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copy number variations

Ye-Qing Qian, Xiao-Qing Wang, Min Chen, Yu-Qin Luo, Kai Yan, Yan-Mei Yang, Bei Liu, Li-Ya Wang, Ying-Zhi Huang, Hong-Ge Li, Hang-Yi Pan, Fan Jin, Min-Yue Dong
BACKGROUND: Fetal chromosome aberrations and sub-chromosomal copy number variations (CNVs) are not rare. There are several ways to detect duplications and deletions; cell-free DNA screening (cfDNA screening) is nowadays an accurate and safe detection method. The objective of this study is to report the feasibility of cfDNA screening as an indicator of parental balanced chromosome translocation. RESULTS: From February 2015 to March 2016, cfDNA screening was offered to 11344 pregnant women...
June 18, 2018: European Journal of Medical Genetics
Wenjia Liu, Yiyang Zhang, Min Chen, Liangliang Shi, Lei Xu, Xiaoping Zou
Esophageal cancer is one of the most common cancers and a leading cause of cancer-related death worldwide. However, the mechanism of esophageal cancer pathogenesis remains poorly understood. Long noncoding RNAs (lncRNAs) dysregulation have been reported to involve in various human cancers, which highlights the potential of lncRNAs used as novel biomarkers for cancer diagnosis. Although more efforts have been made to identify novel lncRNAs signature in esophageal cancer, the expression pattern, prognostic value, and biological function of most lncRNAs in esophageal cancer still need to be systematically investigated...
June 21, 2018: Cancer Medicine
Zhen Liu, Yuling Liu, Fang Liu, Shulin Zhang, Xingxing Wang, Quanwei Lu, Kunbo Wang, Baohong Zhang, Renhai Peng
Long terminal repeat (LTR) retrotransposon is the most abundant DNA component and is largely responsible for plant genome size variation. Although it has been studied in plant species, very limited data is available for cotton, the most important fiber and texture crop. In this study, we performed a comprehensive analysis of LTR retrotransposon families across four cotton species. In tetraploid Gossypium species, LTR retrotransposon families from the progenitor D genome had more copies in D-subgenome, and families from the progenitor A genome had more copies in A-subgenome...
June 20, 2018: Scientific Reports
Xiaoqing Zhang, Bo Wang, Lichen Zhang, Guoling You, Robert A Palais, Luming Zhou, Qihua Fu
BACKGROUND: Copy number variation (CNV) has been implicated in the genetics of multiple human diseases. Spinal muscular atrophy (SMA) and 22q11.2 deletion syndrome (22q11.2DS) are two of the most common diseases which are caused by DNA copy number variations. Genetic diagnostics for these conditions would be enhanced by more accurate and efficient methods to detect the relevant CNVs. METHODS: Competitive PCR with limited deoxynucleotide triphosphates (dNTPs) and high-resolution melting (HRM) analysis was used to detect 22q11...
June 20, 2018: BMC Genomics
Xu Zhang, Yuzhuo Wang, Tian Tian, Gangqiao Zhou, Guangfu Jin
Genome-wide association studies have identified several germline variants in gastric cancer. Meanwhile, sequencing studies have characterized extensive somatic alterations that arise during gastric carcinogenesis. However, the relationship between the germline variants and somatic alterations is still unclear in gastric cancer. A total of 11 susceptibility loci and 276 driver genes of gastric cancer were determined based on previous studies and publicly available database. An enrichment analysis was made to detect whether driver genes were enriched in susceptibility regions...
June 20, 2018: Cancer Medicine
Wei Lu, Yongcan Xu, Jiewei Xu, Zhong Wang, Guochao Ye
Recently, a growing number of evidence has revealed that long noncoding RNAs (lncRNAs) act as key regulators in various cellular biologic processes, and dysregulation of lncRNAs involves in tumorigenesis and cancer progression. However, the expression pattern, clinical relevance, and biologic function of most lncRNAs in human thyroid cancer remain unclear. To identify more thyroid-cancer-associated lncRNAs, we analyzed the expression profile of lncRNAs in thyroid cancer tissues and adjacent normal or non-tumor tissues using RNA sequencing data and gene microarray data from The Cancer Genome Atlas and Gene Expression Omnibus...
June 20, 2018: Cancer Medicine
Irene Jiménez, Mathieu Chicard, Léo Colmet-Daage, Nathalie Clément, Adrien Danzon, Eve Lapouble, Gaelle Pierron, Mylène Bohec, Sylvain Baulande, Dominique Berrebi, Paul Fréneaux, Aurore Coulomb, Louise Galmiche-Rolland, Sabine Sarnacki, Georges Audry, Pascale Philippe-Chomette, Hervé J Brisse, François Doz, Jean Michon, Olivier Delattre, Gudrun Schleiermacher
Circulating tumor DNA (ctDNA) is a powerful tool for the molecular characterization of cancer. The most frequent pediatric kidney tumors (KT) are Wilms' tumors (WT), but other diagnoses may occur. According to the SIOP strategy, in most countries pediatric KT have a presumptive diagnosis of WT if they are clinically and radiologically compatible. The histologic confirmation is established after post-chemotherapy nephrectomy. Thus, there is a risk for a small fraction of patients to receive neoadjuvant chemotherapy that is not adapted to the disease...
June 19, 2018: International Journal of Cancer. Journal International du Cancer
Venugopal S Vineeth, Usha R Dutta, Karthik Tallapakka, Aneek Das Bhowmik, Ashwin Dalal
Rett syndrome is a neurodevelopmental disorder affecting the nervous, musculoskeletal and gastroenteric systems. Affected individuals show normal neonatal development for 6-18 months followed by sudden growth arrest, psychomotor retardation and a broad spectrum of clinical features. Sequence variants in MECP2 gene have been identified as the major genetic etiology accounting for 90-95% of patients. Apart from MECP2, pathogenic sequence variants and copy number variants of FOXG1 gene lead to congenital type of Rett syndrome which is a more severe form and characterised by absence of early normal development as seen in classical Rett syndrome...
June 16, 2018: Gene
Keiko Taniguchi-Ponciano, Daniel Marrero-Rodríguez, Hugo Arreola-De la Cruz, Víctor Huerta-Padilla, Nancy Muñoz, Laura Gómez-Ortiz, Gustavo Ponce-Navarrete, Miriam Rodríguez-Esquivel, Mónica Mendoza-Rodríguez, Laura Gómez-Virgilio, Raúl Peralta, Luis Serna, Guillermo Gómez, Jorge Ortiz, Alejandra Mantilla, Daniel Hernández, Ángeles Hernández, Cindy Bandala, Rosa María Ribas-Aparicio, Mauricio Salcedo
BACKGROUND: Similarities between the pathologic progression of cancer and the physiologic process of placentation have been recognized for many years proposing that both present similar mechanisms and processes. Cervical cancer (CC) is one of the most frequent neoplasia among Mexican women turning it into an important health problem. OBJECTIVE: The aim of this study was to determine the degree of the involvement of pregnancy related genes and in cancer progression by insilico analysis and validated in CC samples...
May 31, 2018: Cancer Biomarkers: Section A of Disease Markers
Jinyu Chen, Shihua Zhang
The increasing availability of high-throughput biological data, especially multi-dimensional genomic data across the same samples, has created an urgent need for modular and integrative analysis tools that can reveal the relationships among different layers of cellular activities. To this end, we present a MATLAB package, Matrix Integration Analysis (MIA), implementing and extending four published methods, designed based on two classical techniques, non-negative matrix factorization (NMF), and partial least squares (PLS)...
2018: Frontiers in Genetics
Eline Overwater, Luisa Marsili, Marieke J H Baars, Annette F Baas, Irma van de Beek, Eelco Dulfer, Johanna M van Hagen, Yvonne Hilhorst-Hofstee, Marlies Kempers, Ingrid P Krapels, Leonie A Menke, Judith M A Verhagen, Kak K Yeung, Petra J G Zwijnenburg, Maarten Groenink, Peter van Rijn, Marjan M Weiss, Els Voorhoeve, J Peter van Tintelen, Arjan C Houweling, Alessandra Maugeri
Simultaneous analysis of multiple genes using next generation sequencing (NGS) technology has become widely available. Copy number variations (CNVs) in disease-associated genes have emerged as a cause for several hereditary disorders. CNVs are, however, not routinely detected using NGS analysis. The aim of this study was to assess the diagnostic yield and the prevalence of CNVs using our panel of Hereditary Thoracic Aortic Disease (H-TAD) associated genes. 810 patients suspected of H-TAD were analysed by targeted NGS analysis of 21 H-TAD associated genes...
June 16, 2018: Human Mutation
Xiaofei Song, Christine R Beck, Renqian Du, Ian M Campbell, Zeynep Coban-Akdemir, Shen Gu, Amy M Breman, Pawel Stankiewicz, Grzegorz Ira, Chad A Shaw, James R Lupski
Alu elements, the short interspersed element numbering >1 million copies per human genome, can mediate the formation of copy number variants (CNVs) between substrate pairs. These Alu/Alu-mediated rearrangements (AAMR) can result in pathogenic variants that cause diseases. To investigate the impact of AAMR on gene variation and human health, we first characterized Alus that are involved in mediating CNVs (CNV-Alus) and observed that these Alus tend to be evolutionarily younger. We then computationally generated, with the assistance of a supercomputer, a test dataset consisting of 78 million Alu pairs and predicted ~18% of them are potentially susceptible to AAMR...
June 15, 2018: Genome Research
Jinxin Zeng, Changwei Lei, Yulong Wang, Yanpeng Chen, Xiuzhong Zhang, Zhuangzhuang Kang, Xiwen Zhai, Xiaolan Ye, Hongning Wang
The aim of this study was to explore the distribution of Salmonella Enteritidis (S. enteritidis) in internal organs and variation of cecum microbiota in newly hatched chicken after oral challenge during a 21-day period. The quantities of S. enteritidis DNA in different internal organs (heart, liver, spleen, stomach, pancreas, small intestine, blood and cecum contents) were determined by real-time fluorescent quantitative polymerase chain reaction (FQ-PCR). The result showed that all of the above-mentioned samples were positive at 12 h post inoculation (PI) after oral challenge...
June 12, 2018: Microbial Pathogenesis
Barbara Vona, Michaela A H Hofrichter, Jörg Schröder, Wafaa Shehata-Dieler, Indrajit Nanda, Thomas Haaf
OBJECTIVES: Despite recent advancements in diagnostic tools, the genomic landscape of hereditary hearing loss remains largely uncharacterized. One strategy to understand genome-wide aberrations includes the analysis of copy number variation that can be mapped using SNP-microarray technology. A growing collection of literature has begun to uncover the importance of copy number variation in hereditary hearing loss. This pilot study underpins a larger effort that involves the stage-wise analysis of hearing loss patients, many of whom have advanced to high-throughput sequencing analysis...
June 14, 2018: BMC Research Notes
Xiaojia Xu, Yulian Li, Yaping Liang, Mingjuan Yin, Yan Zhang, Lingfeng Huang, Zuwei Yu, Jindong Ni
It is known that multiple genetic variants can affect immune responses to the hepatitis B virus (HBV) vaccine. A case-control study was undertaken to examine the possible association of low responsiveness to the HBV vaccine in a Chinese population with genetic polymorphisms in integrin subunit alpha L, CD58, tumor necrosis factor superfamily member 15, C-C motif chemokine ligand 15, transforming growth factor beta 3, and B-cell lymphoma 6 protein. The copy numbers of these six genes were detected in 129 low responders, 129 middle responders and 129 high responders to HBV vaccination...
June 11, 2018: Infection, Genetics and Evolution
Chengyong Lei, Shidong Lv, Hongyi Wang, Chuan Liu, Qiliang Zhai, Shanci Wang, Guixing Cai, Dingheng Lu, Zhen Sun, Qiang Wei
The role of leukemia inhibitory factor receptor (LIFR), which is important in the signal transduction of the interleukin-6 cytokine family, is still undefined in clear cell renal cell carcinoma (ccRCC). Thus, we examined the function and mechanism of LIFR in ccRCC. Low LIFR expression correlated with a poor prognosis and an aggressive tumor phenotype. Moreover, integrated LIFR DNA and mRNA analysis revealed that promoter methylation and copy number variation contributed to the reduced LIFR expression. LIFR knockdown increased 786-O and Caki-2 cell invasion and migration...
June 14, 2018: DNA and Cell Biology
Jean Fan, Hae-Ock Lee, Soohyun Lee, Da-Eun Ryu, Semin Lee, Catherine Xue, Seok Jin Kim, Kihyun Kim, Nikolas Barkas, Peter J Park, Woong-Yang Park, Peter V Kharchenko
Characterization of intratumoral heterogeneity is critical to cancer therapy, as presence of phenotypically diverse cell populations commonly fuels relapse and resistance to treatment. Although genetic variation is a well-studied source of intratumoral heterogeneity, the functional impact of most genetic alterations remains unclear. Even less understood is the relative importance of other factors influencing heterogeneity, such as epigenetic state or tumor microenvironment. To investigate the relationship between genetic and transcriptional heterogeneity in a context of cancer progression, we devised a computational approach called HoneyBADGER to identify copy number variation and loss-of-heterozygosity in individual cells from single-cell RNA-sequencing data...
June 13, 2018: Genome Research
J Sidney Ang, Martin N Aloise, Diana Dawes, Maryn G Dempster, Robert Fraser, Andrea Paterson, Paul Stanley, Adriana Suarez-Gonzalez, Martin Dawes, Hagit Katzov-Eckert
OBJECTIVE: A simple, non-invasive sample collection method is key for the integration of pharmacogenetics into clinical practice. The aim of this study was to gain samples for pharmacogenetic testing and evaluate the variation between dry-flocked and sponge-tipped buccal swabs in yield and quality of DNA isolated. RESULTS: Thirty-one participants collected samples using dry-flocked swabs and sponge-tipped swabs. Samples were assessed for DNA yield, quality and genotyping performance on a qPCR OpenArray platform of 28 pharmacogenetic SNPs and a CYP2D6 TaqMan copy number variant...
June 14, 2018: BMC Research Notes
Yun Wang, Taro Masaki, Sikandar G Khan, Deborah Tamura, Christiane Kuschal, Megan Rogers, John J DiGiovanna, Kenneth H Kraemer
Recent findings of mosaicism (DNA sequence variation) challenge the dogma that each person has a stable genetic constitution. Copy number variations, point mutations and chromosome abnormalities in normal or diseased tissues have been described. We studied normal skin mosaicism of a single nucleotide polymorphism (SNP) [rs1426654, p.Thr111Ala] in SLC24A5, an ion transporter gene. This SNP is unusual in that more than 90% of people of European descent have homozygous germline A/A alleles, while more than 90% of East Asians and Blacks have homozygous germline G/G alleles...
2018: PloS One
Ameen Bakhsh, Ioannis Ladas, Marian Hamshere, Martyn Bullock, George Kirov, Lei Zhang, Peter Taylor, John Welbourn Gregory, David Michael Scott-Coombes, Henry Völzke, Alexander Teumer, Kiran Mantripragada, Dillwyn Williams, Roderick J Clifton-Bligh, Nigel Williams, Marian Ludgate
Euthyroid multinodular goiter (MNG) is common but little is known about the genetic variation conferring predisposition. Previously we reported a family with MNG of adolescent onset in which some family members developed papillary thyroid carcinomas (PTC). We conducted a genome-wide linkage analysis and next generation sequencing to identify genetic variants that may confer disease predisposition. A multipoint nonparametric LOD score of 3.01 was obtained covering 19 cM on chromosome 20p. Haplotype analysis reduced the region of interest to 10 cM; analysis of copy number variation identified an intronic InDel (~1000 bp) in the PLCB1 gene in all 8 affected family members and carriers (an unaffected person who has inherited the genetic trait) but ~1% of 'healthy' Caucasians...
June 13, 2018: Thyroid: Official Journal of the American Thyroid Association
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