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https://www.readbyqxmd.com/read/29334207/screening-for-causative-mutations-of-major-prolificacy-genes-in-iranian-fat-tailed-sheep
#1
Ramin Abdoli, Seyed Ziaeddin Mirhoseini, Navid Ghavi Hossein-Zadeh, Pouya Zamani
Background: The presence of different missense mutations in sheep breeds have shown that the bone morphogenetic protein receptor 1B (BMPR1B), bone morphogenetic protein 15 (BMP15) and growth differentiation factor 9 (GDF9) genes play a vital role in ovulation rate and prolificacy in ewes. Therefore, the present study aims to investigate BMPR1B, BMP15 and GDF9 gene mutations in prolific ewes of Iranian fat-tailed Lori-Bakhtiari sheep. MATERIALS AND METHODS: In the present experimental study, genomic DNA was extracted from whole blood of 10 prolific Lori-Bakhtiari ewes with at least two twinning records in the first four parities to identify point mutations of the BMPR1B, BMP15 and GDF9 genes, using DNA sequencing...
April 2018: International Journal of Fertility & Sterility
https://www.readbyqxmd.com/read/29333594/ras-testing-for-colorectal-cancer-patients-is-reliable-in-european-laboratories-that-pass-external-quality-assessment
#2
V Tack, M J L Ligtenberg, A G Siebers, P D M Rombout, P D Dabir, R D A Weren, J H J M van Krieken, E M C Dequeker
Wild-type status of KRAS and the NRAS gene (exon 2, 3, and 4) in the tumor should be determined before treatment of metastatic colorectal cancer (mCRC) patients with EGFR-targeting agents. There is a large variation in test methods to determine RAS status, and more sensitive detection methods were recently introduced. Data from quality assessment programs indicate substantial error rates. This study assessed the completeness and correctness of RAS testing in European laboratories that successfully passed external quality assessment (EQA)...
January 15, 2018: Virchows Archiv: An International Journal of Pathology
https://www.readbyqxmd.com/read/29332065/a-novel-mutation-of-amhr2-in-two-siblings-with-persistent-m%C3%A3-llerian-duct-syndrome
#3
Aydilek D Çakır, Hande Turan, Hüseyin Onay, Haluk Emir, Senol Emre, Nil Comunoglu, Oya Ercan, Olcay Evliyaoglu
Persistent müllerian duct syndrome (PMDS) is characterized by the presence of müllerian duct derivatives in otherwise phenotypically normal males. It is caused in approximately 85% of the cases by mutations in the AMH gene or its type II receptor (AMHR2). We report on 2 brothers with normal external genitalia but high serum AMH levels. Sequence analysis of the AMHR2 gene in the 2 siblings revealed a novel homozygous missense mutation in exon 10 (p.V458L, c.1372G>T). PMDS is a rare condition, but it has to be considered in differential diagnosis of cryptorchidism with normal male genitalia...
January 13, 2018: Sexual Development: Genetics, Molecular Biology, Evolution, Endocrinology, Embryology, and Pathology of Sex Determination and Differentiation
https://www.readbyqxmd.com/read/29330474/a-de-novo-foxp1-truncating-mutation-in-a-patient-originally-diagnosed-as-c-syndrome
#4
Roser Urreizti, Sarah Damanti, Carla Esteve, Héctor Franco-Valls, Laura Castilla-Vallmanya, Raul Tonda, Bru Cormand, Lluïsa Vilageliu, John M Opitz, Giovanni Neri, Daniel Grinberg, Susana Balcells
De novo FOXP1 mutations have been associated with intellectual disability (ID), motor delay, autistic features and a wide spectrum of speech difficulties. C syndrome (Opitz C trigonocephaly syndrome) is a rare and genetically heterogeneous condition, characterized by trigonocephaly, craniofacial anomalies and ID. Several different chromosome deletions and and point mutations in distinct genes have been associated with the disease in patients originally diagnosed as Opitz C. By whole exome sequencing we identified a de novo splicing mutation in FOXP1 in a patient, initially diagnosed as C syndrome, who suffers from syndromic intellectual disability with trigonocephaly...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330450/c-terminal-short-arginine-serine-repeat-sequence-dependent-regulation-of-y14-rbm8a-localization
#5
Takanori Tatsuno, Yasuhito Ishigaki
Y14 (RBM8A) is an RNA recognition motif-containing protein that forms heterodimers with MAGOH and serves as a core factor of the RNA surveillance machinery for the exon junction complex (EJC). The role of the Y14 C-terminal serine/arginine (RS) repeat-containing region, which has been reported to undergo modifications such as phosphorylation and methylation, has not been sufficiently investigated. Thus, we aimed to explore the functional significance of the Y14 C-terminal region. Deletion or dephosphorylation mimic mutants of the C-terminal region showed a shift in localization from the nucleoplasmic region; in addition, the C-terminal RS repeat-containing sequence itself exhibited the potential for nucleolar localization...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330416/virtual-genome-walking-across-the-32%C3%A2-gb-ambystoma-mexicanum-genome-assembling-gene-models-and-intronic-sequence
#6
Teri Evans, Andrew D Johnson, Matthew Loose
Large repeat rich genomes present challenges for assembly using short read technologies. The 32 Gb axolotl genome is estimated to contain ~19 Gb of repetitive DNA making an assembly from short reads alone effectively impossible. Indeed, this model species has been sequenced to 20× coverage but the reads could not be conventionally assembled. Using an alternative strategy, we have assembled subsets of these reads into scaffolds describing over 19,000 gene models. We call this method Virtual Genome Walking as it locally assembles whole genome reads based on a reference transcriptome, identifying exons and iteratively extending them into surrounding genomic sequence...
January 12, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29330282/population-dependent-intron-retention-and-dna-methylation-in-breast-cancer
#7
Dongwook Kim, Manu Shivakumar, Seonggyun Han, Michael S Sinclair, Youngji Lee, Yonglan Zheng, Olufunmilayo I Olopade, Dokyoon Kim, Younghee Lee
Regulation of gene expression by DNA methylation in gene promoter regions is well-studied; however, the effects of methylation in the gene body (exons and introns) on gene expression are comparatively understudied. Recently, hyper-methylation has been implicated in the inclusion of alternatively spliced exons; moreover, exon recognition can be enhanced by recruiting the methyl-CpG-binding protein (MeCP2) to hyper-methylated sites. This study examines if methylation status of an intron is correlated with how frequently the intron is retained during splicing using DNA methylation and RNA sequencing (RNA-seq) data from breast cancer tissue specimens in The Cancer Genome Atlas (TCGA)...
January 12, 2018: Molecular Cancer Research: MCR
https://www.readbyqxmd.com/read/29329938/pipeline-to-gene-discovery-analysing-familial-parkinsonism-in-the-queensland-parkinson-s-project
#8
Steven R Bentley, Stephanie Bortnick, Ilaria Guella, Javed Y Fowdar, Peter A Silburn, Stephen A Wood, Matthew J Farrer, George D Mellick
INTRODUCTION: Family based study designs provide an informative resource to identify disease-causing mutations. The Queensland Parkinson's Project (QPP) has been involved in numerous genetic screening studies; however, details of the families enrolled into the register have not been comprehensively reported. This article characterises the families enrolled in the QPP and summarises monogenic forms of hereditary Parkinsonism found in the register. METHOD: The presence of pathogenic point mutations and copy number variations (CNVs) were, generally, screened in a sample of over 1000 PD patients from the total of 1725...
January 3, 2018: Parkinsonism & related Disorders
https://www.readbyqxmd.com/read/29328376/identification-of-a-novel-compound-heterozygous-mutation-of-the-cyp21a2-gene-causing-21%C3%A2-hydroxylase-deficiency-in-a-chinese-pedigree
#9
Jia Liu, Xiujuan Zhang, Haiqing Zhang, Li Fang, Jin Xu, Qingbo Guan, Chao Xu
21‑Hydroxylase deficiency (21‑OHD) is the most common cause of congenital adrenal hyperplasia. Inherited in an autosomal recessive manner, 21‑OHD is caused by mutations in the cytochrome P450 family 21 subfamily A member 2 (CYP21A2) gene. The present study was designed to investigate the genetic characteristics of one Chinese pedigree and to identify the genotype‑phenotype association, thereby facilitating the precise diagnosis of 21‑OHD at the molecular level. Members of a Chinese family with 21‑OHD were screened for mutations in the CYP21A2 gene...
January 8, 2018: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29328375/the-role-of-il%C3%A2-16-gene-polymorphisms-in-endometriosis
#10
Michail Matalliotakis, Maria I Zervou, Elias Eliopoulos, Charoula Matalliotaki, Nilufer Rahmioglu, Ioannis Kalogiannidis, Krina Zondervan, Demetrios A Spandidos, Ioannis Matalliotakis, George N Goulielmos
Endometriosis is one of the most common gynecological diseases affecting up to 10% of the female population of childbearing age and a major cause of pain and infertility. It is influenced by multiple genetic, epigenetic and environmental factors. Interleukin‑16 (IL‑16) is a proinflammatory cytokine playing a pivotal role in many inflammatory and autoimmune diseases as well as in the pathogenesis of endometriosis. The aim of the present study was to evaluate the association of two IL‑16 gene single nucleotide polymorphisms (SNPs), rs4072111 and rs11556218, with the risk of endometriosis in women from Greece as well as to gain insight about the structural consequences of these two exonic SNPs regarding development of the disease...
January 9, 2018: International Journal of Molecular Medicine
https://www.readbyqxmd.com/read/29327506/next-generation-sequencing-characterizes-the-extent-of-hla-diversity-in-an-argentinian-registry-population
#11
C K Hurley, L Hou, A Lazaro, J Gerfen, E Enriquez, P Galarza, M Belen Rodriguez Cardozo, M Halagan, M Maiers, D Behm, J Ng
Next generation DNA sequencing is used to determine the HLA-A, -B, -C, -DRB1, and -DQB1 assignments of 1472 unrelated volunteers for the unrelated donor registry in Argentina. The analysis characterized all HLA exons and introns for class I alleles; at least exons 2, 3 for HLA-DRB1; and exons 2-6 for HLA-DQB1. Of the distinct alleles present, there are 330 class I and 98 class II. The majority (~98%) of the cumulative allele frequency at each locus is contributed by alleles that appear at a frequency of at least 1 in 1000...
January 12, 2018: HLA
https://www.readbyqxmd.com/read/29325903/gata4-loss-of-function-mutation-and-the-congenitally-bicuspid-aortic-valve
#12
Ruo-Gu Li, Ying-Jia Xu, Juan Wang, Xing-Yuan Liu, Fang Yuan, Ri-Tai Huang, Song Xue, Li Li, Hua Liu, Yan-Jie Li, Xin-Kai Qu, Hong-Yu Shi, Min Zhang, Xing-Biao Qiu, Yi-Qing Yang
Aggregating evidence suggests that genetic determinants play a pivotal role in the pathogenesis of the congenitally bicuspid aortic valve (BAV). BAV is of pronounced genetic heterogeneity, and the genetic components underlying BAV in an overwhelming majority of patients remain elusive. In the current study, the whole coding exons and adjacent introns, as well as 5' and 3' untranslated regions of the GATA4 gene, which codes for a zinc-finger transcription factor crucial for the normal development of the aortic valve, were screened by direct sequencing in 150 index patients with congenital BAV...
November 23, 2017: American Journal of Cardiology
https://www.readbyqxmd.com/read/29325454/down-expression-of-p2rx2-kcnq5-erbb3-and-socs3-through-dna-hypermethylation-in-elderly-women-with-presbycusis
#13
Amal Bouzid, Ibtihel Smeti, Leila Dhouib, Magali Roche, Imen Achour, Aida Khalfallah, Abdullah Ahmed Gibriel, Ilhem Charfeddine, Hammadi Ayadi, Joel Lachuer, Abdelmonem Ghorbel, Christine Petit, Saber Masmoudi
CONTEXT: Presbycusis, an age-related hearing impairment (ARHI), represents the most common sensory disability in adults. Today, the molecular mechanisms underlying presbycusis remain unclear. This is in particular due to the fact that ARHI is a multifactorial complex disorder resulting from several genomic factors interacting with lifelong cumulative effects of: disease, diet, and environment. OBJECTIVE: Identification of novel biomarkers for presbycusis. MATERIALS AND METHODS: We selectively ascertained eighteen elderly unrelated women lacking environmental and metabolic risk factors...
January 11, 2018: Biomarkers: Biochemical Indicators of Exposure, Response, and Susceptibility to Chemicals
https://www.readbyqxmd.com/read/29325334/-analysis-on-the-novel-compound-heterozygous-mutation-f%C3%A2-%C2%AA-of-a-patient-with-hereditary-factor-%C3%A2-%C2%AA-deficiency
#14
K Xu, K Y Shu, F F Li, T Chen, J Liu, S S Jin, J J Guo, Z H Zhang, M H Jiang
Objective: To investigate the clinical phenotype and genotype characteristics of a Chinese hereditary factor Ⅺ deficiency pedigree. Methods: The activated partial thromboplastin time (APTT), prothrombin time (PT), FⅪ activity (FⅪ: C) were measured by clotting method using automatic coagulation analyzer. The FⅪ antigen (FⅪ: Ag) was assayed by enzyme-linked immunosorbent assay (ELISA). Fifteen exons of F11 from the proband and his pedigree members were amplified by polymerase chain reaction (PCR), then sequenced...
December 26, 2017: Zhonghua Yi Xue za Zhi [Chinese medical journal]
https://www.readbyqxmd.com/read/29325310/-clinical-characteristics-and-whole-exon-sequence-study-of-a-chinese-family-with-autosomal-dominant-lateral-temporal-lobe-epilepsy
#15
C Y Li, H H Yang, R J Lyu, Q Wang
Objective: To explore the genetic characteristics in a Chinese family with autosomal dominant lateral temporal lobe epilepsy (ADLTE) and analyze the correlation between genotype and phenotype. Methods: The natural history, clinical data and peripheral blood sample were collected in all patients and two healthy members of this ADLTE family. Whole exon sequence (WES) analysis strategy was used to explore the underlying mutations. Possible causative genetic variation was further confirmed by direct PCR and Sanger sequencing...
January 1, 2018: Zhonghua Nei Ke za Zhi [Chinese Journal of Internal Medicine]
https://www.readbyqxmd.com/read/29325170/ecology-of-paracoccidioides-brasiliensis-p-lutzii-and-related-species-infection-in-armadillos-soil-occurrence-and-mycological-aspects
#16
Marluce Francisca Hrycyk, Hans Garcia Garces, Sandra de Moraes Gimenes Bosco, Sílvio Luis de Oliveira, Sílvio Alencar Marques, Eduardo Bagagli
Paracoccidioides brasiliensis and the related species P. americana, P. restrepiensis, P. venezuelensis, and P. lutzii (Ascomycota, Ajellomycetaceae) are the etiological agents of paracoccidoidoimycosis (PCM), one of the most important systemic mycoses in Latin America. They are dimorphic fungi, with a mycelial life cycle in soil and a yeast phase associated with tissues of mammalian hosts. This study aimed to detect Paracoccidioides spp. in armadillo tissues and associated soil samples in three well-defined geographic areas, including the Alta Floresta, an area not only endemic for PCM in the central region of Brazil but also of probable P...
January 6, 2018: Medical Mycology: Official Publication of the International Society for Human and Animal Mycology
https://www.readbyqxmd.com/read/29324689/characterization-of-translationally-controlled-tumour-protein-from-the-sea-anemone-anemonia-viridis-and-transcriptome-wide-identification-of-cnidarian-homologues
#17
Aldo Nicosia, Carmelo Bennici, Girolama Biondo, Salvatore Costa, Marilena Di Natale, Tiziana Masullo, Calogera Monastero, Maria Antonietta Ragusa, Marcello Tagliavia, Angela Cuttitta
Gene family encoding translationally controlled tumour protein (TCTP) is defined as highly conserved among organisms; however, there is limited knowledge of non-bilateria. In this study, the first TCTP homologue from anthozoan was characterised in the Mediterranean Sea anemone, Anemonia viridis. The release of the genome sequence of Acropora digitifera, Exaiptasia pallida, Nematostella vectensis and Hydra vulgaris enabled a comprehensive study of the molecular evolution of TCTP family among cnidarians. A comparison among TCTP members from Cnidaria and Bilateria showed conserved intron exon organization, evolutionary conserved TCTP signatures and 3D protein structure...
January 11, 2018: Genes
https://www.readbyqxmd.com/read/29323541/development-of-a-targeted-next-generation-sequencing-assay-to-detect-diagnostically-relevant-mutations-of-jak2-calr-and-mpl-in-myeloproliferative-neoplasms
#18
Thomas Frawley, Cathal P O'Brien, Eibhlin Conneally, Elisabeth Vandenberghe, Melanie Percy, Stephen E Langabeer, Karl Haslam
BACKGROUND: The classical Philadelphia chromosome-negative myeloproliferative neoplasms (MPNs), consisting of polycythemia vera, essential thrombocythemia, and primary myelofibrosis, are a heterogeneous group of neoplasms that harbor driver mutations in the JAK2, CALR, and MPL genes. The detection of these mutations has been incorporated into the recent World Health Organization (WHO) diagnostic criteria for MPN. Given a pressing clinical need to screen for these mutations in a routine diagnostic setting, a targeted next-generation sequencing (NGS) assay for the detection of MPN-associated mutations located in JAK2 exon 14, JAK2 exon 12, CALR exon 9, and MPL exon 10 was developed to provide a single platform alternative to reflexive, stepwise diagnostic algorithms...
January 11, 2018: Genetic Testing and Molecular Biomarkers
https://www.readbyqxmd.com/read/29323238/human-complement-receptor-type-1-cr1-protein-levels-and-genetic-variants-in-chronic-chagas-disease
#19
Thaisa Lucas Sandri, Kárita Cláudia Freitas Lidani, Fabiana Antunes Andrade, Christian G Meyer, Peter G Kremsner, Iara J de Messias-Reason, Thirumalaisamy P Velavan
Complement is an essential element in both innate and acquired immunity contributing to the immunopathogenesis of many disorders, including Chagas Disease (CD). Human complement receptor 1 (CR1) plays a role in the clearance of complement opsonized molecules and may facilitate the entry of pathogens into host cells. Distinct CR1 exon 29 variants have been found associated with CR1 expression levels, increased susceptibility and pathophysiology of several diseases. In this study, CR1 plasma levels were assessed by ELISA and CR1 variants in exon 29 by sequencing in a Brazilian cohort of 232 chronic CD patients and 104 healthy controls...
January 11, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29322437/deep-computational-circular-rna-analytics-from-rna-seq-data
#20
Tobias Jakobi, Christoph Dieterich
Circular RNAs (circRNAs) have been first described as "scrambled exons" in the 1990s. CircRNAs originate from back splicing or exon skipping of linear RNA templates and have continuously gained attention in recent years due to the availability of high-throughput whole-transcriptome sequencing methods. Numerous manuscripts describe thousands of circRNAs throughout uni- and multicellular eukaryote species and demonstrated that they are conserved, stable, and abundant in specific tissues or conditions. This manuscript provides a walk-through of our bioinformatics toolbox, which covers all aspects of in silico circRNA analysis, starting from raw sequencing data and back-splicing junction discovery to circRNA quantitation and reconstruction of internal the circRNA structure...
2018: Methods in Molecular Biology
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