A genome-wide association study of copy number variations with umbilical hernia in swine

2016 ◽  
Vol 47 (3) ◽  
pp. 298-305 ◽  
Author(s):  
Yi Long ◽  
Ying Su ◽  
Huashui Ai ◽  
Zhiyan Zhang ◽  
Bin Yang ◽  
...  
Keyword(s):  
Association Study ◽  
Copy Number ◽  
Umbilical Hernia ◽  
Genome Wide Association Study ◽  
Copy Number Variations ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals The correlation of copy number variations with longevity in a genome-wide association study of Han Chinese

Aging ◽  
2018 ◽  
Vol 10 (6) ◽  
pp. 1206-1222 ◽  
Author(s):  
Xin Zhao ◽  
Xiaomin Liu ◽  
Aiping Zhang ◽  
Huashuai Chen ◽  
Qing Huo ◽  
...  
Keyword(s):  
Association Study ◽  
Copy Number ◽  
Genome Wide Association Study ◽  
Copy Number Variations ◽  
Han Chinese ◽  
Genome Wide Association ◽  
Genome Wide ◽  
A Genome

scholarly journals A Genome-Wide Association Study to Identify Potential Germline Copy Number Variants for Sporadic Breast Cancer Susceptibility

2016 ◽  
Vol 149 (3) ◽  
pp. 156-164 ◽  
Author(s):  
Yadav Sapkota ◽  
Ashok Narasimhan ◽  
Mahalakshmi Kumaran ◽  
Badan S. Sehrawat ◽  
Sambasivarao Damaraju
Keyword(s):  
Breast Cancer ◽  
Association Study ◽  
Copy Number ◽  
Genome Wide Association Study ◽  
Genome Wide Association ◽  
Frequency Effect ◽  
Potential Candidate ◽  
Disease Etiology ◽  
Genome Wide ◽  
A Genome

Breast cancer (BC) predisposition in populations arises from both genetic and nongenetic risk factors. Structural variations such as copy number variations (CNVs) are heritable determinants for disease susceptibility. The primary objectives of this study are (1) to identify CNVs associated with sporadic BC using a genome-wide association study (GWAS) design; (2) to utilize 2 distinct CNV calling algorithms to identify concordant CNVs as a strategy to reduce false positive associations in the hypothesis-generating GWAS discovery phase, and (3) to identify potential candidate CNVs for follow-up replication studies. We used Affymetrix SNP Array 6.0 data profiled on Caucasian subjects (422 cases/348 controls) to call CNVs using algorithms implemented in Nexus Copy Number and Partek Genomics Suite software. Nexus algorithm identified CNVs associated with BC (731 autosomal CNVs with >5% frequency in the total sample and Q < 0.05). Thirteen CNVs were identified when Partek algorithm-called CNVs were overlapped with Nexus-identified CNVs; these CNVs showed concordances for frequency, effect size, and direction. Coding genes present within BC-associated CNVs were known to play a role in disease etiology and prognosis. Long noncoding RNAs identified within CNVs showed tissue-specific expression, indicating potential functional relevance of the findings. The identified candidate CNVs warrant independent replication.

Genome-wide association study identified copy number variants associated with sporadic colorectal cancer risk

2017 ◽  
Vol 55 (3) ◽  
pp. 181-188 ◽  
Author(s):  
Lai Fun Thean ◽  
Yee Syuen Low ◽  
Michelle Lo ◽  
Yik-Ying Teo ◽  
Woon-Puay Koh ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Association Study ◽  
Copy Number ◽  
Genome Wide Association Study ◽  
Copy Number Variants ◽  
Genome Wide Association ◽  
Copy Number Loss ◽  
Genome Wide ◽  
A Genome

BackgroundMultiple single nucleotide polymorphisms (SNPs) have been associated with colorectal cancer (CRC) risk. The role of structural or copy number variants (CNV) in CRC, however, remained unclear. We investigated the role of CNVs in patients with sporadic CRC.MethodsA genome-wide association study (GWAS) was performed on 1000 Singapore Chinese patients aged 50 years or more with no family history of CRC and 1000 ethnicity-matched, age-matched and gender-matched healthy controls using the Affymetrix SNP 6 platform. After 16 principal component corrections, univariate and multivariate segmentations followed by association testing were performed on 1830 samples that passed quality assurance tests.ResultsA rare CNV region (CNVR) at chromosome 14q11 (OR=1.92 (95% CI 1.59 to 2.32), p=2.7e-12) encompassing CHD8, and common CNVR at chromosomes 3q13.12 (OR=1.54 (95% CI 1.33 to 1.77), p=2.9e-9) and 12p12.3 (OR=1.69 (95% CI 1.41 to 2.01), p=2.8e-9) encompassing CD47 and RERG/ARHGDIB, respectively, were significantly associated with CRC risk. CNV loci were validated in an independent replication panel using an optimised copy number assay. Whole-genome expression data in matched tumours of a subset of cases demonstrated that copy number loss at CHD8 was significantly associated with dysregulation of several genes that perturb the Wnt, TP53 and inflammatory pathways.ConclusionsA rare CNVR at 14q11 encompassing the chromatin modifier CHD8 was significantly associated with sporadic CRC risk. Copy number loss at CHD8 altered expressions of genes implicated in colorectal tumourigenesis.

scholarly journals Genome-Wide Association Study of Copy Number Variations (CNVs) with Opioid Dependence

2014 ◽  
Vol 40 (4) ◽  
pp. 1016-1026 ◽  
Author(s):  
Dawei Li ◽  
Hongyu Zhao ◽  
Henry R Kranzler ◽  
Ming D Li ◽  
Kevin P Jensen ◽  
...  
Keyword(s):  
Association Study ◽  
Copy Number ◽  
Opioid Dependence ◽  
Genome Wide Association Study ◽  
Copy Number Variations ◽  
Genome Wide Association ◽  
Genome Wide
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