scholarly journals VCS: Tool for Visualizing Copy Number Variation and Single Nucleotide Polymorphism

2014 ◽  
Vol 27 (12) ◽  
pp. 1691-1694 ◽  
Author(s):  
HyoYoung Kim ◽  
Samsun Sung ◽  
Seoae Cho ◽  
Tae-Hun Kim ◽  
Kangseok Seo ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Copy Number Variation ◽  
Copy Number ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Number Variation

scholarly journals A genome-wide single nucleotide polymorphism and copy number variation analysis for number of piglets born alive

BMC Genomics ◽  
2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Nedenia Bonvino Stafuzza ◽  
Rafael Medeiros de Oliveira Silva ◽  
Breno de Oliveira Fragomeni ◽  
Yutaka Masuda ◽  
Yijian Huang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Copy Number Variation ◽  
Copy Number ◽  
Variation Analysis ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Copy Number Variation Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Number Variation

scholarly journals Single-Nucleotide Polymorphism and Copy Number Variation of the Multidrug Resistance-1 Locus of Plasmodium vivax: Local and Global Patterns

2012 ◽  
Vol 87 (5) ◽  
pp. 813-821 ◽  
Author(s):  
Rosa del Carmen Miluska Vargas-Rodríguez ◽  
Maria José Menezes ◽  
Pamela Orjuela-Sánchez ◽  
Marcelo U. Ferreira ◽  
Melissa da Silva Bastos
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Multidrug Resistance ◽  
Copy Number Variation ◽  
Plasmodium Vivax ◽  
Copy Number ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Number Variation ◽  
Global Patterns

scholarly journals The genetic sequences prone to copy number variation and single nucleotide polymorphism are linked to the repair of the poisoned DNA topoisomerase II

2020 ◽  
Author(s):  
Chuo Jiang ◽  
Cong Ma ◽  
Detao Wang ◽  
Li Liu ◽  
Chunxiu Zhang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Copy Number Variation ◽  
Copy Number ◽  
Topoisomerase Ii ◽  
Chromosome Translocation ◽  
Nucleotide Polymorphism ◽  
Dna Topoisomerase ◽  
Single Nucleotide ◽  
Topoisomerase Ii Poisons ◽  
Number Variation

AbstractTOP2-poisoning bioflavonoids and pesticides are linked to the copy number variation-related autism and chromosome translocation-related leukemia. On the other hand, the poisoned DNA topoisomerase II (TOP2) can lead to chromosome aberration. However, except a limited number of genes such as the MLL fusion, other poisoned TOP2-targeted genes, as well as their relationships with any specific diseases, are not defined. We applied the γH2A.X antibodies to genome-widely immunoprecipitate the chromatins that were associated with the repair of the TOP2 poison etoposide-induced DNA double strand breaks. We identified many transcriptable protein- and nonprotein-coding DNA sequences that are the candidates of or associated with many gene copy number variation- and/or single nucleotide polymorphism-associated diseases, including but not limited to microdeletion and microduplication syndromes (which are phenotypically presented as developmental, autistic, neurological, psychiatric, diabetic, autoimmune, and neoplastic diseases among many others) as well as stature, obesity, metabolic syndrome, hypertension, coronary artery disease, ischemic stroke, aortic aneurysm and dissection, leukemia, cancer, osteoporosis, Alzheimer disease, Parkinson disease, and Huntington disease. Our data raise the possibility that the poisoned TOP2 might be linked to the specific genetic alterations contributing to these diseases, additional to the known copy number variation-related autism and chromosome translocation-related leukemia. According to our and others’ data, we propose a model that may interpret the features, such as mosaicism, polygenic traits and pleiotropy, of these diseases.Author SummaryFor the past several decades, the morbidity rate of many diseases, including autism, mental disorders, cancer, cardiovascular diseases, diabetes, and senile dementia, has world-widely been rising. Analysis of the genome of the patients and their family members has identified the genes, whose alterations, so called copy number variation (CNV) and single nucleotide polymorphism (SNP), contribute to the diseases. Moreover, the CNVs and SNPs are de novo, that is, they have occurred only in the recent generations. Epidemiologically, this indicates that for the past several decades, there have existed some unknown world-wide etiologies to which human beings are exposed. If the etiologies are identified, avoiding human’s exposure may reduce the morbidity of the diseases. We have found that the repair of the poisoned topoisomerase II involves many genes that contribute to the aforementioned diseases. As the topoisomerase II is known to be located at the genomic sites where the disease-associated CNVs occur, as the poisoned topoisomerase II is susceptible to chromosome aberration, and as the topoisomerase II poisons, such as dietary bioflavonoids, are widely distributed in the environment, our data raise the yet-to-be-confirmed possibility that the environmental topoisomerase II poisons might etiologically contribute to many CNV-associated diseases.

scholarly journals Atypical Molecular Basis for Drug Resistance to Mitochondrial Function Inhibitors in Plasmodium falciparum

2020 ◽  
Vol 65 (3) ◽  
Author(s):  
Heather J. Painter ◽  
Joanne M. Morrisey ◽  
Michael W. Mather ◽  
Lindsey M. Orchard ◽  
Cuyler Luck ◽  
...  
Keyword(s):  
Drug Resistance ◽  
Single Nucleotide Polymorphism ◽  
Plasmodium Falciparum ◽  
Copy Number Variation ◽  
Copy Number ◽  
De Novo ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pyrimidine Synthesis ◽  
Number Variation

ABSTRACT The continued emergence of drug-resistant Plasmodium falciparum parasites hinders global attempts to eradicate malaria, emphasizing the need to identify new antimalarial drugs. Attractive targets for chemotherapeutic intervention are the cytochrome (cyt) bc1 complex, which is an essential component of the mitochondrial electron transport chain (mtETC) required for ubiquinone recycling and mitochondrially localized dihydroorotate dehydrogenase (DHODH) critical for de novo pyrimidine synthesis. Despite the essentiality of this complex, resistance to a novel acridone class of compounds targeting cyt bc1 was readily attained, resulting in a parasite strain (SB1-A6) that was panresistant to both mtETC and DHODH inhibitors. Here, we describe the molecular mechanism behind the resistance of the SB1-A6 parasite line, which lacks the common cyt bc1 point mutations characteristic of resistance to mtETC inhibitors. Using Illumina whole-genome sequencing, we have identified both a copy number variation (∼2×) and a single-nucleotide polymorphism (C276F) associated with pfdhodh in SB1-A6. We have characterized the role of both genetic lesions by mimicking the copy number variation via episomal expression of pfdhodh and introducing the identified single nucleotide polymorphism (SNP) using CRISPR-Cas9 and assessed their contributions to drug resistance. Although both of these genetic polymorphisms have been previously identified as contributing to both DSM-1 and atovaquone resistance, SB1-A6 represents a unique genotype in which both alterations are present in a single line, suggesting that the combination contributes to the panresistant phenotype. This novel mechanism of resistance to mtETC inhibition has critical implications for the development of future drugs targeting the bc1 complex or de novo pyrimidine synthesis that could help guide future antimalarial combination therapies and reduce the rapid development of drug resistance in the field.

scholarly journals Including copy number variation in association studies to predict genotypic values

2010 ◽  
Vol 92 (2) ◽  
pp. 115-125 ◽  
Author(s):  
M. P. L. CALUS ◽  
D. J. DE KONING ◽  
C. S. HALEY
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Genetic Variation ◽  
Copy Number ◽  
Association Studies ◽  
Simulated Data ◽  
Continuous Measure ◽  
Nucleotide Polymorphism ◽  
Copy Number Polymorphism ◽  
Single Nucleotide ◽  
Number Variation

SummaryThe objective of this study was to investigate, both empirically and deterministically, the ability to explain genetic variation resulting from a copy number polymorphism (CNP) by including the CNP, either by its genotype or by a continuous derivation thereof, alone or together with a nearby single nucleotide polymorphism (SNP) in the model. This continuous measure of a CNP genotype could be a raw hybridization measurement, or a predicted CNP genotype. Results from simulations showed that the linkage disequilibrium (LD) between an SNP and CNP was lower than LD between two SNPs, due to the higher mutation rate at the CNP loci. The model R2 values from analysing the simulated data were very similar to the R2 values predicted with the deterministic formulae. Under the assumption that x copies at a CNP locus lead to the effect of x times the effect of 1 copy, including a continuous measure of a CNP locus in the model together with the genotype of a nearby SNP increased power to explain variation at the CNP locus, even when the continuous measure explained only 15% of the variation at the CNP locus.

scholarly journals Detection of copy number variation associated with ventriculomegaly in fetuses using single nucleotide polymorphism arrays

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Huili Xue ◽  
Aili Yu ◽  
Na Lin ◽  
Xuemei Chen ◽  
Min Lin ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphism ◽  
Copy Number ◽  
Snp Array ◽  
Copy Number Variations ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Group I ◽  
Number Variation ◽  
Fetal Ventriculomegaly ◽  
Cns Anomalies

AbstractEtiopathogenesis of fetal ventriculomegaly is poorly understood. Associations between fetal isolated ventriculomegaly and copy number variations (CNVs) have been previously described. We investigated the correlations between fetal ventriculomegaly—with or without other ultrasound anomalies—and chromosome abnormalities. 222 fetuses were divided into four groups: (I) 103 (46.4%) cases with isolated ventriculomegaly, (II) 41 (18.5%) cases accompanied by soft markers, (III) 33 (14.9%) cases complicated with central nervous system (CNS) anomalies, and (IV) 45 (20.3%) cases with accompanying anomalies. Karyotyping and single nucleotide polymorphism (SNP) array were used in parallel. Karyotype abnormalities were identified in 15/222 (6.8%) cases. Karyotype abnormalities in group I, II, III, and IV were 4/103 (3.9%), 2/41 (4.9%), 4/33 (12.1%), and 5/45 (11.1%), respectively. Concerning the SNP array analysis results, 31/222 (14.0%) were CNVs, CNVs in groups I, II, III, and IV were 11/103 (10.7%), 6/41 (14.6%), 9/33 (27.3%), and 5/45 fetuses (11.1%), respectively. Detections of clinical significant CNVs were higher in non-isolated ventriculomegaly than in isolated ventriculomegaly (16.81% vs 10.7%, P = 0.19). SNP arrays can effectively identify CNVs in fetuses with ventriculomegaly and increase the abnormal chromosomal detection rate by approximately 7.2%, especially ventriculomegaly accompanied by CNS anomalies.

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