nayir Ahmet, Richard Sandford, Nurcan Cengiz, Per M Knappskog, Helge Boman, Bolan Linghu, Fan Yang, Edward J Oakeley, Pierre Saint Mézard, Andreas W Sailer, Stefan Johansson, Eyvind Rødahl, Sophie Saunier, Friedhelm Hildebrandt, Alexandre Benmerah
No abstract text is available yet for this article.
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28157542/the-rare-variant-generalized-disequilibrium-test-for-association-analysis-of-nuclear-and-extended-pedigrees-with-application-to-alzheimer-disease-wgs-data
#9
Zongxiao He, Di Zhang, Alan E Renton, Biao Li, Linhai Zhao, Gao T Wang, Alison M Goate, Richard Mayeux, Suzanne M Leal
No abstract text is available yet for this article.
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28157541/the-genetic-architecture-of-gene-expression-in-peripheral-blood
#10
Luke R Lloyd-Jones, Alexander Holloway, Allan McRae, Jian Yang, Kerrin Small, Jing Zhao, Biao Zeng, Andrew Bakshi, Andres Metspalu, Manolis Dermitzakis, Greg Gibson, Tim Spector, Grant Montgomery, Tonu Esko, Peter M Visscher, Joseph E Powell
No abstract text is available yet for this article.
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28157540/large-intragenic-deletion-in-dstyk-underlies-autosomal-recessive-complicated-spastic-paraparesis-spg23
#11
John Y W Lee, Chao-Kai Hsu, Magdalene Michael, Arti Nanda, Lu Liu, James R McMillan, Celine Pourreyron, Takuya Takeichi, Jakub Tolar, Evan Reid, Thomas Hayday, Sergiu C Blumen, Saif Abu-Mouch, Rachel Straussberg, Lina Basel-Vanagaite, Yael Barhum, Yasmin Zouabi, Hejab Al-Ajmi, Hsin-Yu Huang, Ting-Chien Lin, Masashi Akiyama, Julia Y Y Lee, W H Irwin McLean, Michael A Simpson, Maddy Parsons, John A McGrath
SPG23 is an autosomal-recessive neurodegenerative subtype of lower limb spastic paraparesis with additional diffuse skin and hair dyspigmentation at birth followed by further patchy pigment loss during childhood. Previously, genome-wide linkage in an Arab-Israeli pedigree mapped the gene to an approximately 25 cM locus on chromosome 1q24-q32. By using whole-exome sequencing in a further Palestinian-Jordanian SPG23 pedigree, we identified a complex homozygous 4-kb deletion/20-bp insertion in DSTYK (dual serine-threonine and tyrosine protein kinase) in all four affected family members...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28157539/the-undiagnosed-diseases-network-accelerating-discovery-about-health-and-disease
#12
Rachel B Ramoni, John J Mulvihill, David R Adams, Patrick Allard, Euan A Ashley, Jonathan A Bernstein, William A Gahl, Rizwan Hamid, Joseph Loscalzo, Alexa T McCray, Vandana Shashi, Cynthia J Tifft, Anastasia L Wise
Diagnosis at the edges of our knowledge calls upon clinicians to be data driven, cross-disciplinary, and collaborative in unprecedented ways. Exact disease recognition, an element of the concept of precision in medicine, requires new infrastructure that spans geography, institutional boundaries, and the divide between clinical care and research. The National Institutes of Health (NIH) Common Fund supports the Undiagnosed Diseases Network (UDN) as an exemplar of this model of precise diagnosis. Its goals are to forge a strategy to accelerate the diagnosis of rare or previously unrecognized diseases, to improve recommendations for clinical management, and to advance research, especially into disease mechanisms...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28132693/biallelic-mutation-of-arhgef18-involved-in-the-determination-of-epithelial-apicobasal-polarity-causes-adult-onset-retinal-degeneration
#13
Gavin Arno, Keren J Carss, Sarah Hull, Ceniz Zihni, Anthony G Robson, Alessia Fiorentino, Alison J Hardcastle, Graham E Holder, Michael E Cheetham, Vincent Plagnol, Anthony T Moore, F Lucy Raymond, Karl Matter, Maria S Balda, Andrew R Webster
Mutations in more than 250 genes are implicated in inherited retinal dystrophy; the encoded proteins are involved in a broad spectrum of pathways. The presence of unsolved families after highly parallel sequencing strategies suggests that further genes remain to be identified. Whole-exome and -genome sequencing studies employed here in large cohorts of affected individuals revealed biallelic mutations in ARHGEF18 in three such individuals. ARHGEF18 encodes ARHGEF18, a guanine nucleotide exchange factor that activates RHOA, a small GTPase protein that is a key component of tight junctions and adherens junctions...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28132692/a-recurrent-de-novo-variant-in-nacc1-causes-a-syndrome-characterized-by-infantile-epilepsy-cataracts-and-profound-developmental-delay
#14
Kelly Schoch, Linyan Meng, Szabolcs Szelinger, David R Bearden, Asbjorg Stray-Pedersen, Oyvind L Busk, Nicholas Stong, Eriskay Liston, Ronald D Cohn, Fernando Scaglia, Jill A Rosenfeld, Jennifer Tarpinian, Cara M Skraban, Matthew A Deardorff, Jeremy N Friedman, Zeynep Coban Akdemir, Nicole Walley, Mohamad A Mikati, Peter G Kranz, Joan Jasien, Allyn McConkie-Rosell, Marie McDonald, Stephanie Burns Wechsler, Michael Freemark, Sujay Kansagra, Sharon Freedman, Deeksha Bali, Francisca Millan, Sherri Bale, Stanley F Nelson, Hane Lee, Naghmeh Dorrani, David B Goldstein, Rui Xiao, Yaping Yang, Jennifer E Posey, Julian A Martinez-Agosto, James R Lupski, Michael F Wangler, Vandana Shashi
Whole-exome sequencing (WES) has increasingly enabled new pathogenic gene variant identification for undiagnosed neurodevelopmental disorders and provided insights into both gene function and disease biology. Here, we describe seven children with a neurodevelopmental disorder characterized by microcephaly, profound developmental delays and/or intellectual disability, cataracts, severe epilepsy including infantile spasms, irritability, failure to thrive, and stereotypic hand movements. Brain imaging in these individuals reveals delay in myelination and cerebral atrophy...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28132691/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, 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
Degradation of proteins by the ubiquitin-proteasome system (UPS) is an essential biological process in the development of eukaryotic organisms. Dysregulation of this mechanism leads to numerous human neurodegenerative or neurodevelopmental disorders. Through a multi-center collaboration, we identified six de novo genomic deletions and four de novo point mutations involving PSMD12, encoding the non-ATPase subunit PSMD12 (aka RPN5) of the 19S regulator of 26S proteasome complex, in unrelated individuals with intellectual disability, congenital malformations, ophthalmologic anomalies, feeding difficulties, deafness, and subtle dysmorphic facial features...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28132690/mutations-in-extl3-cause-neuro-immuno-skeletal-dysplasia-syndrome
#16
Machteld M Oud, Paul Tuijnenburg, Maja Hempel, Naomi van Vlies, Zemin Ren, Sacha Ferdinandusse, Machiel H Jansen, René Santer, Jessika Johannsen, Chiara Bacchelli, Marielle Alders, Rui Li, Rosalind Davies, Lucie Dupuis, Catherine M Cale, Ronald J A Wanders, Steven T Pals, Louise Ocaka, Chela James, Ingo Müller, Kai Lehmberg, Tim Strom, Hartmut Engels, Hywel J Williams, Phil Beales, Ronald Roepman, Patricia Dias, Han G Brunner, Jan-Maarten Cobben, Christine Hall, Taila Hartley, Polona Le Quesne Stabej, Roberto Mendoza-Londono, E Graham Davies, Sérgio B de Sousa, Davor Lessel, Heleen H Arts, Taco W Kuijpers
EXTL3 regulates the biosynthesis of heparan sulfate (HS), important for both skeletal development and hematopoiesis, through the formation of HS proteoglycans (HSPGs). By whole-exome sequencing, we identified homozygous missense mutations c.1382C>T, c.1537C>T, c.1970A>G, and c.2008T>G in EXTL3 in nine affected individuals from five unrelated families. Notably, we found the identical homozygous missense mutation c.1382C>T (p.Pro461Leu) in four affected individuals from two unrelated families. Affected individuals presented with variable skeletal abnormalities and neurodevelopmental defects...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28132689/biallelic-mutations-in-dnajc12-cause-hyperphenylalaninemia-dystonia-and-intellectual-disability
#17
Yair Anikster, Tobias B Haack, Thierry Vilboux, Ben Pode-Shakked, Beat Thöny, Nan Shen, Virginia Guarani, Thomas Meissner, Ertan Mayatepek, Friedrich K Trefz, Dina Marek-Yagel, Aurora Martinez, Edward L Huttlin, Joao A Paulo, Riccardo Berutti, Jean-François Benoist, Apolline Imbard, Imen Dorboz, Gali Heimer, Yuval Landau, Limor Ziv-Strasser, May Christine V Malicdan, Corinne Gemperle-Britschgi, Kirsten Cremer, Hartmut Engels, David Meili, Irene Keller, Rémy Bruggmann, Tim M Strom, Thomas Meitinger, James C Mullikin, Gerard Schwartz, Bruria Ben-Zeev, William A Gahl, J Wade Harper, Nenad Blau, Georg F Hoffmann, Holger Prokisch, Thomas Opladen, Manuel Schiff
Phenylketonuria (PKU, phenylalanine hydroxylase deficiency), an inborn error of metabolism, can be detected through newborn screening for hyperphenylalaninemia (HPA). Most individuals with HPA harbor mutations in the gene encoding phenylalanine hydroxylase (PAH), and a small proportion (2%) exhibit tetrahydrobiopterin (BH4) deficiency with additional neurotransmitter (dopamine and serotonin) deficiency. Here we report six individuals from four unrelated families with HPA who exhibited progressive neurodevelopmental delay, dystonia, and a unique profile of neurotransmitter deficiencies without mutations in PAH or BH4 metabolism disorder-related genes...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28132688/intervar-clinical-interpretation-of-genetic-variants-by-the-2015-acmg-amp-guidelines
#18
Quan Li, Kai Wang
In 2015, the American College of Medical Genetics and Genomics (ACMG) and the Association for Molecular Pathology (AMP) published updated standards and guidelines for the clinical interpretation of sequence variants with respect to human diseases on the basis of 28 criteria. However, variability between individual interpreters can be extensive because of reasons such as the different understandings of these guidelines and the lack of standard algorithms for implementing them, yet computational tools for semi-automated variant interpretation are not available...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28132687/neurocalcin-delta-suppression-protects-against-spinal-muscular-atrophy-in-humans-and-across-species-by-restoring-impaired-endocytosis
#19
Markus Riessland, Anna Kaczmarek, Svenja Schneider, Kathryn J Swoboda, Heiko Löhr, Cathleen Bradler, Vanessa Grysko, Maria Dimitriadi, Seyyedmohsen Hosseinibarkooie, Laura Torres-Benito, Miriam Peters, Aaradhita Upadhyay, Nasim Biglari, Sandra Kröber, Irmgard Hölker, Lutz Garbes, Christian Gilissen, Alexander Hoischen, Gudrun Nürnberg, Peter Nürnberg, Michael Walter, Frank Rigo, C Frank Bennett, Min Jeong Kye, Anne C Hart, Matthias Hammerschmidt, Peter Kloppenburg, Brunhilde Wirth
Homozygous SMN1 loss causes spinal muscular atrophy (SMA), the most common lethal genetic childhood motor neuron disease. SMN1 encodes SMN, a ubiquitous housekeeping protein, which makes the primarily motor neuron-specific phenotype rather unexpected. SMA-affected individuals harbor low SMN expression from one to six SMN2 copies, which is insufficient to functionally compensate for SMN1 loss. However, rarely individuals with homozygous absence of SMN1 and only three to four SMN2 copies are fully asymptomatic, suggesting protection through genetic modifier(s)...
February 2, 2017: American Journal of Human Genetics
https://www.readbyqxmd.com/read/28132686/decreased-stard10-expression-is-associated-with-defective-insulin-secretion-in-humans-and-mice
#20
Gaelle R Carrat, Ming Hu, Marie-Sophie Nguyen-Tu, Pauline Chabosseau, Kyle J Gaulton, Martijn van de Bunt, Afshan Siddiq, Mario Falchi, Matthias Thurner, Mickaël Canouil, Francois Pattou, Isabelle Leclerc, Timothy J Pullen, Matthew C Cane, Priyanka Prabhala, William Greenwald, Anke Schulte, Piero Marchetti, Mark Ibberson, Patrick E MacDonald, Jocelyn E Manning Fox, Anna L Gloyn, Philippe Froguel, Michele Solimena, Mark I McCarthy, Guy A Rutter
Genetic variants near ARAP1 (CENTD2) and STARD10 influence type 2 diabetes (T2D) risk. The risk alleles impair glucose-induced insulin secretion and, paradoxically but characteristically, are associated with decreased proinsulin:insulin ratios, indicating improved proinsulin conversion. Neither the identity of the causal variants nor the gene(s) through which risk is conferred have been firmly established. Whereas ARAP1 encodes a GTPase activating protein, STARD10 is a member of the steroidogenic acute regulatory protein (StAR)-related lipid transfer protein family...
February 2, 2017: American Journal of Human Genetics
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