keyword
MENU ▼
Read by QxMD icon Read
search

Copy number variation

keyword
https://www.readbyqxmd.com/read/28109442/label-free-and-standard-free-absolute-quantitative-proteomics-using-the-total-protein-and-proteomic-ruler-approaches
#1
J R Wiśniewski
Understanding biological systems and their variation upon stimuli requires knowledge on their composition, primarily including information on organization and dynamics of proteomes. The total protein approach (TPA) is a label- and standard-free method for absolute protein quantitation of proteins using large-scale proteomic data. The method relies on the assumption that the total MS signal from all identified proteins in the dataset reflects-in a biochemical sense-the total protein and the MS signal from a single protein corresponds its abundance in the studied sample...
2017: Methods in Enzymology
https://www.readbyqxmd.com/read/28107356/integrity-of-induced-pluripotent-stem-cell-ipsc-derived-megakaryocytes-as-assessed-by-genetic-and-transcriptomic-analysis
#2
Kai Kammers, Margaret A Taub, Ingo Ruczinski, Joshua Martin, Lisa R Yanek, Alyssa Frazee, Yongxing Gao, Dixie Hoyle, Nauder Faraday, Diane M Becker, Linzhao Cheng, Zack Z Wang, Jeff T Leek, Lewis C Becker, Rasika A Mathias
Previously, we have described our feeder-free, xeno-free approach to generate megakaryocytes (MKs) in culture from human induced pluripotent stem cells (iPSCs). Here, we focus specifically on the integrity of these MKs using: (1) genotype discordance between parent cell DNA to iPSC cell DNA and onward to the differentiated MK DNA; (2) genomic structural integrity using copy number variation (CNV); and (3) transcriptomic signatures of the derived MK lines compared to the iPSC lines. We detected a very low rate of genotype discordance; estimates were 0...
2017: PloS One
https://www.readbyqxmd.com/read/28104681/copy-number-variations-of-e2f1-a-new-genetic-risk-factor-for-testicular-cancer
#3
Maria Santa Rocca, Andrea Di Nisio, Arianna Marchiori, Marco Ghezzi, Giuseppe Opocher, Carlo Foresta, Alberto Ferlin
Testicular germ cell tumor (TGCT) is one of the most heritable forms of cancer. In last years many evidence suggested that constitutional genetic factors, mainly single nucleotide polymorphisms, can increase its risk. However, the possible contribution of copy-number variations (CNVs) in TGCT susceptibility has not been substantially addressed. Indeed, an increasing number of studies have focused on the effect of CNVs on gene expression and on the role of these structural genetic variations as risk factors for different forms of cancer...
January 19, 2017: Endocrine-related Cancer
https://www.readbyqxmd.com/read/28104311/comprehensive-profiling-of-the-androgen-receptor-in-liquid-biopsies-from-castration-resistant-prostate-cancer-reveals-novel-intra-ar-structural-variation-and-splice-variant-expression-patterns
#4
Bram De Laere, Pieter-Jan van Dam, Tom Whitington, Markus Mayrhofer, Emanuela Henao Diaz, Gert Van den Eynden, Jean Vandebroek, Jurgen Del-Favero, Steven Van Laere, Luc Dirix, Henrik Grönberg, Johan Lindberg
BACKGROUND: Expression of the androgen receptor splice variant 7 (AR-V7) is associated with poor response to second-line endocrine therapy in castration-resistant prostate cancer (CRPC). However, a large fraction of nonresponding patients are AR-V7-negative. OBJECTIVE: To investigate if a comprehensive liquid biopsy-based AR profile may improve patient stratification in the context of second-line endocrine therapy. DESIGN, SETTING, AND PARTICIPANTS: Peripheral blood was collected from patients with CRPC (n=30) before initiation of a new line of systemic therapy...
January 16, 2017: European Urology
https://www.readbyqxmd.com/read/28101908/recurrent-rearrangements-of-human-amylase-genes-create-multiple-independent-cnv-series
#5
Nzar A A Shwan, Sandra Louzada, Fengtang Yang, John A L Armour
The human amylase gene cluster includes the human salivary (AMY1) and pancreatic amylase genes (AMY2A and AMY2B), and is a highly variable and dynamic region of the genome. Copy number variation of AMY1 has been implicated in human dietary adaptation, and in population association with obesity, but neither of these findings has been independently replicated. Despite these functional implications, the structural genomic basis of copy number variation (CNV) has only been defined in detail very recently. In this work we use high-resolution analysis of copy number, and analysis of segregation in trios, to define new, independent allelic series of amylase CNVs in sub-Saharan Africans, including a series of higher-order expansions of a unit consisting of one copy each of AMY1, AMY2A and AMY2B...
January 19, 2017: Human Mutation
https://www.readbyqxmd.com/read/28100915/whole-exome-sequencing-study-reveals-common-copy-number-variants-in-protocadherin-genes-associated-with-childhood-obesity-in-koreans
#6
S Moon, M Y Hwang, H B Jang, S Han, Y J Kim, J-Y Hwang, H-J Lee, S I Park, J Song, B-J Kim
Recently, the prevalence of childhood obesity has significantly increased in industrialized countries, including Korea, and now controlling obesity is becoming an economic burden. However, knowledge of the risk factors associated with obesity is still limited. In this study, we aimed to discover additional obesity-associated loci in children. To achieve this, we conducted an exome-wide association analysis of copy number variation (CNV) using whole-exome sequencing (WES) data from a total of 102 cases and 86 controls...
January 19, 2017: International Journal of Obesity: Journal of the International Association for the Study of Obesity
https://www.readbyqxmd.com/read/28100372/-research-on-potential-interaction-between-mitochondrial-dna-copy-number-and-related-factors-on-risk-of-hypertension-in-coal-miners
#7
J Y Guo, L J Lei, N Qiao, G Q Fan, C M Sun, J J Huang, T Wang
Objective: To investigate the effects of mitochondrial DNA (mtDNA) copy number in peripheral blood and related factors on the risk of hypertension in coal miners. Methods: A case-control study was conducted in 378 coal miners with hypertension and 325 healthy coal miners recruited from Datong Coal Mine Group. A standard questionnaire was used to collect their general information, such as demographic characteristics, habits and occupational history. Fluorescence quantitative PCR was performed to detect the copy number of mtDNA...
January 10, 2017: Zhonghua Liu Xing Bing Xue za Zhi, Zhonghua Liuxingbingxue Zazhi
https://www.readbyqxmd.com/read/28100184/cnvs-into-the-wild-screening-the-genomes-of-conifer-trees-picea-spp-reveals-fewer-gene-copy-number-variations-in-hybrids-and-links-to-adaptation
#8
Julien Prunier, Sébastien Caron, John MacKay
BACKGROUND: Copy number variations (CNVs) have been linked to different phenotypes in human, including many diseases. A genome-scale understanding of CNVs is available in a few plants but none are wild species, leaving a knowledge gap regarding their genome biology and evolutionary role. We developed a reliable CNV detection method for species lacking contiguous reference genome. We selected multiple probes within 14,078 gene sequences and developed comparative genome hybridization on arrays...
January 18, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28097046/molecular-classification-of-tissue-from-a-transformed-non-hogkin-s-lymphoma-case-with-unexpected-long-time-remission
#9
Julie Støve Bødker, Marianne Tang Severinsen, Tarec Christoffer El-Galaly, Rasmus Froberg Brøndum, Maria Bach Laursen, Steffen Falgreen, Mette Nyegaard, Alexander Schmitz, Lasse Hjort Jakobsen, Anna Amanda Schönherz, Hanne Due, Linn Reinholdt, Martin Bøgsted, Karen Dybkær, Hans Erik Johnsen
BACKGROUND: The concept of precision medicine in cancer includes individual molecular studies to predict clinical outcomes. In the present N = 1 case we retrospectively have analysed lymphoma tissue by exome sequencing and global gene expression in a patient with unexpected long-term remission following relaps. The goals were to phenotype the diagnostic and relapsed lymphoma tissue and evaluate its pattern. Furthermore, to identify mutations available for targeted therapy and expression of genes to predict specific drug effects by resistance gene signatures (REGS) for R-CHOP as described at http://www...
2017: Experimental Hematology & Oncology
https://www.readbyqxmd.com/read/28096781/a-replication-study-of-schizophrenia-related-rare-copy-number-variations-in-a-han-southern-chinese-population
#10
Jianmin Yuan, Jianlin Hu, Zhiqiang Li, Fuquan Zhang, Dexiang Zhou, Chunhui Jin
BACKGROUND: Schizophrenia (SCZ) is a common, complex and severe psychiatric disorder associated with many different genetic and environmental risk factors. Evidence from genetic studies has revealed the role of genome structural variations, specifically copy number variants (CNVs), in the etiology of SCZ. Nevertheless, the occurrence of CNVs and their relation to SCZ has remained relatively unstudied in the diverse Han Chinese population. RESULTS: We used a case/control paradigm, including 476 cases and 1023 controls...
2017: Hereditas
https://www.readbyqxmd.com/read/28094446/deep-sequencing-of-a-candidate-region-harboring-the-sox9-gene-for-the-canine-xx-disorder-of-sex-development
#11
J Nowacka-Woszuk, I Szczerbal, H Pausch, S Hundi, M K Hytönen, A Grzemski, K Flisikowski, H Lohi, M Switonski, M Szydlowski
A disorder of sex development (DSD) in dogs with female sex chromosomes (78, XX), a lack of the SRY gene and the presence of testes or ovotestes is commonly diagnosed in numerous breeds. The molecular background of DSD is not fully recognized but has been linked to the copy number variation in the region harboring the SOX9 gene. We applied a genome-wide association study and targeted next-generation sequencing techniques to compare DSD and normal female dogs. The genome-wide association study did not indicate a significant chromosome region...
January 17, 2017: Animal Genetics
https://www.readbyqxmd.com/read/28093616/rare-germline-alterations-in-cancer-related-genes-associated-with-the-risk-of-multiple-primary-tumor-development
#12
Rolando A R Villacis, Tatiane R Basso, Luisa M Canto, Maísa Pinheiro, Karina M Santiago, Juliana Giacomazzi, Cláudia A A de Paula, Dirce M Carraro, Patrícia Ashton-Prolla, Maria I Achatz, Silvia R Rogatto
: Multiple primary tumors (MPT) have been described in carriers of inherited cancer predisposition genes. However, the genetic etiology of a large proportion of MPT cases remains unclear. We reviewed 267 patients with hereditary cancer predisposition syndromes (HCPS) that underwent genetic counseling and selected 22 patients with MPT to perform genomic analysis (CytoScan HD Array, Affymetrix) aiming to identify new alterations related to a high risk of developing MPT. Twenty patients had a positive family history of cancer and 11 met phenotypic criteria for HCPS...
January 16, 2017: Journal of Molecular Medicine: Official Organ of the "Gesellschaft Deutscher Naturforscher und Ärzte"
https://www.readbyqxmd.com/read/28093083/genetic-analysis-of-teat-number-in-pigs-reveals-some-developmental-pathways-independent-of-vertebra-number-and-several-loci-which-only-affect-a-specific-side
#13
Gary A Rohrer, Dan J Nonneman
BACKGROUND: Number of functional teats is an important trait in commercial swine production. As litter size increases, the number of teats must also increase to supply nutrition to all piglets. Therefore, a genome-wide association analysis was conducted to identify genomic regions that affect this trait in a commercial swine population. Genotypic data from the Illumina Porcine SNP60v1 BeadChip were available for 2951 animals with total teat number (TTN) records. A subset of these animals (n = 1828) had number of teats on each side recorded...
January 4, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28093068/potential-of-gene-drives-with-genome-editing-to-increase-genetic-gain-in-livestock-breeding-programs
#14
Serap Gonen, Janez Jenko, Gregor Gorjanc, Alan J Mileham, C Bruce A Whitelaw, John M Hickey
BACKGROUND: This paper uses simulation to explore how gene drives can increase genetic gain in livestock breeding programs. Gene drives are naturally occurring phenomena that cause a mutation on one chromosome to copy itself onto its homologous chromosome. METHODS: We simulated nine different breeding and editing scenarios with a common overall structure. Each scenario began with 21 generations of selection, followed by 20 generations of selection based on true breeding values where the breeder used selection alone, selection in combination with genome editing, or selection with genome editing and gene drives...
January 4, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28091623/comparative-genomics-of-canine-isolated-leishmania-leishmania-amazonensis-from-an-endemic-focus-of-visceral-leishmaniasis-in-governador-valadares-southeastern-brazil
#15
Hugo O Valdivia, Laila V Almeida, Bruno M Roatt, João Luís Reis-Cunha, Agnes Antônia Sampaio Pereira, Celia Gontijo, Ricardo Toshio Fujiwara, Alexandre B Reis, Mandy J Sanders, James A Cotton, Daniella C Bartholomeu
Leishmaniasis is a highly diverse group of diseases caused by kinetoplastid of the genus Leishmania. These parasites are taxonomically diverse, with human pathogenic species separated into two subgenera according to their development site inside the alimentary tract of the sand fly insect vector. The disease encompasses a variable spectrum of clinical manifestations with tegumentary or visceral symptoms. Among the causative species in Brazil, Leishmania (Leishmania) amazonensis is an important etiological agent of human cutaneous leishmaniasis that accounts for more than 8% of all cases in endemic regions...
January 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28090239/the-screening-and-ranking-algorithm-for-change-points-detection-in-multiple-samples
#16
Chi Song, Xiaoyi Min, Heping Zhang
The chromosome copy number variation (CNV) is the deviation of genomic regions from their normal copy number states, which may associate with many human diseases. Current genetic studies usually collect hundreds to thousands of samples to study the association between CNV and diseases. CNVs can be called by detecting the change-points in mean for sequences of array-based intensity measurements. Although multiple samples are of interest, the majority of the available CNV calling methods are single sample based...
December 2016: Annals of Applied Statistics
https://www.readbyqxmd.com/read/28089650/neither-quantification-by-qpcr-nor-quantitative-elisa-can-be-used-to-discriminate-angus-cattle-for-resistance-susceptibility-to-babesia-bovis
#17
Rodrigo Giglioti, Henrique Nunes Oliveira, Adriana Mércia Guaratini Ibelli, Talita Barban Bilhassi, Thalita Athiê Néo, Clarissa Helena Santana, Márcio Dias Rabelo, Rosângela Zacarias Machado, Ana Carolina de Souza Chagas, Márcia Cristina de Sena Oliveira
With the aim of finding quantitative phenotypic traits that can be used to discriminate the levels of resistance/susceptibility to Babesia bovis, we estimated the repeatability and correlation between the level of infection, determined by the number of copies of a fragment of the gene that encodes cytochrome B (NC mt-cyB) of B. bovis, and the levels of the anti-B. bovis antibodies, in blood samples collected from 51 Angus cattle on two different occasions. Samples with the anticoagulant EDTA were used for DNA extraction and without anticoagulant for separation of the blood serum...
November 21, 2016: Ticks and Tick-borne Diseases
https://www.readbyqxmd.com/read/28087982/the-impact-of-ces1-genotypes-on-the-pharmacokinetics-of-methylphenidate-in-healthy-danish-subjects
#18
Claus Stage, Gesche Jürgens, Louise Schow Guski, Ragnar Thomsen, Ditte Bjerre, Laura Ferrero-Miliani, Yassine Kamal Lyauk, Henrik Berg Rasmussen, Kim Dalhoff
AIM: This study investigated the influence of CES1 variations, including the SNP rs71647871 (G143E) and variation in copy number, on the pharmacokinetics of a single oral dose of 10 mg methylphenidate. METHODS: CES1 genotype was obtained from 200 healthy Danish Caucasian volunteers. Based on the genotype, 44 (19 males and 25 females) were invited to participate in an open, prospective trial involving six predefined genotypes: three groups with two, three, and four CES1 copies, respectively; a group of carriers of the CES1 143E allele; a group of individuals homozygous for CES1A1c (CES1VAR); and a group having three CES1 copies, in which the duplication, CES1A2, had increased transcriptional activity...
January 14, 2017: British Journal of Clinical Pharmacology
https://www.readbyqxmd.com/read/28081277/comparative-genomic-hybridization-analysis-of-rice-dwarf-mutants-induced-by-gamma-irradiation
#19
J E Hwang, S-H Kim, I J Jung, S M Han, J-W Ahn, S-J Kwon, S H Kim, S-Y Kang, D S Kim, J-B Kim
Comparative genomic hybridization (CGH) is a powerful tool used to analyze changes in copy number, polymorphisms, and structural variations in the genome. Gene copy number variation (CNV) is a common form of natural diversity in the genome, which can create new genes and alter gene structure. Thus, CNVs may influence phenotypic variation and gene expression. In this study, to detect CNVs, we irradiated rice seeds with gamma rays (300 Gy) and selected two dwarf mutagenized plants, GA-III-189 and -1052, in the M3 generation...
December 23, 2016: Genetics and Molecular Research: GMR
https://www.readbyqxmd.com/read/28079130/association-of-nsv823469-copy-number-loss-with-decreased-risk-of-chronic-obstructive-pulmonary-disease-and-pulmonary-function-in-chinese
#20
Xiaoliang Chen, Xiaoxiao Lu, Jiansong Chen, Di Wu, Fuman Qiu, Huali Xiong, Zihua Pan, Lei Yang, Binyao Yang, Chenli Xie, Yifeng Zhou, Dongsheng Huang, Yumin Zhou, Jiachun Lu
It is highly possible that copy number variations (CNVs) in susceptible regions have effects on chronic obstructive pulmonary disease (COPD) development, while long noncoding RNA (lncRNAs) have been shown to cause COPD. We hypothesized that the common CNV, named nsv823469 located on 6p22.1, and covering lncRNAs (major histocompatibility complex, class I, A (HLA-A) and HLA complex group 4B (HCG4B)) has an effect on COPD risk. This association was assessed through a two-stage case-control study, and was further confirmed with COPD and pulmonary function-based family analyses, respectively...
January 12, 2017: Scientific Reports
keyword
keyword
17243
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"