scholarly journals Fine-tuned characterization of RCCX copy number variants and their relationship with extended MHC haplotypes

2012 ◽  
Vol 13 (7) ◽  
pp. 530-535 ◽  
Author(s):  
Z Bánlaki ◽  
M Doleschall ◽  
K Rajczy ◽  
G Fust ◽  
Á Szilágyi
Keyword(s):  
Copy Number ◽  
Copy Number Variants

An approach to rapid characterization of DMD copy number variants for prenatal risk assessment

2021 ◽  
Author(s):  
Hui‐Lin Chin ◽  
Kieran O'Neill ◽  
Kristal Louie ◽  
Lindsay Brown ◽  
Kamilla Schlade‐Bartusiak ◽  
...  
Keyword(s):  
Risk Assessment ◽  
Copy Number ◽  
Copy Number Variants ◽  
Prenatal Risk ◽  
Rapid Characterization

scholarly journals Characterization of Single Gene Copy Number Variants in Schizophrenia

2020 ◽  
Vol 87 (8) ◽  
pp. 736-744 ◽  
Author(s):  
Jin P. Szatkiewicz ◽  
Menachem Fromer ◽  
Randal J. Nonneman ◽  
NaEshia Ancalade ◽  
Jessica S. Johnson ◽  
...  
Keyword(s):  
Copy Number ◽  
Single Gene ◽  
Copy Number Variants ◽  
Gene Copy Number ◽  
Gene Copy

Characterization of copy number variants for CCL3L1 gene in rheumatoid arthritis for French trio families and Tunisian cases and controls

2016 ◽  
Vol 35 (8) ◽  
pp. 1917-1922 ◽  
Author(s):  
Mohamed Sahbi Ben Kilani ◽  
Yosser Achour ◽  
Javier Perea ◽  
François Cornelis ◽  
Thomas Bardin ◽  
...  
Keyword(s):  
Rheumatoid Arthritis ◽  
Copy Number ◽  
Copy Number Variants

Identification of Copy Number Variants and Characterization of Novel Key Genes Associated with Genitourinary Birth Defects.

2010 ◽  
pp. P1-318-P1-318
Author(s):  
Shuo Han ◽  
Mounia Tannour-Louet ◽  
Sean T Corbett ◽  
Svetlana Yatsenko ◽  
Lindsay Meyers ◽  
...  
Keyword(s):  
Birth Defects ◽  
Copy Number ◽  
Copy Number Variants ◽  
Key Genes

scholarly journals Detection of copy number variants in African goats using whole genome sequence data

2020 ◽  
Author(s):  
Wilson Nandolo ◽  
Gábor Mészáros ◽  
Maria Wurzinger ◽  
Liveness J. Banda ◽  
Timothy N. Gondwe ◽  
...  
Keyword(s):  
Copy Number ◽  
Genetic Characterization ◽  
Sequence Data ◽  
Copy Number Variants ◽  
Whole Genome Sequence ◽  
African Countries ◽  
Body Of Knowledge ◽  
Number Variation ◽  
Cellular Components

Abstract BackgroundCopy number variations (CNV) are a significant source of variation in the genome, as such they are essential to the genetic characterization of animal breeds. The aim of this study was to develop a fine-scaled copy number variation map for African goats. We used sequence data from multiple breeds and from multiple African countries. ResultsA total of 253,553 CNV (244,876 deletions and 8,677 duplications) were identified, corresponding to an overall average of 1,393 CNV per animal. The mean CNV length was 3.3 kb, with a median of 1.3 kb. There was substantial differentiation between the populations for some CNV, suggestive of the effect of population-specific selective pressures. A total of 6,231 global CNV regions (CNVR) were found across all animals, representing 59.2 Mb (2.4%) of the goat genome. About 1.6% of the CNVR were present in all 34 breeds and 28.7% were present in all 5 geographical areas across Africa, where animals had been sampled. The CNVR had genes that were highly enriched in important biological functions, molecular functions, and cellular components including retrograde endocannabinoid signaling, glutamatergic synapse and circadian entrainment. ConclusionsThis study presents the first fine CNV map of African goat based on WGS data and adds to the growing body of knowledge on the genetic characterization of goats.

scholarly journals Global characterization of copy number variants in epilepsy patients from whole genome sequencing

2017 ◽  
Author(s):  
Jean Monlong ◽  
Simon L. Girard ◽  
Caroline Meloche ◽  
Maxime Cadieux-Dion ◽  
Danielle M. Andrade ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Copy Number Variants ◽  
Genetic Variations ◽  
Genome Wide Association Studies ◽  
Whole Genome ◽  
Loss Of Function ◽  
Genome Wide

AbstractEpilepsy will affect nearly 3% of people at some point during their lifetime. Previous copy number variants (CNVs) studies of epilepsy have used array-based technology and were restricted to the detection of large or exonic events. In contrast, whole-genome sequencing (WGS) has the potential to more comprehensively profile CNVs but existing analytic methods suffer from limited accuracy. We show that this is in part due to the non-uniformity of read coverage, even after intra-sample normalization. To improve on this, we developed PopSV, an algorithm that uses multiple samples to control for technical variation and enables the robust detection of CNVs. Using WGS and PopSV, we performed a comprehensive characterization of CNVs in 198 individuals affected with epilepsy and 301 controls. For both large and small variants, we found an enrichment of rare exonic events in epilepsy patients, especially in genes with predicted loss-of-function intolerance. Notably, this genome-wide survey also revealed an enrichment of rare non-coding CNVs near previously known epilepsy genes. This enrichment was strongest for non-coding CNVs located within 100 Kbp of an epilepsy gene and in regions associated with changes in the gene expression, such as expression QTLs or DNase I hypersensitive sites. Finally, we report on 21 potentially damaging events that could be associated with known or new candidate epilepsy genes. Our results suggest that comprehensive sequence-based profiling of CNVs could help explain a larger fraction of epilepsy cases.Author summaryEpilepsy is a common neurological disorder affecting around 3% of the population. In some cases, epilepsy is caused by brain trauma or other brain anomalies but there are often no clear causes. Genetic factors have been associated with epilepsy in the past such as rare genetic variations found by linkage studies as well as common genetic variations found by genome-wide association studies and large copy-number variants. We sequenced the genome of ∼200 epilepsy patients and ∼300 healthy controls and compared the distribution of deletion (loss of a copy) and duplication (additional copy) of genomic regions. Thanks to the sequencing technology and a new method that takes advantage of the large sample size, we could compare the distribution of small copy- number variants between epilepsy patients and controls. Overall, we found that small variants are also associated with epilepsy. Indeed, the genome of epilepsy patients had more exonic copy- number variants, especially when rare or affecting genes with predicted loss-of-function intolerance. Focusing on regions around genes that have been previously associated with epilepsy, we also found more non-coding variants in epilepsy patients, especially deletions or variants in regulatory regions. Finally, we provide a list of 21 regions in which we found likely pathogenic variants.

scholarly journals Global characterization of copy number variants in epilepsy patients from whole genome sequencing

PLoS Genetics ◽  
2018 ◽  
Vol 14 (4) ◽  
pp. e1007285 ◽  
Author(s):  
Jean Monlong ◽  
Simon L. Girard ◽  
Caroline Meloche ◽  
Maxime Cadieux-Dion ◽  
Danielle M. Andrade ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Copy Number Variants ◽  
Whole Genome

scholarly journals Characterization of clinically relevant copy-number variants from exomes of patients with inherited heart disease and unexplained sudden cardiac death

2020 ◽  
Vol 23 (1) ◽  
pp. 86-93
Author(s):  
Emma S. Singer ◽  
Samantha B. Ross ◽  
Jon R. Skinner ◽  
Robert G. Weintraub ◽  
Jodie Ingles ◽  
...  
Keyword(s):  
Heart Disease ◽  
Sudden Cardiac Death ◽  
Copy Number ◽  
Cardiac Death ◽  
Copy Number Variants

Understanding Schizophrenia: Genetic Causes and Treatment

2019 ◽  
Vol 1 (1) ◽  
pp. 6-12
Author(s):  
Fatima Javeria ◽  
Shazma Altaf ◽  
Alishah Zair ◽  
Rana Khalid Iqbal
Keyword(s):  
Copy Number ◽  
Drug Targets ◽  
Disease Risk ◽  
Mental Disease ◽  
Copy Number Variants ◽  
Aminobutyric Acid ◽  
Epigenetic Mechanisms ◽  
Gamma Aminobutyric Acid ◽  
Wide Range ◽  
Severe Mental Disease

Schizophrenia is a severe mental disease. The word schizophrenia literally means split mind. There are three major categories of symptoms which include positive, negative and cognitive symptoms. The disease is characterized by symptoms of hallucination, delusions, disorganized thinking and speech. Schizophrenia is related to many other mental and psychological problems like suicide, depression, hallucinations. Including these, it is also a problem for the patient’s family and the caregiver. There is no clear reason for the disease, but with the advances in molecular genetics; certain epigenetic mechanisms are involved in the pathophysiology of the disease. Epigenetic mechanisms that are mainly involved are the DNA methylation, copy number variants. With the advent of GWAS, a wide range of SNPs is found linked with the etiology of schizophrenia. These SNPs serve as ‘hubs’; because these all are integrating with each other in causing of schizophrenia risk. Until recently, there is no treatment available to cure the disease; but anti-psychotics can reduce the disease risk by minimizing its symptoms. Dopamine, serotonin, gamma-aminobutyric acid, are the neurotransmitters which serve as drug targets in the treatment of schizophrenia. Due to the involvement of genetic and epigenetic mechanisms, drugs available are already targeting certain genes involved in the etiology of the disease.

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