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https://www.readbyqxmd.com/read/29458049/a-comprehensive-brca1-2-ngs-pipeline-for-an-immediate-copy-number-variation-cnv-detection-in-breast-and-ovarian-cancer-molecular-diagnosis
#1
Paola Concolino, Roberta Rizza, Flavio Mignone, Alessandra Costella, Donatella Guarino, Ilaria Carboni, Ettore Capoluongo, Concetta Santonocito, Andrea Urbani, Angelo Minucci
No abstract text is available yet for this article.
February 16, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
https://www.readbyqxmd.com/read/29458007/a-genomically-characterized-collection-of-high-grade-serous-ovarian-cancer-xenografts-for-preclinical-testing
#2
Paulina Cybulska, Jocelyn M Stewart, Azin Sayad, Carl Virtanen, Patricia A Shaw, Blaise Clarke, Natalie Stickle, Marcus Q Bernardini, Benjamin G Neel
High-grade serous ovarian cancer (HGSC) is the leading cause of morbidity and mortality from gynecologic malignancy. Overall survival remains low, due to the nearly ubiquitous emergence of platinum-resistance and the paucity of effective next-line treatments. Current cell culture-based models show limited similarity to HGSC and are therefore unreliable predictive models for pre-clinical evaluation of investigational drugs. This deficiency could help explain the low overall rate of successful drug development and the decades of largely unchanged approaches to HGSC treatment...
February 16, 2018: American Journal of Pathology
https://www.readbyqxmd.com/read/29457755/novel-approach-for-ces1-genotyping-integrating-single-nucleotide-variants-and-structural-variation
#3
Ditte Bjerre, Henrik Berg Rasmussen
AIM: Development of a specific procedure for genotyping of CES1A1 (CES1) and CES1A2, a hybrid of CES1A1 and the pseudogene CES1P1. MATERIALS & METHODS: The number of CES1A1 and CES1A2 copies and that of CES1P1 were determined using real-time PCR. Long range PCRs followed by secondary PCRs allowed sequencing of single nucleotide variants in CES1A1 and CES1A2. Results & conlusion: A procedure consisting of two main steps was developed. Its first main step, the copy number determination, informed about presence of CES1A2 ...
February 19, 2018: Pharmacogenomics
https://www.readbyqxmd.com/read/29456827/impairment-of-social-behaviors-in-arhgef10-knockout-mice
#4
Dai-Hua Lu, Hsiao-Mei Liao, Chia-Hsiang Chen, Huang-Ju Tu, Houng-Chi Liou, Susan Shur-Fen Gau, Wen-Mei Fu
Background: Impaired social interaction is one of the essential features of autism spectrum disorder (ASD). Our previous copy number variation (CNV) study discovered a novel deleted region associated with ASD. One of the genes included in the deleted region is ARHGEF10 . A missense mutation of ARHGEF10 has been reported to be one of the contributing factors in several diseases of the central nervous system. However, the relationship between the loss of ARHGEF10 and the clinical symptoms of ASD is unclear...
2018: Molecular Autism
https://www.readbyqxmd.com/read/29455316/investigation-of-major-genetic-alterations-in-neuroblastoma
#5
Régis Afonso Costa, Héctor N Seuánez
Neuroblastoma (NB) is the most common extracranial solid tumor in childhood. This malignancy shows a wide spectrum of clinical outcome and its prognosis is conditioned by manifold biological and genetic factors. We investigated the tumor genetic profile and clinical data of 29 patients with NB by multiplex ligation-dependent probe amplification (MLPA) to assess therapeutic risk. In 18 of these tumors, MYCN status was assessed by fluorescence in situ hybridization (FISH). Copy number variation was also determined for confirming MLPA findings in two 6p loci...
February 17, 2018: Molecular Biology Reports
https://www.readbyqxmd.com/read/29454353/genetics-of-the-human-y-chromosome-and-its-association-with-male-infertility
#6
REVIEW
Stacy Colaco, Deepak Modi
The human Y chromosome harbors genes that are responsible for testis development and also for initiation and maintenance of spermatogenesis in adulthood. The long arm of the Y chromosome (Yq) contains many ampliconic and palindromic sequences making it predisposed to self-recombination during spermatogenesis and hence susceptible to intra-chromosomal deletions. Such deletions lead to copy number variation in genes of the Y chromosome resulting in male infertility. Three common Yq deletions that recur in infertile males are termed as AZF (Azoospermia Factor) microdeletions viz...
February 17, 2018: Reproductive Biology and Endocrinology: RB&E
https://www.readbyqxmd.com/read/29452578/clinical-and-genetic-study-of-20-patients-from-china-with-cornelia-de-lange-syndrome
#7
Mingyan Hei, Xiangyu Gao, Lingqian Wu
BACKGROUND: Cornelia de Lange syndrome (CdLS) is a rare congenital syndrome with no racial difference. The objective of this study is to report the clinical characteristics and genetic study of 20 CdLS cases from China. METHODS: This is an observational study. Suspected patients were referred for further confirmation, clinical treatment, and genetic testing under voluntary condition. Demographic data and family history, data of clinical manifestations including facial dysmorphism and developmental delay of each patient were collected...
February 16, 2018: BMC Pediatrics
https://www.readbyqxmd.com/read/29449410/conserved-microrna-targeting-reveals-preexisting-gene-dosage-sensitivities-that-shaped-amniote-sex-chromosome-evolution
#8
Sahin Naqvi, Daniel W Bellott, Kathy S Lin, David C Page
Mammalian X and Y Chromosomes evolved from an ordinary autosomal pair. Genetic decay of the Y led to X Chromosome inactivation (XCI) in females, but some Y-linked genes were retained during the course of sex chromosome evolution, and many X-linked genes did not become subject to XCI. We reconstructed gene-by-gene dosage sensitivities on the ancestral autosomes through phylogenetic analysis of microRNA (miRNA) target sites and compared these preexisting characteristics to the current status of Y-linked and X-linked genes in mammals...
February 15, 2018: Genome Research
https://www.readbyqxmd.com/read/29448085/plk2-loss-commonly-occurs-in-colorectal-carcinomas-but-not-adenomas-relationship-to-mtor-signaling
#9
Elizabeth M Matthew, Zhaohai Yang, Suraj Peri, Mark Andrake, Roland Dunbrack, Eric Ross, Wafik S El-Deiry
Plk2 is a target of p53. Our previous studies demonstrated that with wild-type p53, Plk2 impacts mTOR signaling in the same manner as TSC1, and Plk2-deficient tumors grew larger than control. Other investigators have demonstrated that Plk2 phosphorylates mutant p53 in a positive feedback loop. We investigated Plk2's tumor suppressor functions in relationship to mTOR signaling. Archival specimens from 12 colorectal adenocarcinomas were stained for markers including Plk2, phosphorylated mTOR (serine 2448) and ribosomal S6 (Serine 235/236)...
February 12, 2018: Neoplasia: An International Journal for Oncology Research
https://www.readbyqxmd.com/read/29447663/prenatal-diagnosis-by-chromosomal-microarray-analysis
#10
REVIEW
Brynn Levy, Ronald Wapner
Chromosomal microarray analysis (CMA) is performed either by array comparative genomic hybridization or by using a single nucleotide polymorphism array. In the prenatal setting, CMA is on par with traditional karyotyping for detection of major chromosomal imbalances such as aneuploidy and unbalanced rearrangements. CMA offers additional diagnostic benefits by revealing sub-microscopic imbalances or copy number variations that are too small to be seen on a standard G-banded chromosome preparation. These submicroscopic imbalances are also referred to as microdeletions and microduplications, particularly when they include specific genomic regions that are associated with clinical sequelae...
February 2018: Fertility and Sterility
https://www.readbyqxmd.com/read/29441681/sv40-intron-a-potent-strong-intron-element-that-effectively-increases-transgene-expression-in-transfected-chinese-hamster-ovary-cells
#11
Dan-Hua Xu, Xiao-Yin Wang, Yan-Long Jia, Tian-Yun Wang, Zheng-Wei Tian, Xin Feng, Yin-Na Zhang
Chinese hamster ovary (CHO) cells have become the most widely utilized mammalian cell line for the production of recombinant proteins. However, the product yield and transgene instability need to be further increased and solved. In this study, we investigated the effect of five different introns on transgene expression in CHO cells. hCMV intron A, adenovirus tripartite leader sequence intron, SV40 intron, Chinese hamster EF-1alpha gene intron 1 and intervening sequence intron were cloned downstream of the eGFP expression cassette in a eukaryotic vector, which was then transfected into CHO cells...
February 14, 2018: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/29439256/chromosome-nomenclature-and-cytological-characterization-of-sacred-lotus
#12
Zhuang Meng, Xiaoxu Hu, Zhiliang Zhang, Zhanjie Li, Qingfang Lin, Mei Yang, Pingfang Yang, Ray Ming, Qingyi Yu, Kai Wang
Sacred lotus is a basal eudicot plant that has been cultivated in Asia for over 7,000 years for its agricultural, ornamental, religious, and medicinal importance. A notable characteristic of lotus is the seed longevity. Extensive endeavors have been devoted to dissect its genome assembly, including the variety China Antique, which germinated from a 1,300-year-old seed. Here, cytogenetic markers representing the 10 largest megascaffolds, which constitute approximately 70% of the lotus genome assembly, were developed...
February 14, 2018: Cytogenetic and Genome Research
https://www.readbyqxmd.com/read/29435129/computational-methods-reveal-novel-functionalities-of-piwi-interacting-rnas-in-human-papillomavirus-induced-head-and-neck-squamous-cell-carcinoma
#13
Aswini R Krishnan, Yuanhao Qu, Pin Xue Li, Angela E Zou, Joseph A Califano, Jessica Wang-Rodriguez, Weg M Ongkeko
Human papillomavirus (HPV) infection is the fastest growing cause of head and neck squamous cell carcinoma (HNSCC) today, but its role in malignant transformation remains unclear. This study aimed to conduct a comprehensive investigation of PIWI-interacting RNA (piRNA) alterations and functionalities in HPV-induced HNSCC. Using 77 RNA-sequencing datasets from TCGA, we examined differential expression of piRNAs between HPV16(+) HNSCC and HPV(-) Normal samples, identifying a panel of 30 HPV-dysregulated piRNAs...
January 12, 2018: Oncotarget
https://www.readbyqxmd.com/read/29434842/comprehensive-characterization-of-cancer-genes-in-hepatocellular-carcinoma-genomes
#14
Zhihao Zhang, Liping Xu, Changyu Sun
The present study was performed to detect moderate or low-frequency mutated cancer driver genes in hepatocellular carcinoma (HCC), using OncodriveFM and Dendrix. Following this, integrated analyses were conducted on these novel cancer driver genes. A total of 112,980 somatic mutations were retrieved from TCGA and classified into 11 categories based on their function. Driver genes and pathways were predicted by OncodriveFM and Dendrix, followed by differential expression, DNA-methylation, copy number variations and survival analyses...
February 2018: Oncology Letters
https://www.readbyqxmd.com/read/29434669/copy-number-variation-and-regions-of-homozygosity-analysis-in-patients-with-m%C3%A3-llerian-aplasia
#15
Durkadin Demir Eksi, Yiping Shen, Munire Erman, Lynn P Chorich, Megan E Sullivan, Meric Bilekdemir, Elanur Yılmaz, Guven Luleci, Hyung-Goo Kim, Ozgul M Alper, Lawrence C Layman
Background: Little is known about the genetic contribution to Müllerian aplasia, better known to patients as Mayer-Rokitansky-Küster-Hauser (MRKH) syndrome. Mutations in two genes (WNT4 and HNF1B) account for a small number of patients, but heterozygous copy number variants (CNVs) have been described. However, the significance of these CNVs in the pathogenesis of MRKH is unknown, but suggests possible autosomal dominant inheritance. We are not aware of CNV studies in consanguineous patients, which could pinpoint genes important in autosomal recessive MRKH...
2018: Molecular Cytogenetics
https://www.readbyqxmd.com/read/29434467/genomic-analysis-using-regularized-regression-in-high-grade-serous-ovarian-cancer
#16
Yanina Natanzon, Madalene Earp, Julie M Cunningham, Kimberly R Kalli, Chen Wang, Sebastian M Armasu, Melissa C Larson, David Dl Bowtell, Dale W Garsed, Brooke L Fridley, Stacey J Winham, Ellen L Goode
High-grade serous ovarian cancer (HGSOC) is a complex disease in which initiation and progression have been associated with copy number alterations, epigenetic processes, and, to a lesser extent, germline variation. We hypothesized that, when summarized at the gene level, tumor methylation and germline genetic variation, alone or in combination, influence tumor gene expression in HGSOC. We used Elastic Net (ENET) penalized regression method to evaluate these associations and adjust for somatic copy number in 3 independent data sets comprising tumors from more than 470 patients...
2018: Cancer Informatics
https://www.readbyqxmd.com/read/29433585/characterization-and-validation-of-potential-therapeutic-targets-based-on-the-molecular-signature-of-patient-derived-xenografts-in-gastric-cancer
#17
Zuhua Chen, Wenwen Huang, Tiantian Tian, Wanchun Zang, Jingyuan Wang, Zhentao Liu, Zhongwu Li, Yumei Lai, Zhi Jiang, Jing Gao, Lin Shen
BACKGROUND: Patient-derived xenograft (PDX) models with definite molecular signature are attractive preclinical models for development of novel targeted drugs. Here, we profiled and explored potential therapeutic targets based on characterized PDX models for advanced gastric cancer (AGC). METHODS: The genomic variation and molecular profile of 50 PDX models from AGC patients were analyzed by targeted next-generation sequencing, in situ hybridization, and immunohistochemistry...
February 13, 2018: Journal of Hematology & Oncology
https://www.readbyqxmd.com/read/29433456/exome-sequencing-of-primary-breast-cancers-with-paired-metastatic-lesions-reveals-metastasis-enriched-mutations-in-the-a-kinase-anchoring-protein-family-akaps
#18
Una Kjällquist, Rikard Erlandsson, Nicholas P Tobin, Amjad Alkodsi, Ikram Ullah, Gustav Stålhammar, Eva Karlsson, Thomas Hatschek, Johan Hartman, Sten Linnarsson, Jonas Bergh
BACKGROUND: Tumor heterogeneity in breast cancer tumors is today widely recognized. Most of the available knowledge in genetic variation however, relates to the primary tumor while metastatic lesions are much less studied. Many studies have revealed marked alterations of standard prognostic and predictive factors during tumor progression. Characterization of paired primary- and metastatic tissues should therefore be fundamental in order to understand mechanisms of tumor progression, clonal relationship to tumor evolution as well as the therapeutic aspects of systemic disease...
February 12, 2018: BMC Cancer
https://www.readbyqxmd.com/read/29433355/what-would-be-missed-in-the-first-trimester-if-nuchal-translucency-measurement-is-replaced-by-cell-free-dna-foetal-aneuploidy-screening
#19
Lv-Yin Huang, Min Pan, Jin Han, Li Zhen, Xin Yang, Dong-Zhi Li
The aim of this study was to evaluate which chromosomal abnormalities in our cohort of foetuses with increased nuchal translucency (NT) in the first trimester of pregnancy could be detected by cell free (cf)DNA screening as well. There were 775 singleton pregnancies referred for cytogenetic testing due to an increased NT (≥3.0 mm). Chromosome aberrations were investigated using karyotyping or chromosomal microarray analysis (CMA). Karyotyping had been chosen for foetal cytogenetic testing by 446 patients, and CMA by 329 patients...
February 12, 2018: Journal of Obstetrics and Gynaecology: the Journal of the Institute of Obstetrics and Gynaecology
https://www.readbyqxmd.com/read/29433173/further-investigation-about-copy-number-variations-and-methylation-of-aurka-kif4a-and-nusap1-in-glioblastoma
#20
Sheng Zhong, ShanShan Jiang, YiDa Peng, Yong Chen
No abstract text is available yet for this article.
February 2018: World Neurosurgery
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