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Detection of internal exon deletion with exon Del

Yan Guo, Shilin Zhao, Brian D Lehmann, Quanhu Sheng, Timothy M Shaver, Thomas P Stricker, Jennifer A Pietenpol, Yu Shyr
2014 BMC Bioinformatics  
Internal exon deletions are the absence of consecutive exons in a gene.  ...  Among the many types of variants detectable through exome sequencing, one of the most over looked types of mutation is internal deletion of exons.  ...  The TCGA data was downloaded with approved request 14085-3 from dbGAP of NIH. We would also like to thank Margot Bjoring for editorial support.  ... 
doi:10.1186/1471-2105-15-332 pmid:25322818 pmcid:PMC4288651 fatcat:2d3w3ue62vf3let7qqag2dbaoa

Microarray-based mutation detection in thedystrophingene

Madhuri R. Hegde, Ephrem L.H. Chin, Jennifer G. Mulle, David T. Okou, Stephen T. Warren, Michael E. Zwick
2008 Human Mutation  
The mutational spectrum of disease-causing alleles, including exonic copy number variations (CNVs), is complex. Deletions account for approximately 65% of DMD mutations and 85% of BMD mutations.  ...  Duplications occur in approximately 6 to 10% of males with either DMD or BMD.  ...  Sue Richards of the OHSU DNA Diagnostic Laboratory and Dr. Don Love of LabPLUS, Auckland Hospital, New Zealand for providing positive controls.  ... 
doi:10.1002/humu.20831 pmid:18663755 pmcid:PMC2574813 fatcat:cteu2ac4ufhcjauubopnzvmhem

Detecting exon deletions and duplications of the DMD gene using Multiplex Ligation-dependent Probe Amplification (MLPA)

Kent K.S. Lai, Ivan F.M. Lo, Tony M.F. Tong, Lydia Y.L. Cheng, Stephen T.S. Lam
2006 Clinical Biochemistry  
It should be the method of choice for the detection of exon deletions and duplications of the DMD gene in patients with DMD or BMD, as well as in female carriers.  ...  Objectives: To evaluate the efficacy of Multiplex Ligation-dependent Probe Amplification (MLPA) technique in comparison with the traditional multiplex PCR assay in detection of exon deletions and duplications  ...  Sample no. 45 was found to have deletion of exons 65-76 and was further confirmed by PCR with internal primers.  ... 
doi:10.1016/j.clinbiochem.2005.11.019 pmid:16413013 fatcat:4rm3xp44wveifi5yohrkpxscvi

Log-PCR: A New Tool for Immediate and Cost-Effective Diagnosis of up to 85% of Dystrophin Gene Mutations

A. Trimarco, A. Torella, G. Piluso, V. Maria Ventriglia, L. Politano, V. Nigro
2008 Clinical Chemistry  
Novel techniques with higher detection rates, such as multiplex ligation-dependent probe amplification and multiplex amplifiable probe hybridization, have been introduced.  ...  RESULTS: We observed gross rearrangements in 428 of the patients (84.6%; 74.5% deletions and 10.1% duplications).  ...  We acknowledge the SUN-Naples Human Mutation Gene Bank (Cardiomyology and Medical Genetics), which is a partner of the EuroBioBank network.  ... 
doi:10.1373/clinchem.2007.097881 pmid:18403565 fatcat:5iof5ban7na7dka5hbb6lj3dbq

Exon-level array CGH in a large clinical cohort demonstrates increased sensitivity of diagnostic testing for Mendelian disorders

Swaroop Aradhya, Rachel Lewis, Tahrra Bonaga, Nnenna Nwokekeh, Amanda Stafford, Barbara Boggs, Kathleen Hruska, Nizar Smaoui, John G. Compton, Gabriele Richard, Sharon Suchy
2012 Genetics in Medicine  
Approximately 40% of positive findings were deletions of only one or two exons. A high frequency of deletions was observed for several auto-somal dominant disorders, with a detection rate of 2.9%.  ...  with probes in exonic regions of 589 genes.  ...  For Peutz-Jeghers syndrome, 10 out of 31 patients (32%) with negative sequencing results carried a deletion detected by exon array CGH in the STK11 gene.  ... 
doi:10.1038/gim.2011.65 pmid:22382802 fatcat:oej3dxngbrfzridbzma5uixgti

Apparent Homozygosity of a Novel Frame Shift Mutation in the CFTR Gene Because of a Large Deletion

Feras M. Hantash, Arlene Rebuyon, Mei Peng, Joy B. Redman, Weimin Sun, Charles M. Strom
2009 Journal of Molecular Diagnostics  
We present here a patient with classic cystic fibrosis who has a novel microdeletion in exon 7 on one allele and a large deletion encompassing exon 7 on the second allele.  ...  Patients develop cystic fibrosis because of a variety of homozygous recessive mutations , including single nucleotide polymorphisms , insertions , and deletions, in the cystic fibrosis transmembrane regulator  ...  presence of large exon deletions.  ... 
doi:10.2353/jmoldx.2009.080117 pmid:19324987 pmcid:PMC2671343 fatcat:4eq33pol6rca3cvhvspo7zz32q

Exclusion of Exon 2 Is a Common mRNA Splice Variant of Primate Telomerase Reverse Transcriptases

Johanna B. Withers, Tamara Ashvetiya, Karen L. Beemon, Bin Tian
2012 PLoS ONE  
Internal mammalian exons are usually short, typically only 50 to 300 nucleotides, and most long internal exons are alternatively processed.  ...  We were interested in examining splicing of the 59 half of hTERT mRNA, especially since exon 2 is unusually large (1.3 kb).  ...  Acknowledgments We wish to thank Mohan Bolisetty for contributing to the analysis of hTERT deep sequencing data and for helpful discussions.  ... 
doi:10.1371/journal.pone.0048016 pmid:23110161 pmcid:PMC3480478 fatcat:n4rqfzzmynfm5otej6yndgppzm

Genetic diagnosis of Duchenne/Becker muscular dystrophy using next-generation sequencing: Validation analysis of DMD mutations

M. Okubo, N. Minami, K. Goto, S. Noguchi, S. Mitsuhashi, I. Nishino
2016 Neuromuscular Disorders  
The results were compared with those from MLPA or Sanger sequencing. All deletions were detected. In contrast, 50% of duplications were correctly identified compared with the MLPA method.  ...  Although MLPA can diagnose 70% of DMD/BMD patients having deletions/duplications, the remaining 30% of patients with small mutations require further analysis, such as Sanger sequencing.  ...  This problem can also occur with MLPA when it detects a single exon deletion.  ... 
doi:10.1016/j.nmd.2016.06.041 fatcat:asxihxbi65hxnpj4u7cklzaana

Genetic diagnosis of Duchenne/Becker muscular dystrophy using next-generation sequencing: validation analysis of DMD mutations

Mariko Okubo, Narihiro Minami, Kanako Goto, Yuichi Goto, Satoru Noguchi, Satomi Mitsuhashi, Ichizo Nishino
2016 Journal of Human Genetics  
The results were compared with those from MLPA or Sanger sequencing. All deletions were detected. In contrast, 50% of duplications were correctly identified compared with the MLPA method.  ...  Although MLPA can diagnose 70% of DMD/BMD patients having deletions/duplications, the remaining 30% of patients with small mutations require further analysis, such as Sanger sequencing.  ...  This problem can also occur with MLPA when it detects a single exon deletion.  ... 
doi:10.1038/jhg.2016.7 pmid:26911353 pmcid:PMC4931045 fatcat:p3o54tc2f5girbydzogkdvd2qy

Comparison of Mutation Profiles in the Duchenne Muscular Dystrophy Gene among Populations: Implications for Potential Molecular Therapies

Luz López-Hernández, Benjamín Gómez-Díaz, Alexandra Luna-Angulo, Mónica Anaya-Segura, David Bunyan, Carolina Zúñiga-Guzman, Rosa Escobar-Cedillo, Bladimir Roque-Ramírez, Luis Ruano-Calderón, Héctor Rangel-Villalobos, Julia López-Hernández, Francisco Estrada-Mena (+2 others)
2015 International Journal of Molecular Sciences  
Some of the molecular therapies, such as exon skipping, stop codon read-through and internal ribosome entry site-mediated translation rely on the type and location of mutations.  ...  In view of this, we compared the mutation profiles of the populations represented in the DMD Leiden Open-source Variation Database with original data from Mexican patients (n = 162) with clinical diagnosis  ...  Sample collection was financed with grants from the Secretaría de Salud and Administración del Patrimonio de la Beneficencia Pública (APBP) and Asociación de Distrofia Muscular de Occidente A.C.  ... 
doi:10.3390/ijms16035334 pmid:25761239 pmcid:PMC4394478 fatcat:jft65zdxjjazljzqhhybumk62e

Quantum dots immunofluorescence histochemical detection of EGFR gene mutations in the non-small cell lung cancers using mutation-specific antibodies

Hong-Lei Chen, Yan-Gang Qu, Qian-qian Zhang, Qi Pan, Xian-Da Zhao, Yan-Hua Huang, Fu-Chun Chen
2014 International Journal of Nanomedicine  
Acknowledgment This research is supported by the Natural Science Foundation of China (number 30900652).  ...  Of the 26 patients with positive QDs-IHC staining, all of the EGFR mutations (exon 19 deletion and exon 21 L858R mutation) were detected by ADx-ARMS; however, ADx-ARMS could detect four cases of exon 18  ...  Mutations associated with enhanced sensitivity to EGFR-TKIs are found in exons 18-21 of the TK domain of EGFR; in particular, del E746-A750 in exon 19 and the L858R point mutation in exon 21 account for  ... 
doi:10.2147/ijn.s71310 pmid:25525358 pmcid:PMC4266265 fatcat:chc5aalo6neghikhsgcozamiwm

Whole-gene APC deletions cause classical familial adenomatous polyposis, but not attenuated polyposis or "multiple" colorectal adenomas

O. M. Sieber, H. Lamlum, M. D. Crabtree, A. J. Rowan, E. Barclay, L. Lipton, S. Hodgson, H. J. W. Thomas, K. Neale, R. K. S. Phillips, S. M. Farrington, M. G. Dunlop (+9 others)
2002 Proceedings of the National Academy of Sciences of the United States of America  
We have developed a real-time quantitative multiplex PCR assay to detect APC exon 14 deletions.  ...  Routine mutation detection techniques fail to detect a pathogenic APC germ-line mutation in approximately 30% of patients with classical polyposis and 90% of those with AAPC͞multiple adenomas.  ...  Friedl (University of Bonn), and G. Taylor (St. James's University Hospital, Leeds, U.K.) for kindly providing control samples.  ... 
doi:10.1073/pnas.042699199 pmid:11867715 pmcid:PMC122454 fatcat:tqnxkph4jvcpzhag2ilqaon3cy

Characterization of large rearrangements in autosomal dominant polycystic kidney disease and the PKD1/TSC2 contiguous gene syndrome

Mark B. Consugar, Wai C. Wong, Patrick A. Lundquist, Sandro Rossetti, Vickie J. Kubly, Denise L. Walker, Laureano J. Rangel, Richard Aspinwall, W. Patrick Niaudet, Seza Özen, Albert David, Milen Velinov (+10 others)
2008 Kidney International  
Our assay improves detection levels and the reliability of molecular testing of patients with ADPKD.  ...  All changes in a set of 25 previously defined deletions in PKD1, PKD2 and PKD1/TSC2 were detected by this assay and we also found 14 new mutations at these loci.  ...  (a) MLPA analysis of patient with large deletion of PKD2 region (P964 12 ) and case with deletion of exon 5 (M363).  ... 
doi:10.1038/ki.2008.485 pmid:18818683 pmcid:PMC2756756 fatcat:x237mojls5cc7oa7wqqfcf2rle

Quality Assurance for Duchenne and Becker Muscular Dystrophy Genetic Testing

Lisa Kalman, Jay Leonard, Norman Gerry, Jack Tarleton, Christina Bridges, Julie M. Gastier-Foster, Robert E. Pyatt, Eileen Stonerock, Monique A. Johnson, C. Sue Richards, Iris Schrijver, Tianhui Ma (+5 others)
2011 Journal of Molecular Diagnostics  
Approximately 65% of patients with DMD have deletions, 7% to 10% have duplications, and 25% to 30% have point mutations in one or more of the 79 exons of the dystrophin gene.  ...  Most clinical genetics laboratories test for deletions, and some use technologies that can detect smaller mutations and duplications.  ...  We also thank the patients with DMD and their families, whose donated blood provided an invaluable resource for this project and for biomedical research.  ... 
doi:10.1016/j.jmoldx.2010.11.018 pmid:21354051 pmcid:PMC3128550 fatcat:f6rx4g76nzdt7ag5xrld5btbqe

Identification and characterization of large deletions in the phenylalanine hydroxylase (PAH) gene by MLPA: Evidence for both homologous and non-homologous mechanisms of rearrangement

Libor Kozak, Eva Hrabincova, Jaromir Kintr, Ondrej Horky, Petra Zapletalova, Ivona Blahakova, Pavel Mejstrik, Dagmar Prochazkova
2006 Molecular Genetics and Metabolism  
We conclude that MLPA is a convenient, rapid and reliable method for detection of intragenic deletions in the PAH gene and that a relatively high number of alleles with large deletions are present in the  ...  Nineteen cases exhibited deletion of exon 5, and 12 cases provided evidence for the deletion of exon 3.  ...  This work was supported by Grant IGA NR 8451-3/2005 of the Ministry of Health, Czech Republic.  ... 
doi:10.1016/j.ymgme.2006.06.007 pmid:16931086 fatcat:ykbui5genzgjzksmme5tb5epry
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