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Allelic exclusion

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https://www.readbyqxmd.com/read/28195318/biallelic-loss-of-function-variants-in-dock3-cause-muscle-hypotonia-ataxia-and-intellectual-disability
#1
Katherine L Helbig, Cameron Mroske, Divya Moorthy, Samin A Sajan, Milen Velinov
DOCK3 encodes the dedicator of cytokinesis 3 protein, a member of the DOCK180 family of proteins that are characterized by guanine nucleotide exchange factor activity. DOCK3 is expressed exclusively in the central nervous system and plays an important role in axonal outgrowth and cytoskeleton reorganization. Dock3 knockout mice exhibit motor deficiencies with abnormal ataxic gait and impaired learning. We report two siblings with biallelic loss-of-function variants in DOCK3. Diagnostic whole exome sequencing and chromosomal microarray were performed on a proband with severe intellectual disability, hypotonia, and ataxic gait...
February 14, 2017: Clinical Genetics
https://www.readbyqxmd.com/read/28191856/quantitative-assessment-of-the-effect-of-fgf20-rs12720208-variant-on-the-risk-of-parkinson-s-disease-a-meta-analysis
#2
Xiaoli Wang, Xiaoxuan Sun, Xiaona Zhang, Hong Li, Anmu Xie
OBJECTIVES: Many studies have investigated the association between fibroblast growth factor 20(FGF20) rs12720208(C/T) polymorphism and the susceptibility of Parkinson's disease (PD). However, published data are still controversial. Here, we performed a meta-analysis to evaluate the association of rs12720208 polymorphism with the risk of PD. METHODS: Up to April 2016, Pubmed, EMbase, Web of science, the Chinese National Knowledge Infrastructure, and Wanfang Medicine were reviewed to identify appropriate documents...
February 13, 2017: Neurological Research
https://www.readbyqxmd.com/read/28186609/-analysis-of-genetic-polymorphisms-of-15-str-loci-among-ethnic-hans-from-xiamen
#3
Lili Wu, Peng Ran, Xiujuan Zheng, Juanjuan Zhou, Bin Pei, Xiuyu Song
OBJECTIVE: To assess the value of 15 short tandem repeat (STR) loci selected by an AmpFLSTR Identifiler(TM) system for personal identification and paternity testing among ethnic Hans from Xiamen, Fujian. METHODS: For 400 unrelated individuals, allelic frequencies for the 15 STR loci from the AmpFLSTR Identifiler(TM) kit were determined. Population genetics parameters for forensic usage were calculated. RESULTS: No deviation of the observed allele frequency from Hardy-Weinberg equilibrium expectations was found by Chi-square test (P>0...
February 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
https://www.readbyqxmd.com/read/28185422/the-association-of-the-hla-a-24-02-b-39-01-and-b-39-06-alleles-with-type-1-diabetes-is-restricted-to-specific-hla-dr-dq-haplotypes-in-finns
#4
M-L Mikk, T Heikkinen, M I El-Amir, M Kiviniemi, A-P Laine, T Härkönen, R Veijola, J Toppari, M Knip, J Ilonen
BACKGROUND: We analysed the previously reported association of the HLA-A*24:02, B*18 and B*39 alleles with type 1 diabetes and diabetes associated autoimmunity in the Finnish population applying HLA-DR/DQ stratification. MATERIALS & METHODS: Haplotype transmission was analysed in 2424 nuclear families from the Finnish Paediatric Diabetes Register. Survival analysis was applied to study the development of islet autoantibodies and further progression to clinical diabetes in the prospective follow-up cohort from the Finnish Type 1 Diabetes Prediction and Prevention (DIPP) Study...
February 10, 2017: HLA
https://www.readbyqxmd.com/read/28179390/natural-genetic-variation-in-the-caenorhabditis-elegans-response-to-pseudomonas-aeruginosa
#5
Natalia Martin, Jogender Singh, Alejandro Aballay
Caenorhabditis elegans responds to pathogenic microorganisms by activating its innate immune system, which consists of physical barriers, behavioral responses, and microbial killing mechanisms. We examined whether natural variation plays a role in the response of C. elegans to Pseudomonas aeruginosa using two C. elegans strains that carry the same allele of npr-1, a gene that encodes a G-protein-coupled receptor related to mammalian neuropeptide Y receptors, but that differ in their genetic backgrounds. Strains carrying an allele for the NPR-1 215F isoform have been shown to exhibit lack of pathogen avoidance behavior and deficient immune response towards P...
February 7, 2017: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/28168762/developing-a-new-nonbinary-snp-fluorescent-multiplex-detection-system-for-forensic-application-in-china
#6
Yanfang Liu, Huidan Liao, Ying Liu, Juanjuan Guo, Yi Sun, Xiaoliang Fu, Ding Xiao, Jifeng Cai, Lingmei Lan, Pingli Xie, Lagabaiyila Zha
Nonbinary single-nucleotide polymorphisms (SNPs) are potential forensic genetic markers because that their discrimination power is greater than that of normal binary SNPs, and that they can detect highly degraded samples. We previously developed a nonbinary SNP multiplex typing assay. In the present study, we selected additional 20 nonbinary SNPs from the NCBI SNP database and verified them through pyrosequencing. These 20 nonbinary SNPs were analyzed using the fluorescent-labeled SNaPshot multiplex SNP typing method...
February 6, 2017: Electrophoresis
https://www.readbyqxmd.com/read/28167604/gs-dreadd-knock-in-mice-for-tissue-specific-temporal-stimulation-of-camp-signaling
#7
Dmitry Akhmedov, Maria G Mendoza-Rodriguez, Kavitha Rajendran, Mario Rossi, Jürgen Wess, Rebecca Berdeaux
Hundreds of hormones and ligands stimulate cAMP signaling in different tissues through activation of G protein-coupled receptors (GPCRs). Although functions and individual effectors of cAMP signaling are well characterized in many tissues, pleiotropic effects of GPCR agonists limit investigation of physiologic functions of cAMP signaling in individual cell types at different developmental stages in vivo To facilitate studies of cAMP signaling in specific cell populations in vivo, we harnessed the power of DREADD (Designer Receptors Exclusively Activated by Designer Drugs) technology by creating ROSA26-based knock-in mice for conditional expression of a Gs-coupled DREADD (rM3Ds-GFP, or "GsD")...
February 6, 2017: Molecular and Cellular Biology
https://www.readbyqxmd.com/read/28160964/association-between-the-20210g-a-prothrombin-gene-polymorphism-and-arterial-ischemic-stroke-in-children-and-young-adults-two-meta-analyses-of-3586-cases-and-6440-control-subjects-in-total
#8
Beata Sarecka-Hujar, Ilona Kopyta, Michal Skrzypek, Joanna Sordyl
BACKGROUND: Previous data have shown that the 20210G>A polymorphism of the Factor II gene is related to an increased prothrombin level, which may in turn lead to a procoagulant state. The heterogeneous and multifactorial character of arterial ischemic stroke often results in contradictory reports describing the association between the 20210G>A polymorphism and arterial ischemic stroke in different populations. We performed a meta-analysis of available data addressing the relation between the FII 20210G>A polymorphism and arterial ischemic stroke, both in young adults and children...
January 4, 2017: Pediatric Neurology
https://www.readbyqxmd.com/read/28159756/structure-and-origin-of-the-white-cap-locus-and-its-role-in-evolution-of-grain-color-in-maize
#9
Bao-Cai Tan, Jiahn-Chou Guan, Shou Ding, Shan Wu, Jonathan W Saunders, Karen E Koch, Donald R McCarty
Selection for yellow and white grain types has been central to post-domestication improvement of maize. While genetic control of carotenoid biosynthesis in endosperm is attributed primarily to the Yellow1 (Y1) phytoene synthase gene, less is known about the role of the dominant white endosperm factor White Cap (Wc). We show that the Wc locus contains multiple, tandem copies of a Carotenoid cleavage dioxygenase 1 (Ccd1) gene that encodes a carotenoid-degrading enzyme. A survey of 111 maize inbreds and landraces, together with 22 teosinte accessions, reveals that Wc is exclusive to maize, where it is prevalent in white-grain (y1) varieties...
February 3, 2017: Genetics
https://www.readbyqxmd.com/read/28152414/coexisting-and-cooperating-mutations-in-npm1-mutated-acute-myeloid-leukemia
#10
Jay L Patel, Jonathan A Schumacher, Kimberly Frizzell, Shelly Sorrells, Wei Shen, Adam Clayton, Rakhi Jattani, Todd W Kelley
NPM1 insertion mutations represent a common recurrent genetic abnormality in acute myeloid leukemia (AML) patients. The frequency of these mutations varies from approximately 30% overall up to 50% in patients with a normal karyotype. Several recent studies have exploited advances in massively parallel sequencing technology to shed light on the complex genomic landscape of AML. We hypothesize that variant allele fraction (VAF) data derived from massively parallel sequencing studies may provide further insights into the clonal architecture and pathogenesis of NPM1-driven leukemogenesis...
January 23, 2017: Leukemia Research
https://www.readbyqxmd.com/read/28129724/identification-of-traditional-chinese-medicinal-pipefish-and-exclusion-of-common-adulterants-by-multiplex-pcr-based-on-12s-sequences-of-specific-alleles
#11
Linhui Gao, Yan Yin, Jia Li, Yuan Yuan, Chao Jiang, Wei Gao, Xianan Zhang, Luqi Huang
We aimed to establish a rapid and accurate allele-specific diagnostic Polymerase Chain Reaction (PCR) method for medicinal pipefish. To achieve this, pipefish genomic DNA was extracted, sequenced bi-directionally, and the data were analyzed. On this basis, specific identification primers were designed and a facile multiplex PCR system was established and optimized. Phylogenetic tree analysis showed that the six species of pipefish were strictly clustered in separate single branches. The reaction was optimized for ease of application, to be used in a reaction volume of 20 μL with template DNA amounts in the range of 5-100 ng, and an annealing temperature from 43 to 55 °C...
January 27, 2017: Mitochondrial DNA. Part A. DNA Mapping, Sequencing, and Analysis
https://www.readbyqxmd.com/read/28123851/the-fate-of-brca1-related-germline-mutations-in-triple-negative-breast-tumors
#12
Vassiliki Kotoula, Florentia Fostira, Kyriaki Papadopoulou, Paraskevi Apostolou, Eleftheria Tsolaki, Georgios Lazaridis, Kyriaki Manoussou, Flora Zagouri, Dimitrios Pectasides, Ioannis Vlachos, Ioannis Tikas, Sotiris Lakis, Irene Konstantopoulou, George Pentheroudakis, Helen Gogas, Pavlos Papakostas, Christos Christodoulou, Dimitrios Bafaloukos, Evangelia Razis, Vasilios Karavasilis, Christina Bamias, Drakoulis Yannoukakos, George Fountzilas
The preservation of pathogenic BRCA1/2 germline mutations in tumor tissues is usually not questioned, while it remains unknown whether these interact with somatic genotypes for patient outcome. Herein we compared germline and tumor genotypes in operable triple-negative breast cancer (TNBC) and evaluated their combined effects on prognosis. We analyzed baseline germline and primary tumor genotype data obtained by Sanger and Next Generation Sequencing in 194 TNBC patients. We also performed multiple tests interrogating the preservation of germline mutations in matched tumors and breast tissue from carriers with available material...
2017: American Journal of Cancer Research
https://www.readbyqxmd.com/read/28122493/association-between-the-159c-t-polymorphism-in-the-promoter-region-of-the-cd14-gene-and-sepsis-a-meta-analysis
#13
Qin Wu, Xiaomeng Xu, Jianan Ren, Song Liu, Xuelian Liao, Xiuwen Wu, Dong Hu, Gefei Wang, Guosheng Gu, Yan Kang, Jieshou Li
BACKGROUND: The association between CD14-159C/T polymorphism and sepsis has been assessed but results of current studies appeared conflicting and inconstant. This analysis was aimed to determine whether the CD14-159C/T polymorphism confers susceptibility to sepsis or is associated with increased risk of death from sepsis. METHOD: The authors conducted a comprehensive search of PubMed, EMBASE, ISI Web of Science, Cochrane library, ScienceDirect, Wiley Online Library and CNKI databases according to a prespecified protocol...
January 25, 2017: BMC Anesthesiology
https://www.readbyqxmd.com/read/28102864/transthyretin-v122i-pv142i-cardiac-amyloidosis-an-age-dependent-autosomal-dominant-cardiomyopathy-too-common-to-be-overlooked-as-a-cause-of-significant-heart-disease-in-elderly-african-americans
#14
REVIEW
Joel N Buxbaum, Frederick L Ruberg
Since the identification of a valine-to-isoleucine substitution at position 122 (TTR V122I; pV142I) in the transthyretin (TTR)-derived fibrils extracted from the heart of a patient with late-onset cardiac amyloidosis, it has become clear that the amyloidogenic mutation and the disease occur almost exclusively in individuals of identifiable African descent. In the United States, the amyloidogenic allele frequency is 0.0173 and is carried by 3.5% of community-dwelling African Americans. Genotyping across Africa indicates that the origin of the allele is in the West African countries that were the major source of the slave trade to North America...
January 19, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28099358/the-gender-specific-association-of-rs334558-in-gsk3%C3%AE-with-major-depressive-disorder
#15
Sha Liu, Le Wang, Ning Sun, Chunxia Yang, Zhifen Liu, Xinrong Li, Xiaohua Cao, Yong Xu, Kerang Zhang
Major depressive disorder (MDD) is one of the most prevalent psychiatric illnesses with a heritability ranging from 40% to 50%. The single nucleotide polymorphism (SNP) rs334558 on the glycogen synthase kinase-3β (GSK3β) gene has been identified as a genetic risk loci associated with schizophrenia and bipolar disorder. However, results from replication studies examining the association between rs334558 and MDD remain inconsistent.In the present study, first, we conducted a meta-analysis of the association between rs334558 and MDD by combining 5 available case-control samples totaling 2311 cases and 2535 controls...
January 2017: Medicine (Baltimore)
https://www.readbyqxmd.com/read/28088785/the-igh-locus-3-cis-regulatory-super-enhancer-co-opts-aid-for-allelic-transvection
#16
Sandrine Le Noir, Brice Laffleur, Claire Carrion, Armand Garot, Sandrine Lecardeur, Eric Pinaud, Yves Denizot, Jane Skok, Michel Cogné
Immunoglobulin heavy chain (IgH) alleles have ambivalent relationships: they feature both allelic exclusion, ensuring monoallelic expression of a single immunoglobulin (Ig) allele, and frequent inter-allelic class-switch recombination (CSR) reassembling genes from both alleles. The IgH locus 3' regulatory region (3'RR) includes several transcriptional cis-enhancers promoting activation-induced cytidine deaminase (AID)-dependent somatic hypermutation (SHM) and CSR, and altogether behaves as a strong super-enhancer...
January 10, 2017: Oncotarget
https://www.readbyqxmd.com/read/28069897/impact-of-estrogen-receptor-%C3%AE-gene-and-oxytocin-receptor-gene-polymorphisms-on-female-sexuality
#17
Anastasia K Armeni, Konstantinos Assimakopoulos, Dimitra J Marioli, Vasiliki Koika, Eftychia Michailidou, Niki Mourtzi, Gregoris Iconomou, Neoklis A Georgopoulos
Over the past decades, research attention has increasingly been paid to the neurobiological component of sexual behaviour. The aim of the present study was to investigate the correlation of estrogen receptor α (ERα) gene polymorphism (rs2234693-PvuII) (T→C substitution) and oxytocin receptor gene polymorphism (rs53576) (G→A substitution) with sexuality parameters of young, healthy women. One hundred thirty-three Greek heterosexual women, students in higher education institutions, 20-25 years of age, sexually active, with normal menstrual cycles (28-35 days), were recruited in the study...
January 9, 2017: Endocrine Connections
https://www.readbyqxmd.com/read/28069890/apobec1-complementation-factor-a1cf-is-not-required-for-c-to-u-rna-editing-in-vivo
#18
Elizabeth M Snyder, Christopher McCarty, Adrienne Mehalow, Karen Svenson, Stephen Murray, Ron Korstanje, Robert E Braun
Editing of the human and murine ApoB mRNA by APOBEC1, the catalytic enzyme of the protein complex that catalyzes C-to-U RNA editing, creates an internal stop codon within the APOB coding sequence, generating two protein isoforms. It has been long held that APOBEC1-mediated editing activity is dependent on the RNA binding protein A1CF. The importance of A1CF in adult tissues has been unclear as a previously reported null allele displays embryonic lethality. This work aimed to address the function of A1CF in adult mouse tissues using a conditional A1cf allele...
January 9, 2017: RNA
https://www.readbyqxmd.com/read/28058572/population-genetic-analyses-and-evaluation-of-22-autosomal-strs-in-indian-populations
#19
Mugdha Singh, Madhusudan R Nandineni
The allele frequencies and forensically relevant parameters for the 22 autosomal short tandem repeats (STRs) present in PowerPlex® Fusion (Promega, Madison, WI) were determined for 357 unrelated individuals from 11 states across India. The combined power of discrimination and probability of exclusion were 0.99999999999999999999999999875 and 0.999999997200846, respectively. The panel was found to be informative for Indian populations and generated a total of 275 alleles. Further, analyses with these loci did not show any noticeable clustering among the Indian populations...
January 6, 2017: International Journal of Legal Medicine
https://www.readbyqxmd.com/read/28057861/cellular-context-dependent-consequences-of-apc-mutations-on-gene-regulation-and-cellular-behavior
#20
Kyoichi Hashimoto, Yosuke Yamada, Katsunori Semi, Masaki Yagi, Akito Tanaka, Fumiaki Itakura, Hitomi Aoki, Takahiro Kunisada, Knut Woltjen, Hironori Haga, Yoshiharu Sakai, Takuya Yamamoto, Yasuhiro Yamada
The spectrum of genetic mutations differs among cancers in different organs, implying a cellular context-dependent effect for genetic aberrations. However, the extent to which the cellular context affects the consequences of oncogenic mutations remains to be fully elucidated. We reprogrammed colon tumor cells in an Apc(Min/+) (adenomatous polyposis coli) mouse model, in which the loss of the Apc gene plays a critical role in tumor development and subsequently, established reprogrammed tumor cells (RTCs) that exhibit pluripotent stem cell (PSC)-like signatures of gene expression...
January 24, 2017: Proceedings of the National Academy of Sciences of the United States of America
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