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Copy number variation

Takuma Iguchi, Noriyo Niino, Satoshi Tamai, Ken Sakurai, Kazuhiko Mori
RT-qPCR is one of the most common methods to assess individual target miRNAs. MiRNAs levels are generally measured relative to a reference sample. This approach is appropriate for examining physiological changes in target gene expression levels. However, absolute quantification using better statistical analysis is preferable for a comprehensive assessment of gene expression levels. Absolute quantification is still not in common use. This report describes a protocol for measuring the absolute levels of plasma miRNA, using RT-qPCR with or without pre-amplification...
February 12, 2018: Journal of Visualized Experiments: JoVE
Lichen Zhang, Xiaoqing Zhang, Guoling You, Yongguo Yu, Qihua Fu
BACKGROUND: Williams-Beuren syndrome (WBS) is caused by a microdeletion of chromosome arm 7q11.23. A rapid and inexpensive genotyping method to detect microdeletion on 7q11.23 needs to be developed for the diagnosis of WBS. This study describes the development of a new type of molecular diagnosis method to detect microdeletion on 7q11.23 based upon high-resolution melting (HRM). METHODS: Four genes on 7q11.23 were selected as the target genes for the deletion genotyping...
March 14, 2018: Clinica Chimica Acta; International Journal of Clinical Chemistry
Jokthan Guivarch, Clarisse Chatel, Jeremie Mortreux, Chantal Missirian, Nicole Philip, François Poinso
BACKGROUND: Autism spectrum disorders are serious neurodevelopmental disorders that affect approximately 1% of the population. These disorders are substantially influenced by genetics. Several recent linkage analyses have examined copy number variations associated with autism risk. Microdeletion of the 2q13 region is considered a pathogenic copy number variation. This microdeletion is involved in developmental delays, congenital heart defects, dysmorphism, and various psychiatric disorders, including autism spectrum disorders...
March 18, 2018: Journal of Medical Case Reports
François-Xavier Nouhaud, France Blanchard, Richard Sesboue, Jean-Michel Flaman, Jean-Christophe Sabourin, Christian Pfister, Frédéric Di Fiore
BACKGROUND: Gene copy number variations (CNVs) have been reported to be frequent in renal cell carcinoma (RCC), with potential prognostic value for some. However, their clinical utility, especially to guide treatment of metastatic disease remains to be established. Our objectives were to assess CNVs on a panel of selected genes and determine their clinical relevance in patients who underwent treatment of metastatic RCC. PATIENTS AND METHODS: The genetic assessment was performed on frozen tissue samples of clear cell metastatic RCC using quantitative multiplex polymerase chain reaction of short fluorescent fragment method to detect CNVs on a panel of 14 genes of interest...
February 23, 2018: Clinical Genitourinary Cancer
Yi Pang, Yunfeng Guan, Xing Jin, Hongmei Shen, Lixiang Liu, Qingzhen Jia, Fangang Meng, Xiaoye Zhang
Thyroid-stimulating hormone (TSH) is secreted by the pituitary gland and promotes thyroid growth and function, with increased TSH levels typically associated with hypothyroidism. By consulting the literature, we found that the TSHR, PAX8, and PDE4B genes are associated with thyroid function. Recently, copy number variations (CNVs) have been used as genetic markers to investigate inter-individual variation. Therefore, we investigated the relationship between the TSHR, PAX8, and PDE4B gene CNVs and TSH abnormalities, by calculating variations in gene copy number...
March 15, 2018: Biological Trace Element Research
Qing Mao, Robert Chin, Weiwei Xie, Yuqing Deng, Wenwei Zhang, Huixin Xu, Rebecca Yu Zhang, Quan Shi, Erin E Peters, Natali Gulbahce, Zhenyu Li, Fang Chen, Radoje Drmanac, Brock A Peters
BACKGROUND: Amniocentesis is a common procedure, the primary purpose of which is to collect cells from the fetus to allow testing for abnormal chromosomes, altered chromosomal copy number, or a small number of genes that have small single- to multibase defects. Here we demonstrate the feasibility of generating an accurate whole-genome sequence of a fetus from either the cellular or cell-free DNA (cfDNA) of an amniotic sample. METHODS: cfDNA and DNA isolated from the cell pellet of 31 amniocenteses were sequenced to approximately 50× genome coverage by use of the Complete Genomics nanoarray platform...
March 15, 2018: Clinical Chemistry
He Chen, Jiacheng Yao, Yusi Fu, Yuhong Pang, Jianbin Wang, Yanyi Huang
The next generation sequencing (NGS) technologies have been rapidly evolved and applied to various research fields, but often suffer from losing long-range information due to short library size and read length. Here, we develop a simple, cost-efficient and versatile NGS library preparation method, called tagmentation on microbeads (TOM). This method is capable of recovering long-range information through tagmentation mediated by microbead-immobilized transposomes. Using transposomes with DNA barcodes to identically labeling adjacent sequences during tagmentation, we can restore inter-read connection of each fragment from original DNA molecule by fragment-barcode linkage after sequencing...
March 15, 2018: ACS Applied Materials & Interfaces
Janaina de Freitas Nascimento, Steven Kelly, Jack Sunter, Mark Carrington
Selective transcription of individual protein coding genes does not occur in trypanosomes and the cellular copy number of each mRNA must be determined post-transcriptionally. Here, we provide evidence that codon choice directs the levels of constitutively expressed mRNAs. First, a novel codon usage metric, the gene expression codon adaptation index (geCAI), was developed that maximised the relationship between codon choice and the measured abundance for a transcriptome. Second, geCAI predictions of mRNA levels were tested using differently coded GFP transgenes and were successful over a 25-fold range, similar to the variation in endogenous mRNAs...
March 15, 2018: ELife
Kelly Kyker-Snowman, Bracha Erlanger Avigdor, Mansoor Nasim, Ashley Cimino-Mathews, Sarah J Wheelan, Pedram Argani, Ben Ho Park
BACKGROUND/PURPOSE: Tumor heterogeneity is a now well-recognized phenomenon that can affect the classification, prognosis and treatment of human cancers. Heterogeneity is often described in primary breast cancers based upon histologic subtypes, hormone- and HER2-receptor status, and immunolabeling for various markers, which can be seen within a single tumor as mixed cellular populations, or as separate discrete foci. EXPERIMENTAL DESIGN/METHODS: Here, we present a case report of a patient's primary breast cancer that had two separate but adjacent histologic components, one that was estrogen receptor (ER) positive, and the other ER negative...
March 15, 2018: Breast Cancer Research and Treatment
Hema Singh, Pradeep Tiwari, Vijay Bhavi, Praveen Singh Chaudhary, Prashanth Suravajhala, M Krishna Mohan, Sandeep Kumar Mathur
Background: Human height is a classic polygenic trait and currently available data explains only 10% of the phenotypic variation in height. Almost 60%-80% of the children coming to pediatric and endocrinology outpatient department for the evaluation of short stature are still labeled as idiopathic. Objectives: The aim of this study is to identify various chromosomal alterations causing idiopathic short stature (ISS) and short stature with dysmorphic features not pertaining to known genetic syndromes...
January 2018: Indian Journal of Endocrinology and Metabolism
Adrian F Daly, Emily Castermans, Lindsey Oudijk, Mirtha A Guitelman, Pablo Beckers, Iulia Potorac, Sebastian J C M M Neggers, Nathalie Sacre, Aj Van der Lely, Vincent Bours, Wouter W de Herder, Albert Beckers
Copy number variations (CNV), an important genetic mechanism in inherited tumor genetics, can affect large genetic regions or can be limited to smaller regions within genes, such deletions of single exons. Such exon deletions can be challenging to identify and sequencing can be normal in these cases. Multiplex ligation dependent probe amplification (MLPA) can identify CNV of individual exons. Mutations in the MAX gene are associated with a risk of sporadic and hereditary pheochromocytoma. As mutations in other pheochromocytoma related genes can also cause pituitary tumors (3P-Association), we studied whether MAX exon deletions were involved in the etiology of patients with an unexplained association of multiple endocrine neoplasia including pituitary adenoma and pheochromocytoma...
March 13, 2018: Endocrine-related Cancer
Mengmeng Wang, Shengqian Xu, Xu Zhang, Mengya Chen, Renfang Han, Xingxing Hu, Yaping Yuan, Yubo Ma, Jiajia Yang, Meng Wu, Rui Liu, Guangming Jiang, Faming Pan
OBJECTIVES: To explore the association of TLR7 gene copy number variations (CNVs) with the susceptibility of ankylosing spondylitis (AS). METHODS: The case control study was performed in 649 Chinese Han patients with AS and 628 healthy controls. The copy numbers of TLR7 gene (2 fragments) were measured by AccuCopyTM methods. Chi-square and logistic regression models were performed to investigate the association of TLR7 gene CNVs with AS. Odds ratio (ORs) and 95% confidence intervals (CIs) was calculated to estimate AS risk and the Bonferroni correction was applied owing to multiple testing...
February 28, 2018: Clinical and Experimental Rheumatology
Mehdi Zarrei, Geoffrey G Hicks, James N Reynolds, Bhooma Thiruvahindrapuram, Worrawat Engchuan, Molly Pind, Sylvia Lamoureux, John Wei, Zhouzhi Wang, Christian R Marshall, Richard F Wintle, Albert E Chudley, Stephen W Scherer
Fetal alcohol spectrum disorder (FASD) is characterized by a combination of neurological, developmental, and congenital defects that may occur as a consequence of prenatal alcohol exposure. Earlier reports showed that large chromosomal anomalies may link to FASD. Here, we examined the prevalence and types of copy number variations (CNVs) in FASD cases previously diagnosed by a multidisciplinary FASD team in sites across Canada. We genotyped 95 children with FASD and 87 age-matched, typically developing controls on the Illumina Human Omni2...
March 13, 2018: Biochemistry and Cell Biology, Biochimie et Biologie Cellulaire
Aditi Jain, Saurabh Anand, Neer K Singh, Sandip Das
The impact of polyploidy on functional diversification of cis-regulatory elements is poorly understood. This is primarily on account of lack of well-defined structure of cis-elements and a universal regulatory code. To the best of our knowledge, this is the first report on characterization of sequence and functional diversification of paralogous and homeologous promoter elements associated with MIR164 from Brassica. The availability of whole genome sequence allowed us to identify and isolate a total of 42 homologous copies of MIR164 from diploid species-Brassica rapa (A-genome), Brassica nigra (B-genome), Brassica oleracea (C-genome), and allopolyploids-Brassica juncea (AB-genome), Brassica carinata (BC-genome) and Brassica napus (AC-genome)...
March 12, 2018: Functional & Integrative Genomics
Dal-Hoe Koo, William T Molin, Christopher A Saski, Jiming Jiang, Karthik Putta, Mithila Jugulam, Bernd Friebe, Bikram S Gill
Gene amplification has been observed in many bacteria and eukaryotes as a response to various selective pressures, such as antibiotics, cytotoxic drugs, pesticides, herbicides, and other stressful environmental conditions. An increase in gene copy number is often found as extrachromosomal elements that usually contain autonomously replicating extrachromosomal circular DNA molecules (eccDNAs). Amaranthus palmeri , a crop weed, can develop herbicide resistance to glyphosate [ N -(phosphonomethyl) glycine] by amplification of the 5-enolpyruvylshikimate-3-phosphate synthase ( EPSPS ) gene, the molecular target of glyphosate...
March 12, 2018: Proceedings of the National Academy of Sciences of the United States of America
Jianghong Zhong, Lina M Olsson, Vilma Urbonaviciute, Min Yang, Liselotte Bäckdahl, Rikard Holmdahl
A single nucleotide polymorphism in Ncf1 has been found with a major effect on chronic inflammatory autoimmune diseases in the rat with the surprising observation that a lower reactive oxygen response led to more severe diseases. This finding was subsequently reproduced in the mouse and the effect operates in many different murine diseases through different pathogenic pathways; like models for rheumatoid arthritis, encephalomyelitis, lupus, gout, psoriasis and psoriatic arthritis. The human gene is located in an unstable region with many variable sequence repetitions, which means it has not been included in any genome wide associated screens so far...
March 8, 2018: Free Radical Biology & Medicine
Hong Qi, Zhao-Ling Xuan, Yang Du, Li-Rong Cai, Han Zhang, Xiao-Hui Wen, Xiang-Dong Kong, Kai Yang, Yang Mi, Xin-Xin Fu, Shan-Bo Cao, Juan Wang, Chong-Jian Chen, Jun-Bin Liang
OBJECTIVE: Chromosome aberrations are generally considered as one of the most substantial causative factors contributing to spontaneous miscarriages. Cytogenetic analyses like G-banded karyotype and chromosomal microarray analyses are often performed to further investigate the chromosome status of a miscarried fetus. STUDY DESIGN: Here, we describe a novel method, AnnoCNV, to detect DNA copy number variations (CNVs) using low coverage whole genome sequencing (WGS)...
March 8, 2018: European Journal of Obstetrics, Gynecology, and Reproductive Biology
I Maini, I Ivanovski, O Djuric, S G Caraffi, E Errichiello, M Marinelli, F Franchi, V Bizzarri, S Rosato, M Pollazzon, C Gelmini, M Malacarne, C Fusco, G Gargano, S Bernasconi, O Zuffardi, L Garavelli
BACKGROUND: Since 2010, array-CGH (aCGH) has been the first-tier test in the diagnostic approach of children with neurodevelopmental disorders (NDD) or multiple congenital anomalies (MCA) of unknown origin. Its broad application led to the detection of numerous variants of uncertain clinical significance (VOUS). How to appropriately interpret aCGH results represents a challenge for the clinician. METHOD: We present a retrospective study on 293 patients with age range 1 month - 29 years (median 7 years) with NDD and/or MCA and/or dysmorphisms, investigated through aCGH between 2005 and 2016...
March 9, 2018: Italian Journal of Pediatrics
Marcos Vinicius Antunes de Lemos, Elisa Peripolli, Mariana Piatto Berton, Fabiele Loise Braga Feitosa, Bianca Ferreira Olivieri, Nedenia Bonvino Stafuzza, Rafael Lara Tonussi, Sabrina Kluska, Hermenegildo Lucas Justino Chiaia, Lenise Mueller, Adrielli Mathias Ferrinho, Angelica Simone Cravo Prereira, Henrique Nunes de Oliveira, Lucia Galvão de Albuquerque, Fernando Baldi
The aim of this study was to analyze the association between the copy number variation regions (CNVRs) and fatty acid profile phenotypes for saturated (SFA), monosaturated (MUFA), polyunsaturated (PUFA), ω6 and ω3 fatty acids, PUFA/SFA and ω6/ω3 ratios, as well as for their sums, in Nellore cattle (Bos primigenius indicus). A total of 963 males were finished in feedlot and slaughtered with approximately 2 years of age. Animals were genotyped with the BovineHD BeadChip (Illumina Inc., San Diego, CA, USA)...
March 8, 2018: Journal of Applied Genetics
Jacob L Steenwyk, Antonis Rokas
In recent years, copy number (CN) variation has emerged as a new and significant source of genetic polymorphisms contributing to the phenotypic diversity of populations. CN variants are defined as genetic loci that, due to duplication and deletion, vary in their number of copies across individuals in a population. CN variants range in size from 50 base pairs to whole chromosomes, can influence gene activity, and are associated with a wide range of phenotypes in diverse organisms, including the budding yeast Saccharomyces cerevisiae ...
2018: Frontiers in Microbiology
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