scholarly journals Genome‐wide survey of copy number variants finds MAPT duplications in progressive supranuclear palsy

2019 ◽  
Vol 34 (7) ◽  
pp. 1049-1059 ◽  
Author(s):  
Zhongbo Chen ◽  
Jason A. Chen ◽  
Aleksey Shatunov ◽  
Ashley R. Jones ◽  
Stephanie N. Kravitz ◽  
...  
Keyword(s):  
Progressive Supranuclear Palsy ◽  
Copy Number ◽  
Copy Number Variants ◽  
Genome Wide ◽  
Genome Wide Survey

scholarly journals Genome-wide survey implicates the influence of copy number variants (CNVs) in the development of early-onset bipolar disorder

2011 ◽  
Vol 17 (4) ◽  
pp. 421-432 ◽  
Author(s):  
L Priebe ◽  
F A Degenhardt ◽  
S Herms ◽  
B Haenisch ◽  
M Mattheisen ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
Early Onset ◽  
Copy Number ◽  
Copy Number Variants ◽  
Genome Wide ◽  
Genome Wide Survey

scholarly journals Genome-Wide Survey of Large Rare Copy Number Variants in Alzheimer’s Disease Among Caribbean Hispanics

2012 ◽  
Vol 2 (1) ◽  
pp. 71-78 ◽  
Author(s):  
Mahdi Ghani ◽  
Dalila Pinto ◽  
Joseph H. Lee ◽  
Yakov Grinberg ◽  
Christine Sato ◽  
...  
Keyword(s):  
Alzheimer’S Disease ◽  
Alzheimer's Disease ◽  
Copy Number ◽  
Copy Number Variants ◽  
Genome Wide ◽  
Genome Wide Survey

A genome wide survey supports the involvement of large copy number variants in schizophrenia with and without intellectual disability

2013 ◽  
Vol 162 (8) ◽  
pp. 847-854 ◽  
Author(s):  
Eske M. Derks ◽  
Muhammad Ayub ◽  
Kimberly Chambert ◽  
Jurgen Del Favero ◽  
Mandy Johnstone ◽  
...  
Keyword(s):  
Intellectual Disability ◽  
Copy Number ◽  
Copy Number Variants ◽  
Genome Wide ◽  
A Genome ◽  
Genome Wide Survey

scholarly journals Genome-wide Survey of Copy Number Variants Associated with Blood Pressure and Body Mass Index in a Korean Population

2011 ◽  
Vol 9 (4) ◽  
pp. 152-160 ◽  
Author(s):  
Sang-Hoon Moon ◽  
Young-Jin Kim ◽  
Yun-Kyoung Kim ◽  
Dong-Joon Kim ◽  
Ji-Young Lee ◽  
...  
Keyword(s):  
Blood Pressure ◽  
Body Mass Index ◽  
Body Mass ◽  
Copy Number ◽  
Copy Number Variants ◽  
Korean Population ◽  
Genome Wide ◽  
Genome Wide Survey

scholarly journals Detection and characterization of copy number variants based on whole-genome sequencing by DNBSEQ platforms

2019 ◽  
Author(s):  
Junhua Rao ◽  
Lihua Peng ◽  
Fang Chen ◽  
Hui Jiang ◽  
Chunyu Geng ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Copy Number ◽  
Copy Number Variants ◽  
Copy Number Variant ◽  
Whole Genome ◽  
Genome Wide ◽  
Wide Range ◽  
Distribution Sensitivity ◽  
Cnv Detection

AbstractBackgroundNext-generation sequence (NGS) has rapidly developed in past years which makes whole-genome sequencing (WGS) becoming a more cost- and time-efficient choice in wide range of biological researches. We usually focus on some variant detection via WGS data, such as detection of single nucleotide polymorphism (SNP), insertion and deletion (Indel) and copy number variant (CNV), which playing an important role in many human diseases. However, the feasibility of CNV detection based on WGS by DNBSEQ™ platforms was unclear. We systematically analysed the genome-wide CNV detection power of DNBSEQ™ platforms and Illumina platforms on NA12878 with five commonly used tools, respectively.ResultsDNBSEQ™ platforms showed stable ability to detect slighter more CNVs on genome-wide (average 1.24-fold than Illumina platforms). Then, CNVs based on DNBSEQ™ platforms and Illumina platforms were evaluated with two public benchmarks of NA12878, respectively. DNBSEQ™ and Illumina platforms showed similar sensitivities and precisions on both two benchmarks. Further, the difference between tools for CNV detection was analyzed, and indicated the selection of tool for CNV detection could affected the CNV performance, such as count, distribution, sensitivity and precision.ConclusionThe major contribution of this paper is providing a comprehensive guide for CNV detection based on WGS by DNBSEQ™ platforms for the first time.

scholarly journals RefCNV: Identification of Gene-Based Copy Number Variants Using Whole Exome Sequencing

2016 ◽  
Vol 15 ◽  
pp. CIN.S36612 ◽  
Author(s):  
Lun-Ching Chang ◽  
Biswajit Das ◽  
Chih-Jian Lih ◽  
Han Si ◽  
Corinne E. Camalier ◽  
...  
Keyword(s):  
Exome Sequencing ◽  
Whole Exome Sequencing ◽  
Copy Number ◽  
Copy Number Variants ◽  
Estimation Methods ◽  
Single Nucleotide Variants ◽  
False Positive Error ◽  
Reference Set ◽  
Genome Wide ◽  
Whole Exome

With rapid advances in DNA sequencing technologies, whole exome sequencing (WES) has become a popular approach for detecting somatic mutations in oncology studies. The initial intent of WES was to characterize single nucleotide variants, but it was observed that the number of sequencing reads that mapped to a genomic region correlated with the DNA copy number variants (CNVs). We propose a method RefCNV that uses a reference set to estimate the distribution of the coverage for each exon. The construction of the reference set includes an evaluation of the sources of variability in the coverage distribution. We observed that the processing steps had an impact on the coverage distribution. For each exon, we compared the observed coverage with the expected normal coverage. Thresholds for determining CNVs were selected to control the false-positive error rate. RefCNV prediction correlated significantly ( r = 0.96–0.86) with CNV measured by digital polymerase chain reaction for MET (7q31), EGFR (7p12), or ERBB2 (17q12) in 13 tumor cell lines. The genome-wide CNV analysis showed a good overall correlation (Spearman's coefficient = 0.82) between RefCNV estimation and publicly available CNV data in Cancer Cell Line Encyclopedia. RefCNV also showed better performance than three other CNV estimation methods in genome-wide CNV analysis.

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