keyword
MENU ▼
Read by QxMD icon Read
search

Copy number

keyword
https://www.readbyqxmd.com/read/29156725/methylation-of-cpg-sites-in-the-upstream-regulatory-region-physical-status-and-mrna-expression-of-hpv-6-in-adult-onset-laryngeal-papilloma
#1
Zeyi Deng, Taro Ikegami, Asanori Kiyuna, Chunlin Zhang, Tao Zhang, Sen Matayoshi, Takayuki Uehara, Hiroyuki Maeda, Mikio Suzuki, Akira Ganaha
The methylation status of HPV-6 upstream regulatory region (URR) in adult-onset laryngeal papillomatosis (AO-LP) remains unclear. The purpose of this study was to investigate the methylation status of URR and the physical status of HPV-6, as well as the dynamic variations of viral load and mRNA expression in AO-LP. We examined 18 specimens from 11 patients with AO-LP by real-time polymerase chain reaction (PCR), bisulfite-sequencing PCR, and amplification of papilloma oncogene transcripts. HPV-6 was identified in 9 of 11 patients (81...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156722/whole-exome-sequencing-reveals-novel-mutations-and-epigenetic-regulation-in-hypopharyngeal-carcinoma
#2
Ping Wu, Honglong Wu, Yaoyun Tang, Shi Luo, Xing Fang, Chubo Xie, Jian He, Suping Zhao, Xiaofeng Wang, Jiajia Xu, Xi Chen, Dongfang Li, Huanming Yang, Jian Wang
Hypopharyngeal cancer (HPC) frequently presents at an advanced stage, resulting in poor prognosis. Although combined surgical therapy and chemoradiotherapy have improved the survival for patients with HPC over the past 3 decades, the mortality rate in late-stage diagnosis of HPC is unsatisfactory. In this study, we performed whole-exome sequencing (WES) of 23 hypopharyngeal tumor and paired adjacent normal tissue to identify novel candidate driver genes associated with hypopharyngeal carcinoma. We identified several copy number variants (CNVs) and 15 somatic mutation genes that were associated with hypopharyngeal carcinoma...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156716/using-droplet-digital-pcr-to-analyze-mycn-and-alk-copy-number-in-plasma-from-patients-with-neuroblastoma
#3
Marco Lodrini, Annika Sprüssel, Kathy Astrahantseff, Daniela Tiburtius, Robert Konschak, Holger N Lode, Matthias Fischer, Ulrich Keilholz, Angelika Eggert, Hedwig E Deubzer
The invasive nature of surgical biopsies deters sequential application, and single biopsies often fail to reflect tumor dynamics, intratumor heterogeneity and drug sensitivities likely to change during tumor evolution and treatment. Implementing molecular characterization of cell-free neuroblastoma-derived DNA isolated from blood plasma could improve disease assessment for treatment selection and monitoring of patients with high-risk neuroblastoma. We established droplet digital PCR (ddPCR) protocols for MYCN and ALK copy number status in plasma from neuroblastoma patients...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156679/remote-intracranial-recurrence-of-idh-mutant-gliomas-is-associated-with-tp53-mutations-and-an-8q-gain
#4
Shunsuke Nakae, Takema Kato, Kazuhiro Murayama, Hikaru Sasaki, Masato Abe, Masanobu Kumon, Tadashi Kumai, Kei Yamashiro, Joji Inamasu, Mitsuhiro Hasegawa, Hiroki Kurahashi, Yuichi Hirose
Most IDH mutant gliomas harbor either 1p/19q co-deletions or TP53 mutation; 1p/19q co-deleted tumors have significantly better prognoses than tumors harboring TP53 mutations. To investigate the clinical factors that contribute to differences in tumor progression of IDH mutant gliomas, we classified recurrent tumor patterns based on MRI and correlated these patterns with their genomic characterization. Accordingly, in IDH mutant gliomas (N = 66), 1p/19 co-deleted gliomas only recurred locally, whereas TP53 mutant gliomas recurred both locally and in remote intracranial regions...
October 17, 2017: Oncotarget
https://www.readbyqxmd.com/read/29156220/the-epilepsy-phenotype-in-adult-patients-with-intellectual-disability-and-pathogenic-copy-number-variants
#5
Giuseppe d'Orsi, Tommaso Martino, Orazio Palumbo, Maria Grazia Pascarella, Pietro Palumbo, Maria Teresa Di Claudio, Carlo Avolio, Massimo Carella
PURPOSE: To characterize the electroclinical features of epilepsy associated with intellectual disability and pathogenic copy number variations (CNVs) METHODS: we prospectively investigated 61 adult patients with epilepsy and intellectual disability or other neurodevelopmental disorders. We performed high resolution SNP-Array analysis in order to detect clinical relevant chromosomal microdeletions and microduplications. An ordinal logistic regression model was fitted with 34 demographic, clinical and EEG-related variables in order to identify the epilepsy phenotype of patients with pathogenic CNVs...
November 14, 2017: Seizure: the Journal of the British Epilepsy Association
https://www.readbyqxmd.com/read/29156055/analysis-of-an-adtkd-family-with-a-novel-frameshift-mutation-in-muc1-reveals-characteristic-features-of-mutant-muc1-protein
#6
Satoko Yamamoto, Jun-Ya Kaimori, Takuji Yoshimura, Tomoko Namba, Atsuko Imai, Kaori Kobayashi, Ryoichi Imamura, Naotsugu Ichimaru, Kazuto Kato, Akihiro Nakaya, Shiro Takahara, Yoshitaka Isaka
Background: Medullary cystic kidney disease Type 1 is an autosomal dominant tubulointerstitial kidney disease (ADTKD). Recently, mucin 1 ( MUC1 ) was identified as a causal gene of medullary cystic kidney disease (ADTKD-MUC1). However, the MUC1 mutation was found to be a single cytosine insertion in a single copy of the GC-rich variable number of tandem repeats (VNTRs), which are very difficult to analyze by next-generation sequencing. To date, other mutations have not been detected in ADTKD-MUC1, and the mutant MUC1 protein has not been analyzed because of the difficulty of genetically modifying the VNTR sequence...
June 1, 2017: Nephrology, Dialysis, Transplantation
https://www.readbyqxmd.com/read/29155794/an-array-based-comparative-genomic-hybridization-platform-for-efficient-detection-of-copy-number-variations-in-fast-neutron-induced-medicago-truncatula-mutants
#7
Yuhui Chen, Xianfu Wang, Shunfei Lu, Hongcheng Wang, Shibo Li, Rujin Chen
Mutants are invaluable genetic resources for gene function studies. To generate mutant collections, three types of mutagens can be utilized, including biological such as T-DNA or transposon, chemical such as ethyl methanesulfonate (EMS), or physical such as ionization radiation. The type of mutation observed varies depending on the mutagen used. For ionization radiation induced mutants, mutations include deletion, duplication, or rearrangement. While T-DNA or transposon-based mutagenesis is limited to species that are susceptible to transformation, chemical or physical mutagenesis can be applied to a broad range of species...
November 8, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155773/dna-magnetic-particle-binding-analysis-by-dynamic-and-electrophoretic-light-scattering
#8
Yazan Haddad, Simona Dostalova, Jiri Kudr, Ondrej Zitka, Zbynek Heger, Vojtech Adam
Isolation of DNA using magnetic particles is a field of high importance in biotechnology and molecular biology research. This protocol describes the evaluation of DNA-magnetic particles binding via dynamic light scattering (DLS) and electrophoretic light scattering (ELS). Analysis by DLS provides valuable information on the physicochemical properties of particles including particle size, polydispersity, and zeta potential. The latter describes the surface charge of the particle which plays major role in electrostatic binding of materials such as DNA...
November 9, 2017: Journal of Visualized Experiments: JoVE
https://www.readbyqxmd.com/read/29155328/mitochondrial-trna-leu-uur-c3275t-trna-gln-t4363c-and-trna-lys-a8343g-mutations-may-be-associated-with-pcos-and-metabolic-syndrome
#9
Yu Ding, Bo-Hou Xia, Cai-Juan Zhang, Guang-Chao Zhuo
Polycystic ovary syndrome (PCOS) is a very prevalent endocrine disease affecting reproductive women. Clinically, patients with this disorder are more vulnerable to develop type 2 diabetes mellitus (T2DM), cardiovascular events, as well as metabolic syndrome (MetS). To date, the molecular mechanism underlying PCOS remains largely unknown. Previously, we showed that mitochondrial dysfunction caused by mitochondrial DNA (mtDNA) mutation was an important cause for PCOS. In the current study, we described the clinical and biochemical features of a three-generation pedigree with maternally transmitted MetS, combined with PCOS...
November 16, 2017: Gene
https://www.readbyqxmd.com/read/29154001/tri-allelic-patterns-of-strs-and-partially-homologous-non-sister-chromatid-crossover-observed-in-a-parentage-test
#10
Huiyong Jiao, He Ren, Yaran Yang, Bin Ni, Haiyan Zhou, Wei Chen, Yunwang Cao, Chuguang Chen, Yanmei Huang, Jiangwei Yan
A maternity testing case is reported, in which the child showed tri-allelic patterns in two short tandem repeat (STR) loci. The genotypes of Penta D of the mother and the child were 9,13 and 9,10,13, respectively. Those of D21S11 were 32.2,35 and 29,35, respectively, but intensity ratio of alleles 29 and 35 of the child was 1:2. These results suggested the copy number variations (CNVs) or trisomy of chromosome 21. By further examination using STR-based chromosome aneuploidy detection kit, three alleles were detected in D21S1411, LFG21 and Penta D, and 2 alleles with intensity ratio of 1:2 were observed in D21S2502, D21S1435, D21S11 and D21S1246...
October 28, 2017: Legal Medicine
https://www.readbyqxmd.com/read/29153098/high-amplification-levels-of-mdm2-and-cdk4-correlate-with-poor-outcome-in-patients-with-dedifferentiated-liposarcoma-a-cytogenomic-microarray-analysis-of-47-cases
#11
Robert W Ricciotti, Aaron J Baraff, George Jour, McKenna Kyriss, Yu Wu, Yuhua Liu, Shao-Chun Li, Benjamin Hoch, Yajuan J Liu
Dedifferentiated liposarcoma (DDLS) is characterized at the molecular level by amplification of genes within 12q13-15 including MDM2 and CDK4. However, other than FNCLCC grade, prognostic markers are limited. We aim to identify molecular prognostic markers for DDLS to help risk stratify patients. To this end, we studied 49 cases of DDLS in our institutional archives and performed cytogenomic microarray analysis on 47 cases. Gene copy numbers for 12 loci were evaluated and correlated with outcome data retrieved from our institutional electronic medical records...
December 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29153094/differences-between-chronic-lymphocytic-leukaemia-and-small-lymphocytic-lymphoma-cells-by-proteomic-profiling-and-snp-microarray-analysis
#12
Jennifer A Tooze, Edita Hamzic, Fenella Willis, Ruth Pettengell
The majority of malignant cells in chronic lymphocytic leukaemia (CLL) circulate in the peripheral blood whereas small lymphocytic lymphoma (SLL) cells reside in tissues. The aim of this study was to detect differences in chemokine receptor expression, DNA single nucleotide polymorphism (SNP) microarray analysis and proteomic profiling to help elucidate why the cells remain in their respective environments. We identified by flow cytometric studies of chemokine receptors and DNA SNP microarray analysis significant differences between cells from CLL and SLL patients...
December 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29153092/is-intrachromosomal-amplification-of-chromosome-21-iamp21-always-intrachromosomal
#13
Karen D Tsuchiya, Billy Davis, Rebecca A Gardner
Recurrent chromosomal abnormalities in childhood B-cell acute lymphoblastic leukemia (B-ALL) provide prognostic information that is useful in determining treatment stratification. iAMP21 is a more recently recognized cytogenetic entity of B-ALL that was originally described as multiple copies of the RUNX1 gene on a structurally abnormal chromosome 21. Subsequent studies elucidated a common region of highest-level amplification that includes RUNX1. Fluorescence in situ hybridization (FISH) is the most common method used to identify iAMP21, which is defined as the presence of five or more total copies of RUNX1, with three or more extra RUNX1 signals on a single abnormal chromosome 21...
December 2017: Cancer Genetics
https://www.readbyqxmd.com/read/29152132/high-baalc-copy-numbers-in-peripheral-blood-prior-to-allogeneic-transplantation-predict-early-relapse-in-acute-myeloid-leukemia-patients
#14
Madlen Jentzsch, Marius Bill, Juliane Grimm, Julia Schulz, Karoline Goldmann, Stefanie Beinicke, Janine Häntschel, Wolfram Pönisch, Georg-Nikolaus Franke, Vladan Vucinic, Gerhard Behre, Thoralf Lange, Dietger Niederwieser, Sebastian Schwind
High BAALC expression levels at acute myeloid leukemia diagnosis have been linked to adverse outcomes. Recent data indicate that high BAALC expression levels may also be used as marker for residual disease following acute myeloid leukemia treatment. Allogeneic hematopoietic stem cell transplantation (HSCT) offers a curative treatment for acute myeloid leukemia patients. However, disease recurrence remains a major clinical challenge and identification of high-risk patients prior to HSCT is crucial to improve outcomes...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29152119/a-genome-wide-comprehensively-analyses-of-long-noncoding-rna-profiling-and-metastasis-associated-lncrnas-in-renal-cell-carcinoma
#15
Xue Xu, Yongcan Xu, Chuanqin Shi, Baoyu Wang, Xiang Yu, Yanfen Zou, Tao Hu
Recently, a growing number of studies have indicated that long noncoding RNAs (lncRNAs) are emerging as new critical regulators of tumorigenesis and prognostic markers in multiple cancers. However, the expression pattern of lncRNAs and their contributions in renal cell carcinoma (RCC) remains poorly understood. In this study, we performed a genome-wide comprehensively analysis of lncRNAs profiling and clinical relevance to provide valuable lncRNA candidates for the further study in RCC. RCC and non-tumor tissues RNA sequencing data, and microarray data were obtained from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO), then, these data were annotated and analyzed to find dysregulated lncRNAs in RCC...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29152113/the-prognostic-significance-of-mcl1-copy-number-gain-in-esophageal-squamous-cell-carcinoma
#16
Chen Xu, Yalan Liu, Jie Huang, Hao Wang, Lijie Tan, Yifan Xu, Zhengzeng Jiang, Xin Wang, Yingyong Hou, Dongxian Jiang, Qun Wang
Background: MCL1 copy number variations have been reported to be associated with cancer prognosis in several cancers. However, the role of MCL1 gain has not yet been determined in esophageal squamous cell carcinomas (ESCC). Methods: Fluorescence in situ hybridization (FISH) for MCL1 was performed on 262 ESCC samples using tissue microarray (TMA). Results: The median age of ESCC patients was 62 years (range 37-83), with frequencies between women (16...
October 20, 2017: Oncotarget
https://www.readbyqxmd.com/read/29151205/filamentous-bacteriophage-viruses-preparation-magic-angle-spinning-solid-state-nmr-experiments-and-structure-determination
#17
Omry Morag, Nikolaos G Sgourakis, Gili Abramov, Amir Goldbourt
Filamentous bacteriophages are elongated semi-flexible viruses that infect bacteria. They consist of a circular single-stranded DNA (ssDNA) wrapped by a capsid consisting of thousands of copies of a major coat protein subunit. Given the increasing number of discovered phages and the existence of only a handful of structures, the development of methods for phage structure determination is valuable for biophysics and structural virology. In recent years, we developed and applied techniques to elucidate the 3D atomic-resolution structures of intact bacteriophages using experimental magic-angle spinning (MAS) solid-state NMR data...
2018: Methods in Molecular Biology
https://www.readbyqxmd.com/read/29150724/presence-of-chlamydia-trachomatis-and-mycoplasma-spp-but-not-neisseria-gonorrhoeae-and-treponema-pallidum-in-women-undergoing-an-infertility-evaluation-high-prevalence-of-tetracycline-resistance-gene-tet-m
#18
Min Li, Xiaomei Zhang, Ke Huang, Haixiang Qiu, Jilei Zhang, Yuan Kang, Chengming Wang
Chlamydia trachomatis, Mycoplasma spp., Neisseria gonorrhoeae and Treponema pallidum are sexually transmitted pathogens that threaten reproductive health worldwide. In this study, vaginal swabs obtained from women (n = 133) that attended an infertility clinic in China were tested with qPCRs for C. trachomatis, Mycoplasma spp., N. gonorrhoeae, T. pallidum and tetracycline resistance genes. While none of vaginal swabs were positive for N. gonorrhoeae and T. pallidum, 18.8% (25/133) of the swabs were positive for Chlamydia spp...
November 17, 2017: AMB Express
https://www.readbyqxmd.com/read/29149908/exosomal-micrornas-as-potential-circulating-biomarkers-in-gastrointestinal-tract-cancers-a-systematic-review-protocol
#19
Elmira Gheytanchi, Zahra Madjd, Leila Janani, Arezoo Rasti, Roya Ghods, Fatemeh Atyabi, Mohammad Hossein Asadi Lari, Sadegh Babashah
BACKGROUND: Metastasis is the most frequent type of recurrence in gastrointestinal (GI) cancers, and there is an emerging potential for new diagnostic and therapeutic approaches, especially in the cases of metastatic GI carcinomas. The expression profiles of circulating exosomal microRNAs are of particular interest as novel non-invasive diagnostic and prognostic biomarkers for improved detection of GI cancers in body fluids, especially in the serum of patients with recurrent cancers. The aim of this study is to systematically review primary studies and identify the miRNA profiles of serum exosomes of GI cancers...
November 17, 2017: Systematic Reviews
https://www.readbyqxmd.com/read/29149898/detection-of-plasmodium-falciparum-male-and-female-gametocytes-and-determination-of-parasite-sex-ratio-in-human-endemic-populations-by-novel-cheap-and-robust-rtqpcr-assays
#20
Federica Santolamazza, Pamela Avellino, Giulia Siciliano, Franck Adama Yao, Fabrizio Lombardo, Jean Bosco Ouédraogo, David Modiano, Pietro Alano, Valentina Dianora Mangano
BACKGROUND: The presence of Plasmodium falciparum gametocytes in peripheral blood is essential for human to mosquito parasite transmission. The detection of submicroscopic infections with gametocytes and the estimation of the gametocyte sex ratio are crucial to assess the human host potential ability to infect mosquitoes and transmit malaria parasites. AIM AND OBJECTIVES: The aim of this work was to develop sensitive and cheap Real Time qPCR assays for large-scale epidemiological surveys, based on detection and amplification of gametocyte sex specific transcripts selected from the literature: the female-specific pfs25 and pf glycerol kinase (pfGK) and the male-specific pfs230p and pf13 transcripts...
November 17, 2017: Malaria Journal
keyword
keyword
17289
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"