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Intronic Mutation

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https://www.readbyqxmd.com/read/29052111/targeted-massively-parallel-sequencing-characterises-the-mutation-spectrum-of-palb2-in-breast-and-ovarian-cancer-cases-from-poland-and-ukraine
#1
Aleksander Myszka, Tu Nguyen-Dumont, Pawel Karpinski, Maria M Sasiadek, Hayane Akopyan, Fleur Hammet, Helen Tsimiklis, Daniel J Park, Bernard J Pope, Ryszard Slezak, Nataliya Kitsera, Aleksandra Siekierzynska, Melissa C Southey
Loss-of-function germline mutations in the PALB2 gene are associated with an increase of breast cancer risk. The purpose of this study was to characterise the spectrum of PALB2 mutations in women affected with breast or ovarian cancer from South-West Poland and West Ukraine. We applied Hi-Plex, an amplicon-based enrichment method for targeted massively parallel sequencing, to screen the coding exons and proximal intron-exon junctions of PALB2 in germline DNA from unrelated women affected with breast cancer (n = 338) and ovarian cancer (n = 89) from Poland (n = 304) and Ukraine (n = 123)...
October 19, 2017: Familial Cancer
https://www.readbyqxmd.com/read/29048736/novel-recessive-pdzd7-biallelic-mutations-in-two-chinese-families-with-non-syndromic-hearing-loss
#2
Jing Guan, Hongyang Wang, Lan Lan, Li Wang, Ju Yang, Linyi Xie, Zifang Yin, Wenping Xiong, Lidong Zhao, Dayong Wang, Qiuju Wang
Autosomal recessive non-syndromic hearing loss (ARNSHL) is a highly heterogeneous genetic condition. PDZD7 has emerged as a new genetic etiology of ARNSHL. Biallelic mutations in the PDZD7 gene have been reported in two German families, four Iranian families, and a Pakistani family with ARNSHL. The effect of PDZD7 on ARNSHL in other population has yet to be elucidated. Two Chinese ARNSHL families, each of which had two affected siblings, were included in this study. The families underwent target region capture and high-throughput sequencing to analyze the exonic, splice-site, and intronic sequences of 128 genes...
October 19, 2017: American Journal of Medical Genetics. Part A
https://www.readbyqxmd.com/read/29046685/comparative-analysis-of-the-complete-plastomes-of-apostasia-wallichii-and-neuwiedia-singapureana-apostasioideae-reveals-different-evolutionary-dynamics-of-ir-ssc-boundary-among-photosynthetic-orchids
#3
Zhitao Niu, Jiajia Pan, Shuying Zhu, Ludan Li, Qingyun Xue, Wei Liu, Xiaoyu Ding
Apostasioideae, consists of only two genera, Apostasia and Neuwiedia, which are mainly distributed in Southeast Asia and northern Australia. The floral structure, taxonomy, biogeography, and genome variation of Apostasioideae have been intensively studied. However, detailed analyses of plastome composition and structure and comparisons with those of other orchid subfamilies have not yet been conducted. Here, the complete plastome sequences of Apostasia wallichii and Neuwiedia singapureana were sequenced and compared with 43 previously published photosynthetic orchid plastomes to characterize the plastome structure and evolution in the orchids...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/29045058/loop-mediated-isothermal-amplification-lamp-as-an-alternative-to-pcr-a-rapid-on-site-detection-of-gene-doping
#4
Olivier Salamin, Tiia Kuuranne, Martial Saugy, Nicolas Leuenberger
Innovation in medical research has been diverted at multiple occasions to enhance human performance. The predicted great progress in gene therapy has raised some concerns regarding its misuse in the world of sports (gene doping) for several years now. Even though there is no evidence that gene doping has ever been used in sports, the continuous improvement of gene therapy techniques increases the likelihood of abuse. Therefore, since 2004, efforts have been invested by the anti-doping community and WADA for the development of detection methods...
October 17, 2017: Drug Testing and Analysis
https://www.readbyqxmd.com/read/29044877/sustained-fxn-expression-in-dorsal-root-ganglia-from-a-nonreplicative-genomic-hsv-1-vector
#5
Maria Ventosa, Zetang Wu, Filip Lim
BACKGROUND: Friedreich's ataxia (FA) is an autosomal recessive neurodegenerative disease caused by mutations in the frataxin gene (FXN), which lead to reduced levels of the essential mitochondrial protein frataxin. Currently there is no effective cure. METHODS: With the aim of developing a gene therapy for FA neuropathology, here we describe the construction and preliminary characterization of a high capacity nonreplicative genomic herpes simplex virus type 1 vector (H24B-FXNlac vector) carrying a reduced version of the human FXN genomic locus, comprising the 5 kb promoter and the FXN cDNA with the inclusion of intron 1...
October 17, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/29039010/identification-of-pseudogenes-in-brachypodium-distachyon-chromosomes
#6
Salvatore Camiolo, Andrea Porceddu
Pseudogenes are gene copies that have lost the capability to encode a functional protein. Based on their structure, pseudogenes are classified in two types. Processed pseudogenes arise by a process of retrotranscription from a spliced mRNA and subsequent integration into the genome. Nonprocessed (or duplicated) pseudogenes are generated by genomic duplication and subsequent mutations that disable their functionality so that they cannot longer encode a functional protein. Differently from processed pseudogenes, duplicated pseudogenes are expected to conserve the exon-intron structure of their functional paralogs...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29036614/identification-of-a-candidate-mutation-in-the-col1a2-gene-of-a-chow-chow-with-osteogenesis-imperfecta
#7
E M Quist, R Doan, R R Pool, B F Porter, D L Bannasch, S V Dindot
Osteogenesis imperfecta (OI) is a genetic disease that occurs in humans and animals. Individuals with OI exhibit signs of extreme bone fragility and osteopenia with frequent fractures and perinatal lethality in severe cases. In this study, we report the clinical diagnosis of OI in a dog and the use targeted next-generation sequencing to identify a candidate autosomal dominant mutation in the COL1A2 gene. A five-month old male Chow Chow was examined with a fractured left humerus and resolving, bilateral femoral fractures...
September 19, 2017: Journal of Heredity
https://www.readbyqxmd.com/read/29036491/transcription-associated-compositional-skews-in-drosophila-genes
#8
Juraj Bergman, Andrea J Betancourt, Claus Vogl
In many organisms, local deviations from Chargaff's second parity rule are observed around replication and transcription start sites and within intron sequences. Here, we use expression data as well as a whole-genome dataset of nearly 200 haplotypes to investigate such compositional skews in Drosophila melanogaster genes. We find a positive correlation between compositional skew and gene expression, comparable in strength to similar correlations between expression levels and genome-wide sequence features. This correlation is relatively stronger for germline, compared to somatic expression, consistent with the process of transcription-associated mutation bias...
September 25, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/29035608/f508del-cftr-gene-mutation-in-patients-with-allergic-bronchopulmonary-aspergillosis
#9
Maria N Gamaletsou, Gemma Hayes, Chris Harris, Joanna Brock, Eavan G Muldoon, David W Denning
OBJECTIVE: The F508del mutation occurs in approximately 3.5% of Caucasian population of Northern Europe. Heterozygotes have increased risk for asthma and reduced pulmonary function. Allergic bronchopulmonary aspergillosis (ABPA) is more common in patients with cystic fibrosis (CF). We aimed to establish the frequency of F508del mutation in adult patients with ABPA. METHODS: A retrospective matched case-control study of CF genotyped patients with ABPA seen at the National Aspergillosis Centre was undertaken...
October 16, 2017: Journal of Asthma: Official Journal of the Association for the Care of Asthma
https://www.readbyqxmd.com/read/29028823/novel-mutations-in-darier-disease-and-association-to-self-reported-disease-severity
#10
Ivone U S Leong, Alexander Stuckey, Tara Ahanian, Martin Cederlöf, Jakob D Wikstrom
Darier disease is a rare and severe autosomal dominant skin disease characterised by malodorous keratotic papules in seborrheic areas of the skin. Darier disease affects up to 1 in 30 000 people and is caused by mutations in the ATP2A2 gene, which encodes to the sarco/endoplasmic reticulum calcium-ATPase isoform 2 that pumps calcium into the endoplasmic reticulum. Although many ATP2A2 variants have been described, it is not known if genotype correlates with phenotype, which could be important for prognosis and treatment...
2017: PloS One
https://www.readbyqxmd.com/read/29027900/rna-polymerase-ii-stalling-at-pre-mrna-splice-sites-is-enforced-by-ubiquitination-of-the-catalytic-subunit
#11
Laura Milligan, Camille Sayou, Alex Tuck, Tatsiana Auchynnikava, Jane E A Reid, Ross Alexander, Flavia de Lima Alves, Robin Allshire, Christos Spanos, Juri Rappsilber, Jean D Beggs, Grzegorz Kudla, David Tollervey
Numerous links exist between co-transcriptional RNA processing and the transcribing RNAPII. In particular, pre-mRNA splicing was reported to be associated with slowed RNAPII elongation. Here we identify a site of ubiquitination (K1246) in the catalytic subunit of RNAPII close to the DNA entry path. Ubiquitination was increased in the absence of the Bre5-Ubp3 ubiquitin protease complex. Bre5 binds RNA in vivo, with a preference for exon 2 regions of intron-containing pre-mRNAs and poly(A) proximal sites. Ubiquitinated RNAPII showed similar enrichment...
October 13, 2017: ELife
https://www.readbyqxmd.com/read/29023873/juvenile-elastoma-without-germline-mutations-in-lemd3-gene-a-case-of-buschke-ollendorff-syndrome
#12
Alessandra Condorelli, Nicolo Musso, Laura Scuderi, Daniele F Condorelli, Vincenza Barresi, Rocco De Pasquale
We report the case of a 6-year-old Caucasian girl with clinical and histopathologic features of Buschke-Ollendorff syndrome. Histologic examination of skin lesions showed thick, curly, elastic fibers in the derma. Bone lesions compatible with Buschke-Ollendorff syndrome were found in the girl's mother. Mutations in LEMD3 are pathogenic for Buschke-Ollendorff syndrome. Analysis of all exons and exon-intron junctions of LEMD3 did not reveal any germline mutations.
October 10, 2017: Pediatric Dermatology
https://www.readbyqxmd.com/read/28993503/myh9-e1841k-mutation-augments-proteinuria-and-podocyte-injury-and-migration
#13
Sylvia Cechova, Fan Dong, Fang Chan, Michael J Kelley, Phillip Ruiz, Thu H Le
Intronic variants of the MYH9 gene that encodes the nonmuscle myosin heavy chain IIA are associated with diabetic nephropathy in European Americans and with sickle cell disease-associated nephropathy. However, the causal functional variants of MYH9 have remained elusive. Rare missense mutations in MYH9 cause macrothrombocytopenia and are occasionally associated with development of nephropathy. The E1841K mutation is among the common MYH9 missense mutations and has been associated with nephropathy in some carriers...
October 9, 2017: Journal of the American Society of Nephrology: JASN
https://www.readbyqxmd.com/read/28992378/grem2-nucleotide-variants-and-the-risk-of-tooth-agenesis
#14
Adrianna Mostowska, Barbara Biedziak, Małgorzata Zadurska, Agnieszka Bogdanowicz, Aneta Olszewska, Katarzyna Cieślińska, Ewa Firlej, Paweł P Jagodziński
OBJECTIVE: The etiology of tooth agenesis is multifactorial and still not fully understood. The aim of the study was to test whether variants of GREM2, encoding a BMP antagonist, are associated with the risk of this common dental anomaly in a Polish population. SUBJECTS AND METHODS: Direct sequencing of the GREM2 coding sequence including exon/intron boundaries was performed in 95 patients with both hypodontia and oligodontia. All identified GREM2 variants were then further tested in an independent group of patients (n=163) and controls (n=184)...
October 9, 2017: Oral Diseases
https://www.readbyqxmd.com/read/28990043/%C3%AE-he-genetics-of-juvenile-idiopathic-arthritis-searching-for-new-susceptibility-loci
#15
Maria I Zervou, Despoina G Dimopoulou, Elias Eliopoulos, Maria Trachana, Polyxeni Pratsidou-Gkertsi, Athena Andreou, Prodromos Sidiropoulos, Demetrios A Spandidos, Alexandros Garyfallos, George N Goulielmos
Juvenile idiopathic arthritis (JIA) is an autoimmune disease that is characterized by persistent chronic arthritis and affected by genetic and environmental factors. Different genetic variations have been reported as risk factors for JIA. However, given that many results could not be replicated in individuals of different ancestral origin, it was assumed that heterogeneous genetic factors are involved in this disease. In the present study, we analyzed three single nucleotide polymorphisms (SNPs), namely PTPRC (rs10919563), TYK2 (rs34536443) and PRKCQ (rs4750316), which were found to be associated with JIA in previous studies...
October 5, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28984674/targeted-genomic-profiling-reveals-recurrent-kras-mutations-in-mesonephric-like-adenocarcinomas-of-the-female-genital-tract
#16
Jelena Mirkovic, Marie McFarland, Elizabeth Garcia, Lynette M Sholl, Neal Lindeman, Laura MacConaill, Fei Dong, Michelle Hirsch, Marisa R Nucci, Charles M Quick, Christopher P Crum, W Glenn McCluggage, Brooke E Howitt
Mesonephric adenocarcinoma most commonly arises in the cervix and is presumed to be derived from normal or hyperplastic mesonephric remnants. It is characterized by recurrent KRAS mutations and lack of PIK3CA/PTEN alterations. Adenocarcinomas of the uterine corpus and ovary characterized by morphologic and immunophenotypic similarities to mesonephric adenocarcinoma have been reported. The pathogenesis of these tumors, which have been designated "mesonephric-like adenocarcinomas" is unknown, and it has been debated whether these represent mesonephric adenocarcinomas that arise in the endometrium/ovary or endometrioid adenocarcinomas that closely mimic mesonephric adenocarcinoma...
October 3, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28984114/a-novel-de-novo-col6a1-mutation-emphasizes-the-role-of-intron-14-donor-splice-site-defects-as-a-cause-of-moderate-progressive-form-of-colvi-myopathy-a-case-report-and-review-of-the-genotype-phenotype-correlation
#17
Agnieszka A Koppolu, Agnieszka Madej-Pilarczyk, Małgorzata Rydzanicz, Joanna Kosińska, Piotr Gasperowicz, Jolanta Dorszewska, Wojciech Kozubski, Barbara Steinborn, Andrzej M Kochański, Rafał Płoski
Collagen VI-related myopathy is a group of disorders affecting skeletal muscles and connective tissue. The most common symptoms are muscle weakness and joint deformities which limit the movement and progress over time. Several forms of collagen VI-related myopathies have been described: Bethlem myopathy, an intermediate form and Ullrich congenital muscular dystrophy, which is the most severe. Here we report a novel de novo c.1056+3A>C substitution in intron 14 of the COL6A1 gene encoding alpha-chains of collagen VI in a 13-year-old girl suffering from collagen VI (ColVI) myopathy...
2017: Folia Neuropathologica
https://www.readbyqxmd.com/read/28982955/mutation-spectrum-of-ndp-fzd4-and-tspan12-genes-in-indian-patients-with-retinopathy-of-prematurity
#18
Sonika Rathi, Subhadra Jalali, Ganeswara Rao Musada, Satish Patnaik, Divya Balakrishnan, Anjli Hussain, Inderjeet Kaur
AIM: Retinopathy of prematurity (ROP) is a vasoproliferative eye disease in preterm infants. Based on its phenotypic similarities with familial exudative vitreo retinopathy (FEVR), the present study was conducted to screen the Norrin signalling pathway genes (already been implicated in FEVR) for understanding their involvement among Indian patients with ROP. METHODS: The study cohort consisted of patients with ROP (n=246) and controls (n=300) that included full term (n=110) and preterm babies devoid of ROP (n=190)...
October 5, 2017: British Journal of Ophthalmology
https://www.readbyqxmd.com/read/28981938/-mutational-analysis-and-prenatal-diagnosis-of-col1a1-and-col1a2-genes-in-four-chinese-families-affected-with-osteogenesis-imperfecta
#19
Ying Bai, Xiangdong Kong, Ning Liu, Shumin Ren, Hongxiang Guo, Kaihui Zhao
OBJECTIVE: To detect potential mutations of COL1A1 and COL1A2 genes in four Chinese pedigrees affected with osteogenesis imperfecta (OI) and provide prenatal diagnosis for a fetus at 18th gestational week. METHODS: All coding regions and exon/intron boundaries of the COL1A1 and COL1A2 genes were analyzed with targeted next-generation sequencing (NGS). Suspected mutations were confirmed with Sanger sequencing in the probands, unaffected relatives and 200 unrelated healthy individuals...
October 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28981924/-mutation-analysis-of-ntrk1-gene-in-a-family-affected-with-congenital-insensitivity-to-pain-with-anhidrosis
#20
Bingxiao Li, Zhanhui Zhang, Xia Wu, Wenchao Chen, Jianling Chen, Qian Lyu, Guosheng Liu
OBJECTIVE: To screen for mutations of NTRK1 gene in a Chinese family affected with congenital insensitivity to pain with anhidrosis (CIPA). METHODS: Genomic DNA was extracted from the proband and her family members. All of the 17 exons and intron-exon boundaries of the NTRK1 gene were analyzed by direct Sanger sequencing. For the deletional mutation, the PCR products were subjected to T-A cloning and sequencing to verify the mutation. RESULTS: NTRK1 gene analysis revealed that proband has carried a c...
October 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
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