scholarly journals Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

2016 ◽  
Vol 49 (1) ◽  
pp. 27-35 ◽  
Author(s):  
Christian R Marshall ◽  
◽  
Daniel P Howrigan ◽  
Daniele Merico ◽  
Bhooma Thiruvahindrapuram ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Variants ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Study

scholarly journals A genome-wide study shows a limited contribution of rare copy number variants to Alzheimer's disease risk

2012 ◽  
Vol 22 (4) ◽  
pp. 816-824 ◽  
Author(s):  
Jade Chapman ◽  
Elliott Rees ◽  
Denise Harold ◽  
Dobril Ivanov ◽  
Amy Gerrish ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Copy Number ◽  
Disease Risk ◽  
Copy Number Variants ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Study

scholarly journals Evaluation of copy number burden in specific epilepsy types from a genome-wide study of 18,564 subjects

2019 ◽  
Author(s):  
Lisa-Marie Niestroj ◽  
Daniel P. Howrigan ◽  
Eduardo Perez-Palma ◽  
Elmo Saarentaus ◽  
Peter Nürnberg ◽  
...  
Keyword(s):  
Copy Number ◽  
Genetic Architecture ◽  
Focal Epilepsy ◽  
Copy Number Variants ◽  
Epileptic Encephalopathy ◽  
Additional Risk ◽  
Genome Wide ◽  
A Genome ◽  
Generalized Epilepsy ◽  
Genome Wide Study

AbstractRare and large copy number variants (CNVs) around known genomic ‘hotspots’ are strongly implicated in epilepsy etiology. But it remains unclear whether the observed associations are specific to an epilepsy phenotype, and if additional risk signal can be found outside hotspots. Here, we present the largest CNV burden and first CNV breakpoint level association analysis in epilepsy to date with 11,246 European epilepsy cases and 7,318 ancestry-matched controls. We studied five epilepsy phenotypes: genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, epileptic encephalopathy, and unclassified epilepsy. We discovered novel epilepsy-associated CNV loci and further characterized the CNV burden enrichment among phenotype-specific epilepsies. Finally, we provide evidence for deletion burden outside of known hotspot regions and show that CNVs play a significant role in the genetic architecture of lesional focal epilepsies.

scholarly journals A Genome-wide Study Reveals Copy Number Variants Exclusive to Childhood Obesity Cases

2010 ◽  
Vol 87 (5) ◽  
pp. 661-666 ◽  
Author(s):  
Joseph T. Glessner ◽  
Jonathan P. Bradfield ◽  
Kai Wang ◽  
Nagahide Takahashi ◽  
Haitao Zhang ◽  
...  
Keyword(s):  
Childhood Obesity ◽  
Copy Number ◽  
Copy Number Variants ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Study

A Genome-Wide Screen Of Functional Dna Copy Number Variants Identifies Several Novel Asthma Genes

2011 ◽  
Author(s):  
Angela J. Rogers ◽  
Jen-Hwa Chu ◽  
Katayoon Darvishi ◽  
Iuliana Ionita-Laza ◽  
Barbara J. Klanderman ◽  
...  
Keyword(s):  
Copy Number ◽  
Copy Number Variants ◽  
Dna Copy Number ◽  
Genome Wide ◽  
A Genome ◽  
Functional Dna ◽  
Dna Copy Number Variants

scholarly journals Epilepsy subtype-specific copy number burden observed in a genome-wide study of 17 458 subjects

Brain ◽  
2020 ◽  
Vol 143 (7) ◽  
pp. 2106-2118 ◽  
Author(s):  
Lisa-Marie Niestroj ◽  
Eduardo Perez-Palma ◽  
Daniel P Howrigan ◽  
Yadi Zhou ◽  
Feixiong Cheng ◽  
...  
Keyword(s):  
Copy Number ◽  
Focal Epilepsy ◽  
Copy Number Variants ◽  
Epileptic Encephalopathy ◽  
Human Interactome ◽  
Genome Wide ◽  
A Genome ◽  
Wide Scale ◽  
Generalized Epilepsy ◽  
First Time

Abstract Cytogenic testing is routinely applied in most neurological centres for severe paediatric epilepsies. However, which characteristics of copy number variants (CNVs) confer most epilepsy risk and which epilepsy subtypes carry the most CNV burden, have not been explored on a genome-wide scale. Here, we present the largest CNV investigation in epilepsy to date with 10 712 European epilepsy cases and 6746 ancestry-matched controls. Patients with genetic generalized epilepsy, lesional focal epilepsy, non-acquired focal epilepsy, and developmental and epileptic encephalopathy were included. All samples were processed with the same technology and analysis pipeline. All investigated epilepsy types, including lesional focal epilepsy patients, showed an increase in CNV burden in at least one tested category compared to controls. However, we observed striking differences in CNV burden across epilepsy types and investigated CNV categories. Genetic generalized epilepsy patients have the highest CNV burden in all categories tested, followed by developmental and epileptic encephalopathy patients. Both epilepsy types also show association for deletions covering genes intolerant for truncating variants. Genome-wide CNV breakpoint association showed not only significant loci for genetic generalized and developmental and epileptic encephalopathy patients but also for lesional focal epilepsy patients. With a 34-fold risk for developing genetic generalized epilepsy, we show for the first time that the established epilepsy-associated 15q13.3 deletion represents the strongest risk CNV for genetic generalized epilepsy across the whole genome. Using the human interactome, we examined the largest connected component of the genes overlapped by CNVs in the four epilepsy types. We observed that genetic generalized epilepsy and non-acquired focal epilepsy formed disease modules. In summary, we show that in all common epilepsy types, 1.5–3% of patients carry epilepsy-associated CNVs. The characteristics of risk CNVs vary tremendously across and within epilepsy types. Thus, we advocate genome-wide genomic testing to identify all disease-associated types of CNVs.

scholarly journals A contribution of novel CNVs to schizophrenia from a genome-wide study of 41,321 subjects

2016 ◽  
Author(s):  
Christian Marshall ◽  
Daniel Howrigan ◽  
Daniele Merico ◽  
Bhooma Thiruvahindrapuram ◽  
Wenting Wu ◽  
...  
Keyword(s):  
Copy Number Variants ◽  
Synaptic Function ◽  
Analysis Pipeline ◽  
Genomic Copy Number ◽  
Risk Alleles ◽  
Risk Variants ◽  
Genome Wide ◽  
A Genome ◽  
Significant Support ◽  
Genome Wide Study

Genomic copy number variants (CNVs) have been strongly implicated in the etiology of schizophrenia (SCZ). However, apart from a small number of risk variants, elucidation of the CNV contribution to risk has been difficult due to the rarity of risk alleles, all occurring in less than 1% of cases. We sought to address this obstacle through a collaborative effort in which we applied a centralized analysis pipeline to a SCZ cohort of 21,094 cases and 20,227 controls. We observed a global enrichment of CNV burden in cases (OR=1.11, P=5.7e-15), which persisted after excluding loci implicated in previous studies (OR=1.07, P=1.7e-6). CNV burden is also enriched for genes associated with synaptic function (OR = 1.68, P = 2.8e-11) and neurobehavioral phenotypes in mouse (OR = 1.18, P= 7.3e-5). We identified genome-wide significant support for eight loci, including 1q21.1, 2p16.3 (NRXN1), 3q29, 7q11.2, 15q13.3, distal 16p11.2, proximal 16p11.2 and 22q11.2. We find support at a suggestive level for nine additional candidate susceptibility and protective loci, which consist predominantly of CNVs mediated by non-allelic homologous recombination (NAHR).

A genome-wide scan of copy number variants using high-density SNPs in Brown Swiss dairy cattle

2016 ◽  
Vol 191 ◽  
pp. 153-160 ◽  
Author(s):  
R.T.M.M. Prinsen ◽  
M.G. Strillacci ◽  
F. Schiavini ◽  
E. Santus ◽  
A. Rossoni ◽  
...  
Keyword(s):  
Dairy Cattle ◽  
Copy Number ◽  
Copy Number Variants ◽  
High Density ◽  
Brown Swiss ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Scan
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