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https://www.readbyqxmd.com/read/29020724/chromothripsis-in-treatment-resistance-in-multiple-myeloma
#1
Kyoung Joo Lee, Ki Hong Lee, Kyong-Ah Yoon, Ji Yeon Sohn, Eunyoung Lee, Hyewon Lee, Hyeon-Seok Eom, Sun-Young Kong
Multiple myeloma (MM) is a malignant disease caused by an abnormal proliferation of plasma cells, of which the prognostic factors include chromosomal abnormality, β-2 microglobulin, and albumin. Recently, the term chromothripsis has emerged, which is the massive but highly localized chromosomal rearrangement in response to a one-step catastrophic event. Many studies have shown an association of chromothripsis with the prognosis in several cancers; however, few studies have investigated it in MM. Here, we studied the association between chromothripsis-like patterns and treatment resistance or prognosis...
September 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29020723/chromosomal-microarray-testing-in-42-korean-patients-with-unexplained-developmental-delay-intellectual-disability-autism-spectrum-disorders-and-multiple-congenital-anomalies
#2
Sun Ho Lee, Wung Joo Song
Chromosomal microarray (CMA) is a high-resolution, high-throughput method of identifying submicroscopic genomic copy number variations (CNVs). CMA has been established as the first-line diagnostic test for individuals with developmental delay (DD), intellectual disability (ID), autism spectrum disorders (ASDs), and multiple congenital anomalies (MCAs). CMA analysis was performed in 42 Korean patients who had been diagnosed with unexplained DD, ID, ASDs, and MCAs. Clinically relevant CNVs were discovered in 28 patients...
September 2017: Genomics & Informatics
https://www.readbyqxmd.com/read/29018424/sample-preservation-dna-or-rna-extraction-and-data-analysis-for-high-throughput-phytoplankton-community-sequencing
#3
Anita Mäki, Pauliina Salmi, Anu Mikkonen, Anke Kremp, Marja Tiirola
Phytoplankton is the basis for aquatic food webs and mirrors the water quality. Conventionally, phytoplankton analysis has been done using time consuming and partly subjective microscopic observations, but next generation sequencing (NGS) technologies provide promising potential for rapid automated examination of environmental samples. Because many phytoplankton species have tough cell walls, methods for cell lysis and DNA or RNA isolation need to be efficient to allow unbiased nucleic acid retrieval. Here, we analyzed how two phytoplankton preservation methods, three commercial DNA extraction kits and their improvements, three RNA extraction methods, and two data analysis procedures affected the results of the NGS analysis...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/29018163/mtdna-copy-number-associated-with-age-of-onset-in-familial-amyloid-polyneuropathy
#4
Diana Santos, Maria João Santos, Miguel Alves-Ferreira, Teresa Coelho, Jorge Sequeiros, Isabel Alonso, Pedro Oliveira, Alda Sousa, Carolina Lemos, Manuela Grazina
BACKGROUND: Transthyretin-related familial amyloid polyneuropathy (TTR-FAP Val30Met) shows a wide variation in age-at-onset (AO) between generations and genders, as in Portuguese families, where women display a later onset and a larger anticipation (>10 years). Mitochondrial DNA (mtDNA) copy number was assessed to clarify whether it has a modifier effect on AO variability in Portuguese patients. METHODS: The mtDNA copy number of 262 samples (175 Val30Met TTR carriers and 87 controls (proven Val30Val)) was quantified by quantitative real-time PCR...
October 10, 2017: Journal of Neurology, Neurosurgery, and Psychiatry
https://www.readbyqxmd.com/read/29017575/evidence-for-viable-and-stable-triploid-trypanosoma-congolense-parasites
#5
Eliane Tihon, Hideo Imamura, Jean-Claude Dujardin, Jan Van Den Abbeele
BACKGROUND: Recent whole genome sequencing (WGS) analysis identified a viable triploid strain of Trypanosoma congolense. This triploid strain BANANCL2 was a clone of the field isolate BANAN/83/CRTRA/64 that was collected from cattle in Burkina Faso in 1983. RESULTS: We demonstrated the viability and stability of triploidy throughout the complete life-cycle of the parasite by infecting tsetse flies with the triploid clone BANANCL2. Proboscis-positive tsetse flies efficiently transmitted the parasites to mice resulting in systemic infections...
October 10, 2017: Parasites & Vectors
https://www.readbyqxmd.com/read/29017567/impairment-of-igf2-gene-expression-in-prostate-cancer-is-triggered-by-epigenetic-dysregulation-of-igf2-dmr0-and-its-interaction-with-klf4
#6
Undraga Schagdarsurengin, Angela Lammert, Natalie Schunk, Diana Sheridan, Stefan Gattenloehner, Klaus Steger, Florian Wagenlehner, Temuujin Dansranjavin
BACKGROUND: Human cancer cells often exhibit impaired IGF2 expression and the underlying mechanisms are multifaceted and complex. Besides the well-known imprinting control region IGF2/H19-ICR, the involvement of a differentially methylated region in the promoter P0 of IGF2 gene (IGF2-DMR0) has been suggested. Here, we evaluate several mechanisms potentially leading to up- and/or down-regulation of IGF2 expression in prostate cancer and present a novel role of Kruppel-like factor 4 (KLF4) as a transcriptional regulator of IGF2 binding in IGF2-DMR0...
October 10, 2017: Cell Communication and Signaling: CCS
https://www.readbyqxmd.com/read/29016839/prognostic-relevance-of-genetic-alterations-in-diffuse-lower-grade-gliomas
#7
Kosuke Aoki, Hideo Nakamura, Hiromichi Suzuki, Keitaro Matsuo, Keisuke Kataoka, Teppei Shimamura, Kazuya Motomura, Fumiharu Ohka, Satoshi Shiina, Takashi Yamamoto, Yasunobu Nagata, Tetsuichi Yoshizato, Masahiro Mizoguchi, Tatsuya Abe, Yasutomo Momii, Yoshihiro Muragaki, Reiko Watanabe, Ichiro Ito, Masashi Sanada, Hironori Yajima, Naoya Morita, Ichiro Takeuchi, Satoru Miyano, Toshihiko Wakabayashi, Seishi Ogawa, Atsushi Natsume
Background: Diffuse lower-grade gliomas (LGGs) are genetically classified into 3 distinct subtypes based on isocitrate dehydrogenase (IDH) mutation status and codeletion of chromosome 1p and 19q (1p/19q). However, the subtype-specific effects of additional genetic lesions on survival are largely unknown. Methods: Using Cox proportional hazards regression modeling, we investigated the subtype-specific effects of genetic alterations and clinicopathological factors on survival in each LGG subtype, in a Japanese cohort of LGG cases fully genotyped for driver mutations and copy number variations associated with LGGs (n = 308)...
July 18, 2017: Neuro-oncology
https://www.readbyqxmd.com/read/28993849/identification-of-novel-congenital-heart-disease-candidate-genes-using-chromosome-microarray
#8
Enas Shanshen, Janine Rosenberg, Andrew H Van Bergen
While the majority of patients have isolated heart disease, congenital heart disease (CHD) may be associated with other congenital anomalies or syndromes. Our institution utilizes chromosomal microarray (CMA) to identify chromosomal abnormalities, specifically copy number variations (CNVs). While CNVs have been associated with CHD, their direct impact on cardiac development remains unclear. This study sought to identify potential novel CHD candidate genes by comparing CNVs present in our institution's CHD population with those already recognized in the literature...
October 9, 2017: Pediatric Cardiology
https://www.readbyqxmd.com/read/28993626/the-application-of-thermophilic-dna-primase-ttdnag2-to-dna-amplification
#9
De Zhao, Xiuqiang Chen, Kuan Li, Yu V Fu
For DNA replication in vivo, DNA primase uses a complementary single-stranded DNA template to synthesize RNA primers ranging from 4 to 20 nucleotides in length, which are then elongated by DNA polymerase. Here, we report that, in the presence of double-stranded DNA, the thermophilic DNA primase TtDnaG2 synthesizes RNA primers of around 100 nucleotides with low initiation specificity at 70 °C. Analysing the structure of TtDnaG2, we identified that it adopts a compact conformation. The conserved sites in its zinc binding domain are sequestered away from its RNA polymerase domain, which might give rise to the low initiation specificity and synthesis of long RNA segments by TtDnaG2...
October 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28988007/chromosome-copy-number-variation-in-telomerized-human-bone-marrow-stromal-cells-insights-for-monitoring-safe-ex-vivo-expansion-of-adult-stem-cells
#10
Jorge S Burns, Linda Harkness, Abdullah Aldahmash, Laurent Gautier, Moustapha Kassem
Adult human bone marrow stromal cells (hBMSC) cultured for cell therapy require evaluation of potency and stability for safe use. Chromosomal aberrations upsetting genomic integrity in such cells have been contrastingly described as "Limited" or "Significant". Previously reported stepwise acquisition of a spontaneous neoplastic phenotype during three-year continuous culture of telomerized cells (hBMSC-TERT20) didn't alter a diploid karyotype measured by spectral karyotype analysis (SKY). Such screening may not adequately monitor abnormal and potentially tumorigenic hBMSC in clinical scenarios...
September 25, 2017: Stem Cell Research
https://www.readbyqxmd.com/read/28986787/copy-number-variation-analysis-by-droplet-digital-pcr
#11
Suvi K Härmälä, Robert Butcher, Chrissy H Roberts
The health impact of many copy number variants in our genome remains still largely to be discovered. Detecting and genotyping this often complex variation presents a technical challenge. Here we describe a 96-well format droplet digital PCR (ddPCR) protocol for genotyping a common copy variant in the human haptoglobin gene. ddPCR allows for high-throughput and accurate quantitation of gene copy numbers.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28984810/strc-deletion-is-a-frequent-cause-of-slight-to-moderate-congenital-hearing-impairment-in-the-czech-republic
#12
Pavlina Plevova, Martina Paprskarova, Petra Tvrda, Petra Turska, Rastislav Slavkovsky, Eva Mrazkova
OBJECTIVE: This study aimed to clarify the molecular epidemiology of hearing loss by identifying the responsible genes in patients without GJB2 mutations. STUDY DESIGN: Prospective genetic study. SETTING: Tertiary referral hospital. PATIENTS: Fifty one patients with bilateral sensorineural hearing loss, 20 men, and 31 women, mean age 24.9 years, range 3 to 64 years, from 49 families. GJB2 and deltaGJB6-D13S1830 mutations were excluded previously...
October 4, 2017: Otology & Neurotology
https://www.readbyqxmd.com/read/28984711/genomic-organization-of-tbk1-copy-number-variations-in-glaucoma-patients
#13
Adam P DeLuca, L M Alward Wallace, Jeffrey Liebmann, Robert Ritch, Kazuhide Kawase, Young H Kwon, Alan L Robin, Edwin M Stone, Todd E Scheetz, John H Fingert
BACKGROUND: Approximately 1% of normal tension glaucoma cases are caused by TANK binding kinase 1 (TBK1) gene duplications and triplications. However, the precise borders and orientation of these TBK1 gene copy number variations (CNVs) on chromosome 12 are unknown. METHODS: We determined the exact borders of TBK1 CNVs and the orientation of duplicated or triplicated DNA segments in five NTG patients with different TBK1 mutations using whole genome sequencing. RESULTS: Tandemly duplicated chromosome segments spanning the TBK1 gene were detected in four NTG patients, each with unique borders...
September 3, 2017: Journal of Glaucoma
https://www.readbyqxmd.com/read/28984674/targeted-genomic-profiling-reveals-recurrent-kras-mutations-in-mesonephric-like-adenocarcinomas-of-the-female-genital-tract
#14
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/28984673/toward-biological-subtyping-of-papillary-renal-cell-carcinoma-with-clinical-implications-through-histologic-immunohistochemical-and-molecular-analysis
#15
Rola M Saleeb, Fadi Brimo, Mina Farag, Alexis Rompré-Brodeur, Fabio Rotondo, Vidya Beharry, Samantha Wala, Pamela Plant, Michelle R Downes, Kenneth Pace, Andrew Evans, Georg Bjarnason, John M S Bartlett, George M Yousef
Papillary renal cell carcinoma (PRCC) has 2 histologic subtypes. Almost half of the cases fail to meet all morphologic criteria for either type, hence are characterized as PRCC not otherwise specified (NOS). There are yet no markers to resolve the PRCC NOS category. Accurate classification can better guide the management of these patients. In our previous PRCC study we identified markers that can distinguish between the subtypes. A PRCC patient cohort of 108 cases was selected for the current study. A panel of potentially distinguishing markers was chosen from our previous genomic analysis, and assessed by immunohistochemistry...
October 3, 2017: American Journal of Surgical Pathology
https://www.readbyqxmd.com/read/28984479/comprehensive-characterization-of-differentially-expressed-genes-in-thyroid-cancer
#16
Jian Wang, Shumei Chi, Zhongke Huang, Xiaojuan Ye, Guohua Shi, Dongfang Chen, Cen Lou
AIM: To explore the patterns of gene expression and functionally characterize the differentially expressed genes (DEGs) in thyroid cancer. METHODS: DEGs were determined between 57 paired thyroid cancer and noncancerous tissues using DESeq2. Subsequently, the main functions of the DEGs were studied by a variety of analyses. RESULTS: We identified a cohort of 752 upregulated and 309 downregulated DEGs in thyroid cancer. Several hub DEGs were found in the protein-protein interaction networks...
October 6, 2017: Future Oncology
https://www.readbyqxmd.com/read/28984295/r-baclofen-reverses-cognitive-deficits-and-improves-social-interactions-in-two-lines-of-16p11-2-deletion-mice
#17
Laura J Stoppel, Tatiana M Kazdoba, Melanie D Schaffler, Anthony R Preza, Arnold Heynen, Jacqueline N Crawley, Mark F Bear
Human chromosome 16p11.2 microdeletion is among the most common gene copy number variations (CNVs) known to confer risk for intellectual disability (ID) and autism spectrum disorder (ASD), and affects an estimated 3 in 10 000 people. Caused by a single copy deletion of ~27 genes, 16p11.2 microdeletion syndrome is characterized by ID, impaired language, communication and socialization skills, and ASD. Studies in animal models where a single copy of the syntenic 16p11.2 region has been deleted have revealed morphological, behavioral, and electrophysiological abnormalities...
October 6, 2017: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/28984186/penncnv-in-whole-genome-sequencing-data
#18
Leandro de Araújo Lima, Kai Wang
BACKGROUND: The use of high-throughput sequencing data has improved the results of genomic analysis due to the resolution of mapping algorithms. Although several tools for copy-number variation calling in whole genome sequencing have been published, the noisy nature of sequencing data is still a limitation for accuracy and concordance among such tools. To assess the performance of PennCNV original algorithm for array data in whole genome sequencing data, we processed mapping (BAM) files to extract coverage, representing log R ratio (LRR) of signal intensity, and B allele frequency (BAF)...
October 3, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28981949/-result-of-prenatal-diagnosis-for-151-high-risk-women-by-noninvasive-prenatal-screening-based-on-high-throughput-sequencing
#19
Yifang Jia, Yan Zhang, Wanxiao Hao, Donghong Shi, Jinlai Meng, Heyong Zhao, Yan Lian, Luwen Xie, Xietong Wang
OBJECTIVE: To assess the value of combined fetal karyotyping and chromosomal microarray analysis (CMA) for the verification of high-risk pregnancy signaled by noninvasive prenatal screening (NIPS) based on high-throughput sequencing. METHODS: One hundred and fifty-one pregnant women with high risks for aneuploidies of chromosomes 13, 18, 21, X and Y or pathological copy number variations (CNVs) by NIPS were subjected to amniocytic karyotyping and CMA analysis. RESULTS: One hundred and forty-two women were found to have a high risk for fetal chromosomal aneuploidies, which included 83 cases of trisomy 21, 17 cases of trisomy 18, 2 cases of trisomy 13, and 40 cases of sex chromosome aneuploidies...
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/28981937/-application-of-chromosomal-microarray-analysis-for-fetuses-with-ventricular-septal-defects
#20
Qiong Deng, Fang Fu, Ru Li, Xiangyi Jing, Tingying Lei, Xin Yang, Min Pan, Li Zhen, Jin Han, Can Liao
OBJECTIVE: To explore the genetic etiology of fetuses with ventricular septal defects (VSD) using chromosomal microarray analysis (CMA). METHODS: A total of 248 fetuses were divided into isolated VSD group, VSD with other cardiac and/or great vessels malformation group, VSD with extra-cardiac anomalies group (including malformation and sonographic soft markers), and VSD with both cardiac and extra-cardiac anomalies group. Standard karyotyping was carried out for all fetuses, and CMA was performed for 6 fetuses with an abnormal karyotype and a proportion of fetuses with a normal karyotype...
October 10, 2017: Zhonghua Yi Xue Yi Chuan Xue za Zhi, Zhonghua Yixue Yichuanxue Zazhi, Chinese Journal of Medical Genetics
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