scholarly journals Population‐wide copy number variation calling using variant call format files from 6,898 individuals

2019 ◽  
Vol 44 (1) ◽  
pp. 79-89
Author(s):  
Grace Png ◽  
Daniel Suveges ◽  
Young‐Chan Park ◽  
Klaudia Walter ◽  
Kousik Kundu ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Variant Call Format ◽  
Variant Call ◽  
Number Variation ◽  
Copy Number Variation Calling

scholarly journals Using Family Data as a Verification Standard to Evaluate Copy Number Variation Calling Strategies for Genetic Association Studies

2012 ◽  
Vol 36 (3) ◽  
pp. 253-262 ◽  
Author(s):  
Xiaojing Zheng ◽  
John R. Shaffer ◽  
Caitlin P. McHugh ◽  
Cathy C. Laurie ◽  
Bjarke Feenstra ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Genetic Association ◽  
Copy Number ◽  
Association Studies ◽  
Genetic Association Studies ◽  
Family Data ◽  
Number Variation ◽  
Copy Number Variation Calling

scholarly journals Population-wide copy number variation calling using variant call format files from 6,898 individuals

2018 ◽  
Author(s):  
Grace Png ◽  
Daniel Suveges ◽  
Young-Chan Park ◽  
Klaudia Walter ◽  
Kousik Kundu ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Copy Number Variants ◽  
Regression Tree ◽  
Low Frequency ◽  
Protein Product ◽  
Supplementary Information ◽  
Variant Call ◽  
Large Deletions ◽  
Number Variation

MotivationCopy number variants (CNVs) are large deletions or duplications at least 50 to 200 base pairs long. They play an important role in multiple disorders, but accurate calling of CNVs remains challenging. Most current approaches to CNV detection use raw read alignments, which are computationally intensive to process.ResultsWe use a regression tree-based approach to call CNVs from whole-genome sequencing (WGS, > 18x) variant call-sets in 6,898 samples across four European cohorts, and describe a rich large variation landscape comprising 1,320 CNVs. 61.8% of detected events have been previously reported in the Database of Genomic Variants. 23% of high-quality deletions affect entire genes, and we recapitulate known events such as theGSTM1andRHDgene deletions. We test for association between the detected deletions and 275 protein levels in 1,457 individuals to assess the potential clinical impact of the detected CNVs. We describe the LD structure and copy number variation underlying the association between levels of the CCL3 protein and a complex structural variant (MAF = 0.15, p = 3.6×10-12) affectingCCL3L3, a paralog of theCCL3gene. We also identify acis-association between a low-frequencyNOMO1deletion and the protein product of this gene (MAF = 0.02, p = 2.2×10-7), for which nocis-ortrans-single nucleotide variant-driven protein quantitative trait locus (pQTL) has been documented to date. This work demonstrates that existing population-wide WGS call-sets can be mined for CNVs with minimal computational overhead, delivering insight into a less well-studied, yet potentially impactful class of genetic variant.AvailabilityThe regression tree based approach, UN-CNVc, is available as an R and bash executable on GitHub athttps://github.com/agilly/[email protected];[email protected] InformationSupplementary information is appended.

Identification of Novel Germline and Tumor-Specific Nucleotide Variants and Copy Number Variation in Clival Chordomas by Exome Sequencing

2015 ◽  
Vol 76 (S 01) ◽  
Author(s):  
Georgios Zenonos ◽  
Peter Howard ◽  
Maureen Lyons-Weiler ◽  
Wang Eric ◽  
William LaFambroise ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Exome Sequencing ◽  
Copy Number ◽  
Number Variation ◽  
Specific Nucleotide

The impact of paralog genes: detection of copy number variation in spinal muscle atrophy patients

BIOCELL ◽  
2018 ◽  
Vol 42 (3) ◽  
pp. 87-91 ◽  
Author(s):  
Sergio LAURITO ◽  
Juan A. CUETO ◽  
Jimena PEREZ ◽  
Mar韆 ROQU�
Keyword(s):  
Copy Number Variation ◽  
Muscle Atrophy ◽  
Copy Number ◽  
Number Variation ◽  
The Impact
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