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A knowledge-based approach to predict intragenic deletions or duplications

Krishna R. Kalari, Thomas L. Casavant, Todd E. Scheetz
2008 Computer applications in the biosciences : CABIOS  
We have developed a novel computational system, SPeeDD (system to prioritize deletions or duplications) that utilizes machine learning techniques to predict likely candidate regions that delete or duplicate  ...  Several studies have identified deletions or duplications occurring within a gene that directly cause or predispose to disease.  ...  ACKNOWLEDGEMENTS The authors thank Dr Andy Peek (IDT-Integrated DNA Technology) for providing early access to the TmAlign program for accurate  ... 
doi:10.1093/bioinformatics/btn370 pmid:18647756 fatcat:5ipivxjcizcjfo7fqh6icrmkem

Next generation sequencing-based copy number analysis reveals low prevalence of deletions and duplications in 46 genes associated with genetic cardiomyopathies

Ozge Ceyhan-Birsoy, Trevor J. Pugh, Mark J. Bowser, Elizabeth Hynes, Ashley L. Frisella, Lisa M. Mahanta, Matt S. Lebo, Sami S. Amr, Birgit H. Funke
2015 Molecular Genetics & Genomic Medicine  
Clinically significant intragenic deletions Four intragenic deletions (in LAMP2, LMNA, MYBPC3, and PKP2) were predicted to lead to truncated or absent proteins and were classified as pathogenic or likely  ...  One consequence of this historical separation of technologies and approaches is a largely unexplored class of small, intragenic single or multi exons deletions and duplications.  ... 
doi:10.1002/mgg3.187 pmid:27066507 pmcid:PMC4799872 fatcat:lrhsfs7f5nd4zjoadrxxlym37u

Epilepsy and outcome inFOXG1-related disorders

Laurie E. Seltzer, Mandy Ma, Sohnee Ahmed, Mary Bertrand, William B. Dobyns, James Wheless, Alex R. Paciorkowski
2014 Epilepsia  
We report on the epilepsy features and developmental outcome of 23 new subjects with deletions or intragenic mutations of FOXG1, and 7 subjects with duplications.  ...  The mean age of epilepsy diagnosis in FOXG1 duplications was significantly younger than those with deletions/intragenic mutations (p=0.0002).  ...  R01NS058721 (to W.B.D.), the Child Neurology Foundation Logan Infantile Spasms Award (to A.R.P), and K08NS078054 (to A.R.P.).  ... 
doi:10.1111/epi.12648 pmid:24836831 pmcid:PMC4265461 fatcat:v6uzcvnm7negnk2sc4c2pyxpea

Clinical utility gene card for: Axenfeld–Rieger syndrome

Nicole Weisschuh, Elfride De Baere, Bernd Wissinger, Zeynep Tümer
2010 European Journal of Human Genetics  
FISH, MLPA, Q-PCR or high-resolution microarrays for detection of submicroscopic deletions/duplications.  ...  In case of large deletions/duplications, confirmation with a second technique.  ... 
doi:10.1038/ejhg.2010.163 pmid:20940740 pmcid:PMC3061995 fatcat:c4rej4hgf5anbnsumgb6tqdjxi

Prevalence and properties of intragenic copy-number variation in Mendelian disease genes

Rebecca Truty, Joshua Paul, Michael Kennemer, Stephen E. Lincoln, Eric Olivares, Robert L. Nussbaum, Swaroop Aradhya
2018 Genetics in Medicine  
We investigated the frequencies and characteristics of intragenic copy-number variants (CNVs) in a deep sampling of disease genes associated with monogenic disorders.  ...  Although exome-based approaches are beginning to shed light on these CNVs, the resolution and confidence of CNV calling with these methods remains limited. 1,2 Exon-focused microarray-based comparative  ...  For at least 30 duplications, we observed putative breakpoints based on splitread sequence data and predicted a tandem arrangement that would disrupt the transcript reading frame.  ... 
doi:10.1038/s41436-018-0033-5 pmid:29895855 pmcid:PMC6752305 fatcat:tblwya576nesfnq4xun74wijhu

Characterization of clinically relevant copy-number variants from exomes of patients with inherited heart disease and unexplained sudden cardiac death

Emma S. Singer, Samantha B. Ross, Jon R. Skinner, Robert G. Weintraub, Jodie Ingles, Christopher Semsarian, Richard D. Bagnall
2020 Genetics in Medicine  
Haplotype analysis of a deletion in ACTN2, found in two families, suggests the deletion was caused by an ancestral event.  ...  Characterization of breakpoint junctions revealed nonhomologous end joining was responsible for four deletions, whereas one duplication was caused by nonallelic homologous recombination between duplicated  ...  Publisher's note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.  ... 
doi:10.1038/s41436-020-00970-5 pmid:32973354 fatcat:yqtwjmiqirb53gnhvnrws24xim

Improved molecular diagnosis by the detection of exonic deletions with target gene capture and deep sequencing

Yanming Feng, David Chen, Guo-Li Wang, Victor Wei Zhang, Lee-Jun C. Wong
2014 Genetics in Medicine  
deletions. results: Thirty-eight samples, each containing 2,134, 2,833, or 4,688 coding exons from different panels, with a total of 103,863 exons, were analyzed by capture-massively parallel sequencing  ...  both point mutations and exonic deletions, thus improving the diagnostic power of massively parallel sequencing-based assays.  ...  This study was partially supported by a Muscular Dystrophy Association grant to L.-J.C.W.  ... 
doi:10.1038/gim.2014.80 pmid:25032985 pmcid:PMC4338802 fatcat:zrq4hmbghrdqlnbynmcuohaykq

New insights into genetic variant spectrum and genotype–phenotype correlations of Rubinstein‐Taybi syndrome in 39 CREBBP‐ positive patients

Virginia Pérez‐Grijalba, Alberto García‐Oguiza, María López, Judith Armstrong, Sixto García‐Miñaur, Jose María Mesa‐Latorre, Mar O'Callaghan, Mercé Pineda Marfa, Maria Antonia Ramos‐Arroyo, Fernando Santos‐Simarro, Verónica Seidel, Elena Domínguez‐Garrido
2019 Molecular Genetics & Genomic Medicine  
A wide range of CREBBP pathogenic variants have been reported so far, including point mutations (30%-50%) and large deletions (10%).  ...  Rubinstein-Taybi syndrome (RSTS) is a rare congenital disorder characterized by broad thumbs and halluces, intellectual disability, distinctive facial features, and growth retardation.  ...  ACKNOWLEDGMENTS We thank the patients and families for participating in this study, with special acknowledgment to the Spanish Rubinstein-Taybi Association.  ... 
doi:10.1002/mgg3.972 pmid:31566936 pmcid:PMC6825870 fatcat:asvf6va4o5e5pmjpraau3iuirq

AR intragenic deletions linked to androgen receptor splice variant expression and activity in models of prostate cancer progression

Y Li, T H Hwang, L A Oseth, A Hauge, R L Vessella, S C Schmechel, B Hirsch, K B Beckman, K A Silverstein, S M Dehm
2012 Oncogene  
In a previous study, we demonstrated that altered AR splicing in CRPCa 22Rv1 cells was linked to a 35-kb intragenic tandem duplication of AR exon 3 and flanking sequences.  ...  Similarly, targeted resequencing of the AR gene in CWR-R1 cells led to the discovery of a 48-kb deletion in AR intron 1.  ...  SMD is a Masonic Scholar of the Masonic Cancer Center, University of Minnesota.  ... 
doi:10.1038/onc.2011.637 pmid:22266865 pmcid:PMC3337879 fatcat:6bg7ojt6b5di5mxd6gfbqke4ai

Non-deletion mutations in Egyptian patients with Duchenne muscular dystrophy

Rabah M. Shawky, Solaf M. Elsayed, Theodor Todorov, Andree Zibert, Salem Alawbathani, Hartmut H.-J. Schmidt
2014 Egyptian Journal of Medical Human Genetics  
Direct sequencing of the whole dystrophin gene was done to those patients who had no deletion or duplication by the previous 2 methods.  ...  Aim: To study non-deletion mutations in a sample of Egyptian patients with DMD as most previous studies focused on deletion mutations.  ...  The authors declared no potential conflicts of interests with respect to the authorship and/or publication of this article.  ... 
doi:10.1016/j.ejmhg.2014.03.004 fatcat:de4fsujz3zh2vlpwhp6phorhja

Mutation update for the SATB2 gene

Yuri A. Zarate, Katherine A. Bosanko, Aislling R. Caffrey, Jonathan A. Bernstein, Donna M. Martin, Marc S. Williams, Elizabeth M. Berry‐Kravis, Paul R. Mark, Melanie A. Manning, Vikas Bhambhani, Marcelo Vargas, Andrea H. Seeley (+36 others)
2019 Human Mutation  
Single nucleotide variants predicted to result in the occurrence of a premature stop codon were the most commonly seen (51/120 = 42.5%) followed by missense variants (31/120 = 25.8%).  ...  Here we present a review of published pathogenic variants in the SATB2 gene to date and report 38 novel alterations found in 57 additional previously unreported individuals.  ...  ACKNOWLEDGMENTS The authors are grateful to all participating families. B.C is a senior clinical investigator of the Research Foundation-Flanders.  ... 
doi:10.1002/humu.23771 pmid:31021519 fatcat:w7wn3kia2vez7ig7s53drhr54u

Molecular Diagnosis of Neuromuscular Disease

Jadranka Sertic
2004 EJIFCC  
Southern blotting Southern blotting is the method for detection of deletions or duplications of one or more exons of the gene.  ...  About 65%-70% of patients show intragenic deletions of one or several exons of the gene that can be detected by multiplex PCR or Southern blotting.  ... 
pmid:29988971 pmcid:PMC6034194 fatcat:227ebdx4uvhv7a3jeuzaty7qka

Aberrant firing of replication origins potentially explains intragenic nonrecurrent rearrangements within genes, including the human DMD gene

A. Ankala, J. N. Kohn, A. Hegde, A. Meka, C. L. H. Ephrem, S. H. Askree, S. Bhide, M. R. Hegde
2011 Genome Research  
To further investigate the mutation mechanisms of these copy number variations (CNVs), we performed breakpoint mapping analysis for 62 clinical cases with intragenic deletions in the human DMD gene (50  ...  With a deeper insight into the complex process of replication and its rescue during origin failure, brought forward by recent studies, we propose a hypothesis based on aberrant firing of replication origins  ...  Acknowledgments This work was supported, in part, by NIH grant 1RC1NS 069541-01 and MDA grant MDA138896 to M.R.H.  ... 
doi:10.1101/gr.123463.111 pmid:22090376 pmcid:PMC3246204 fatcat:ctahskkcrncn7i7hkup3573hee

Duchenne and Becker muscular dystrophies: An Indian update on genetics and rehabilitation

JayshreeJ Nadkarni, RashnaS Dastur, V Viswanathan, PradnyaS Gaitonde, SatishV Khadilkar
2008 Neurology India  
The prediction of Duchenne muscular dystrophy (DMD) patients to have out-framed deletions and Becker's muscular dystrophy (BMD) patients to have in-frame deletions of dystrophin gene holds well in the  ...  [1] Probably, due to the large size of the gene, the rate of mutations is high with the majority of mutations being intragenic deletions or duplications.  ...  Whether this is a polymorphism or, related to the disease phenotype needs further confirmation.  ... 
doi:10.4103/0028-3886.43442 pmid:18974550 fatcat:f6dfz6xwp5gkfdq6nzdzx7e2xa

Long-Read Sequencing Revealed Extragenic and Intragenic Duplications of Exons 56–61 in DMD in an Asymptomatic Male and a DMD Patient

Ying Bai, Ju Liu, Jinghan Xu, Yue Sun, Jingjing Li, Yong Gao, Lina Liu, Cangcang Jia, Xiangdong Kong, Li Wang
2022 Frontiers in Genetics  
To the best of our knowledge, this is the first report of a breakpoint analysis of DMD duplication in two men with different phenotypes.  ...  Expanded carrier screening (ECS) has become an increasingly common technique to assess the genetic risks of individuals in the prenatal or preconception period.  ...  ACKNOWLEDGMENTS The authors are very grateful to the families for participating in this study and appreciate Beijing GrandOmics Biosciences Biotechnology Co., Ltd., for the technical support in Nanopore  ... 
doi:10.3389/fgene.2022.878806 pmid:35615378 pmcid:PMC9125615 fatcat:fuo6eqd3xbhbfjdfiwsqxnomye
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