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https://www.readbyqxmd.com/read/28882788/efficient-detection-of-chromosome-imbalances-and-exome-single-nucleotide-variants-using-targeted-sequencing-in-the-clinical-setting
#1
Darine Villela, Silvia Souza da Costa, Angela M Vianna-Morgante, Ana C V Krepischi, Carla Rosenberg
We evaluated an approach to detect copy number variants (CNVs) and single nucleotide changes (SNVs), using a clinically focused exome panel complemented with a backbone and SNP probes that allows for genome-wide copy number changes and copy-neutral absence of heterozygosity (AOH) calls; this approach potentially substitutes the use of chromosomal microarray testing and sequencing into a single test. A panel of 16 DNA samples with known alterations ranging from megabase-scale CNVs to single base modifications were used as positive controls for sequencing data analysis...
September 4, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28871208/identify-latent-chromosomal-aberrations-relevant-to-myelodysplastic-syndromes
#2
Qibin Song, Yuxin Chu, Yi Yao, Min Peng, Weihong Yang, Xiaoqing Li, Shiang Huang
Myelodysplastic syndromes (MDS) are a group of heterogeneous hematologic malignancies. This study aims to identify latent chromosomal abnormalities relevant to MDS, which may optimize the current diagnosis of MDS. Affymetrix CytoScan 750 K microarray platform was utilized to perform a genome-wide detection of chromosomal aberrations in the bone marrow cells of the patients. The findings were compared with the results from traditional karyotypic analysis and FISH to reveal latent chromosomal aberrations. Chromosomal gain, loss, and UPD, and complex karyotypes were identified in those samples...
September 4, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28864461/somatic-uniparental-disomy-of-chromosome-16p-in-hemimegalencephaly
#3
Nicole G Griffin, Kenneth D Cronin, Nicole M Walley, Christine M Hulette, Gerald A Grant, Mohamad A Mikati, Heather G LaBreche, Catherine W Rehder, Andrew S Allen, Peter B Crino, Erin L Heinzen
Hemimegalencephaly (HME) is a heterogeneous cortical malformation characterized by enlargement of one cerebral hemisphere. Somatic variants in mammalian target of rapamycin (mTOR) regulatory genes have been implicated in some HME cases; however, ∼70% have no identified genetic etiology. Here, we screened two HME patients to identify disease-causing somatic variants. DNA from leukocytes, buccal swabs, and surgically resected brain tissue from two HME patients were screened for somatic variants using genome-wide genotyping arrays or sequencing of the protein-coding regions of the genome...
September 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/28840990/a-unique-mutational-spectrum-of-mlc1-in-korean-patients-with-megalencephalic-leukoencephalopathy-with-subcortical-cysts-p-ala275asp-founder-mutation-and-maternal-uniparental-disomy-of-chromosome-22
#4
Sun Ah Choi, Soo Yeon Kim, Jihoo Yoon, Joongmoon Choi, Sung Sup Park, Moon Woo Seong, Hunmin Kim, Hee Hwang, Ji Eun Choi, Jong Hee Chae, Ki Joong Kim, Seunghyo Kim, Yun Jin Lee, Sang Ook Nam, Byung Chan Lim
BACKGROUND: Megalencephalic leukoencephalopathy with subcortical cysts (MLC) is a rare inherited disorder characterized by infantile-onset macrocephaly, slow neurologic deterioration, and seizures. Mutations in the causative gene, MLC1, are found in approximately 75% of patients and are inherited in an autosomal recessive manner. We analyzed MLC1 mutations in five unrelated Korean patients with MLC. METHODS: Direct Sanger sequencing was used to identify MLC1 mutations...
November 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/28805612/detection-of-paternal-uniparental-disomy-9-in-a-neonate-with-prenatally-detected-mosaicism-for-a-small-supernumerary-marker-chromosome-9-and-a-supernumerary-ring-chromosome-9
#5
Chih-Ping Chen, Ming Chen, Liang-Kai Wang, Schu-Rern Chern, Peih-Shan Wu, Shin-Wen Chen, Shih-Ting Lai, Shun-Ping Chang, Chien-Wen Yang, Chen-Wen Pan, Wayseen Wang
OBJECTIVE: We present the association of paternal uniparental disomy (UPD) 9 with mosaicism for a small supernumerary marker chromosome 9 [sSMC(9)] and a supernumerary ring chromosome 9 [r(9)]. MATERIALS AND METHODS: A 38-year-old woman underwent amniocentesis at 17 weeks of gestation because of advanced maternal age. Amniocentesis revealed a karyotype of 47,XY,+mar [25]/48,XY,+mar,+r(9) [4]/47,XY,+r(9) [1]/46,XY [6]. The parental karyotypes were normal. Array comparative genomic hybridization (aCGH) of cultured amniocytes revealed a result of de novo 9p13...
August 2017: Taiwanese Journal of Obstetrics & Gynecology
https://www.readbyqxmd.com/read/28780152/functional-genomic-exploration-reveals-that-ss-riok-1-is-essential-for-the-development-and-survival-of-strongyloides-stercoralis-larvae
#6
Wang Yuan, Huan Zhou, James B Lok, Weiqiang Lei, Siyuan He, Robin B Gasser, Rui Zhou, Rui Fang, Yanqin Zhou, Junlong Zhao, Min Hu
Protein kinase RIOK-1 is a non-ribosomal factor essential for rRNA cleavage and ribosome small subunit maturation. It is encoded in all eukaryotic organisms. The RIOK-1 encoding gene of Caenorhabditis elegans (Ce-riok-1) is expressed in the neuronal and reproductive systems in larvae and adults of this free-living nematode, and it supports larval growth and development of the adult gonad. In spite of its recognised roles in model organisms such as C. elegans, little is known about the function of this molecule in parasitic nematodes...
August 3, 2017: International Journal for Parasitology
https://www.readbyqxmd.com/read/28770003/formation-of-upd-7-mat-by-trisomic-rescue-snp-array-typing-provides-new-insights-in-chromosomal-nondisjunction
#7
Sandra Chantot-Bastaraud, Svea Stratmann, Frédéric Brioude, Matthias Begemann, Miriam Elbracht, Luitgard Graul-Neumann, Madeleine Harbison, Irène Netchine, Thomas Eggermann
BACKGROUND: Maternal uniparental disomy (UPD) of chromosome 7 (upd(7)mat) accounts for approximately 10% of patients with Silver-Russell syndrome (SRS). For upd(7)mat and trisomy 7, a significant number of mechanisms have been proposed to explain the postzygotic formation of these chromosomal compositions, but all have been based on as small number of cases. To obtain the ratio of isodisomy and heterodisomy in UPDs (hUPD, iUPD) and to determine the underlying formation mechanisms, we analysed a large cohort of upd(7)mat patients (n = 73) by SNP array typing...
2017: Molecular Cytogenetics
https://www.readbyqxmd.com/read/28746920/assessing-the-clinical-utility-of-snp-microarray-for-prader-willi-syndrome-due-to-uniparental-disomy
#8
Stephanie L Santoro, Sayaka Hashimoto, Aimee McKinney, Theresa Mihalic Mosher, Robert Pyatt, Shalini C Reshmi, Caroline Astbury, Scott E Hickey
Maternal uniparental disomy (UPD) 15 is one of the molecular causes of Prader-Willi syndrome (PWS), a multisystem disorder which presents with neonatal hypotonia and feeding difficulty. Current diagnostic algorithms differ regarding the use of SNP microarray to detect PWS. We retrospectively examined the frequency with which SNP microarray could identify regions of homozygosity (ROH) in patients with PWS. We determined that 7/12 (58%) patients with previously confirmed PWS by methylation analysis and microsatellite-positive UPD studies had ROH (>10 Mb) by SNP microarray...
July 27, 2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28675902/the-diagnostic-value-of-igf-2-and-the-igf-igfbp-3-system-in-silver-russell-syndrome
#9
Gerhard Binder, Thomas Eggermann, Karin Weber, Nawfel Ferrand, Roland Schweizer
BACKGROUND/AIMS: Recently, we have described a family of 4 members presenting with intrauterine and postnatal growth failure, low IGF-2 levels, and signs of Silver-Russell syndrome (SRS) who carried a genomic IGF2 mutation. Here, we assess the value of IGF-2 in relation to SRS. METHODS: We collected data from 48 SRS children and 48 short children born small for gestational age (SGA) seen at our center. The SRS children were 4.6 ± 2.0 years of age, and the SGA children were 4...
July 4, 2017: Hormone Research in Pædiatrics
https://www.readbyqxmd.com/read/28668702/differential-expression-of-novel-micrornas-in-response-to-the-infection-of-a-tmv-mutant-with-an-internal-poly-a-tract-in-n-benthamiana
#10
Song Guo, Ya-Chih Hsueh, Greg Tucker-Kellogg, Sek-Man Wong
We first constructed small RNA libraries of TMV- and TMV-43A-infected N. benthamiana for high throughput sequencing. A total number of 181 novel microRNAs (miRNAs) were identified through an improved miRNAs analysis pipeline. We were able to identify consistent miRNA expression changes induced in TMV and TMV-43A-infected plants, as well as differences associated with the UPD substitution in the TMV-43A viral genome. Virally induced miRNAs are associated with distinct processes and functions of predicted mRNA targets, including relation to host target defense...
June 29, 2017: Virus Research
https://www.readbyqxmd.com/read/28647735/uniparental-disomy-of-chromosome-15-in-two-cases-by-chromosome-microarray-a-lesson-worth-thinking
#11
Shu Liu, Kaihui Zhang, Fengling Song, Yali Yang, Yuqiang Lv, Min Gao, Yi Liu, Zhongtao Gai
Prader-Willi syndrome (PWS) and Angelman syndrome (AS) are neurogenetic disorders caused by loss of function of the imprinted genes at 15q11q13. A 5-7 Mb paternal/maternal deletion of chromosomal region 15q11.2q13 is the major genetic cause of PWS/AS, but in a small group of patients, the PWS/AS phenotype can result from maternal/paternal uniparental disomy (UPD) of chromosome 15. Various mechanisms leading to UPD include gametic complementation, trisomy rescue, and compensatory UPD, which can be inferred from the pattern of uniparental heterodisomy (heteroUPD) or uniparental isodisomy (isoUPD)...
2017: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/28640239/temple-syndrome-comprehensive-molecular-and-clinical-findings-in-32-japanese-patients
#12
Masayo Kagami, Keisuke Nagasaki, Rika Kosaki, Reiko Horikawa, Yasuhiro Naiki, Shinji Saitoh, Toshihiro Tajima, Tohru Yorifuji, Chikahiko Numakura, Seiji Mizuno, Akie Nakamura, Keiko Matsubara, Maki Fukami, Tsutomu Ogata
PurposeTemple syndrome (TS14) is a rare imprinting disorder caused by aberrations at the 14q32.2 imprinted region. Here, we report comprehensive molecular and clinical findings in 32 Japanese patients with TS14.MethodsWe performed molecular studies for TS14 in 356 patients with variable phenotypes, and clinical studies in all TS14 patients, including 13 previously reported.ResultsWe identified 19 new patients with TS14, and the total of 32 patients was made up of 23 patients with maternal uniparental disomy (UPD(14)mat), six patients with epimutations, and three patients with microdeletions...
June 22, 2017: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/28624953/genome-wide-analysis-of-differential-dna-methylation-in-silver-russell-syndrome
#13
Di Wu, Chunxiu Gong, Chang Su
Silver-Russell Syndrome (SRS) is clinically heterogeneous disorder characterized by low birth weight, postnatal growth restriction, and variable dysmorphic features. Current evidence strongly implicates imprinted genes as an important etiology of SRS. Although almost half of the patients showed DNA hypomethylation at the H19/IGF2 imprinted domain, and approximately 7%-10% of SRS patients have maternal uniparental disomy of chromosome 7 (UPD (7) mat); the rest of the SRS patients shows unknown etiology. In this study, we investigate whether there are further DNA methylation defects in SRS patients...
July 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28620746/uniparental-disomy-as-an-unexpected-cause-of-meckel-gruber-syndrome-report-of-a-case
#14
Nadia Ortiz Bruechle, Peter Steuernagel, Klaus Zerres, Ingo Kurth, Thomas Eggermann, Cordula Knopp
BACKGROUND: Meckel-Gruber syndrome (MKS, OMIM #607361) is a rare pre- or perinatal lethal autosomal recessive ciliopathy caused by mutations in at least 12 known genes. It has a clinical and genetic overlap with other viable ciliopathies, especially Joubert syndrome and Joubert syndrome-related disorders. MKS is characterized by multicystic kidney dysplasia, central nervous system malformations (usually occipital encephalocele), ductal plate malformation of the liver, and postaxial polydactyly...
June 15, 2017: Pediatric Nephrology: Journal of the International Pediatric Nephrology Association
https://www.readbyqxmd.com/read/28611321/salivary-interleukin-6-a-pioneering-marker-for-correlating-diabetes-and-chronic-periodontitis-a-comparative-study
#15
Anitha Balaji, S C Chandrasekaran, D Subramanium, A B Fernz
BACKGROUND: Periodontitis is a chronic inflammatory disease which is multifactorial. Diabetes mellitus (DM) is one of the major systemic factors to influence the severity of chronic periodontitis. Numerous inflammatory markers are produced in the course of the disease which is secreted in saliva too. This study evaluates the salivary concentrations of interleukin-6 (IL-6) in periodontitis patients with type 2 diabetes. MATERIALS AND METHODS: Whole saliva samples were collected from eighty patients who were further divided into four groups; healthy (control group; n = 20), untreated periodontitis (UPD; n = 20), DM (DM; n = 20), and UPD + DM (n = 20 groups)...
March 2017: Indian Journal of Dental Research: Official Publication of Indian Society for Dental Research
https://www.readbyqxmd.com/read/28602932/postzygotic-telomere-capture-causes-segmental-upd-duplication-and-deletion-of-chromosome-8p-in-a-patient-with-intellectual-disability-and-obesity
#16
Jeroen Knijnenburg, Madiek E W Uytdewilligen, Daniella A C M van Hassel, Rianne Oostenbrink, Bert H J Eussen, Annelies de Klein, Alice S Brooks, Laura J C M van Zutven
Using SNP array and FISH analysis, a patient with moderate intellectual disability and obesity was found to harbour an atypical 1.6 Mb inverted duplication on 8p23.1, directly flanked by a distally located interstitial deletion of 2.3 Mb and a terminal segmental uniparental disomy. The duplicated and deleted regions lie exactly between the two segmental duplication regions. These segmental duplications on chromosome 8p23.1 are known to be involved in chromosomal rearrangements because of mutual homology and homology to other genomic regions...
June 8, 2017: European Journal of Medical Genetics
https://www.readbyqxmd.com/read/28594454/precise-control-of-the-lateral-and-vertical-growth-of-two-dimensional-ag-nanoplates
#17
Taixing Tan, Lili Yao, Huiling Liu, Chengyu Li, Cheng Wang
Tuning localized surface plasmon resonance (LSPR) is crucial for practical applications of two-dimensional Ag nanoplates (AgNPs) and relies on the precise control of their lateral length or/and thickness. In the present seed-mediated synthetic method, by taking advantage of underpotential deposition (UPD) of Cu on the (111) surfaces of AgNPs, a solely lateral growth of AgNPs was achieved when Cu(NO3 )2 was employed, while a vertical growth of AgNPs could be attained by introducing CuCl2 into our growth solutions...
June 8, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28588434/maternal-uniparental-disomy-14-temple-syndrome-as-a-result-of-a-robertsonian-translocation
#18
Veronica Bertini, Antonella Fogli, Rossella Bruno, Alessia Azzarà, Angela Michelucci, Teresa Mattina, Silvano Bertelloni, Angelo Valetto
Maternal uniparental disomy of chromosome 14 (upd(14)mat) or Temple syndrome is an imprinting disorder associated with a relatively mild phenotype. The absence of specific congenital malformations makes this condition underdiagnosed in clinical practice. A boy with a de novo robertsonian translocation 45,XY,rob(13;14)(q10;q10) is reported; a CGH/SNP array showed a loss of heterozygosity in 14q11.2q13.1. The final diagnosis of upd(14)mat was made by microsatellite analysis, which showed a combination of heterodisomy and isodisomy for different regions of chromosome 14...
May 2017: Molecular Syndromology
https://www.readbyqxmd.com/read/28546998/uniparental-disomy-determined-by-whole-exome-sequencing-in-a-spectrum-of-rare-motoneuron-diseases-and-ataxias
#19
Dana M Bis, Rebecca Schüle, Jennifer Reichbauer, Matthis Synofzik, Tim W Rattay, Anne Soehn, Peter de Jonghe, Ludger Schöls, Stephan Züchner
BACKGROUND: The genetic causes of many rare inherited motoneuron diseases and ataxias (MND and ATX) remain largely unresolved, especially for sporadic patients, despite tremendous advances in gene discovery. Whole exome data is often available for patients, but it is rarely evaluated for unusual inheritance patterns, such as uniparental disomy (UPD). UPD is the inheritance of two copies of a chromosomal region from one parent, which may generate homozygosity for a deleterious recessive variant from only one carrier-parent...
May 2017: Molecular Genetics & Genomic Medicine
https://www.readbyqxmd.com/read/28534844/property-analysis-of-the-real-time-uncalibrated-phase-delay-product-generated-by-regional-reference-stations-and-its-influence-on-precise-point-positioning-ambiguity-resolution
#20
Yong Zhang, Qing Wang, Xinyuan Jiang
The real-time estimation of the wide-lane and narrow-lane Uncalibrated Phase Delay (UPD) of satellites is realized by real-time data received from regional reference station networks; The properties of the real-time UPD product and its influence on real-time precise point positioning ambiguity resolution (RTPPP-AR) are experimentally analyzed according to real-time data obtained from the regional Continuously Operating Reference Stations (CORS) network located in Tianjin, Shanghai, Hong Kong, etc. The results show that the real-time wide-lane and narrow-lane UPD products differ significantly from each other in time-domain characteristics; the wide-lane UPDs have daily stability, with a change rate of less than 0...
May 19, 2017: Sensors
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