Somatic mutation and copy number variation associated with malignant transformation of IPMN detected by next-generation sequencing

Pancreatology ◽  
2016 ◽  
Vol 16 (4) ◽  
pp. S72
Author(s):  
Shinichi Takano ◽  
Mitsuharu Fukasawa ◽  
Makoto Kadokura ◽  
Hiroko Shindo ◽  
Ei Takahashi ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variation ◽  
Malignant Transformation ◽  
Somatic Mutation ◽  
Copy Number ◽  
Next Generation ◽  
Number Variation ◽  
Generation Sequencing

scholarly journals Use of next-generation sequencing to detectLDLRgene copy number variation in familial hypercholesterolemia

2017 ◽  
Vol 58 (11) ◽  
pp. 2202-2209 ◽  
Author(s):  
Michael A. Iacocca ◽  
Jian Wang ◽  
Jacqueline S. Dron ◽  
John F. Robinson ◽  
Adam D. McIntyre ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variation ◽  
Familial Hypercholesterolemia ◽  
Copy Number ◽  
Next Generation ◽  
Number Variation ◽  
Generation Sequencing

scholarly journals Comprehensive Assessment of Somatic Copy Number Variation Calling Using Next-Generation Sequencing Data

2021 ◽  
Author(s):  
Yun-Ching Chen ◽  
Fayaz Seifuddin ◽  
Cu Nguyen ◽  
Zhaowei Yang ◽  
Wanqiu Chen ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variation ◽  
Cancer Progression ◽  
Copy Number ◽  
Tissue Sample ◽  
Next Generation Sequencing Data ◽  
Next Generation ◽  
Dna Amount ◽  
Number Variation ◽  
Generation Sequencing

AbstractCopy number variation (CNV) is a common type of mutation that often drives cancer progression. With advances in next-generation sequencing (NGS), CNVs can be detected in a detailed manner via newly developed computational tools but quality of such CNV calls has not been carefully evaluated. We analyzed CNV calls reported by 6 cutting-edge callers for 91 samples which were derived from the same cancer cell line, prepared and sequenced by varying the following factors: type of tissue sample (Fresh vs. Formalin Fixed Paraffin Embedded (FFPE)), library DNA amount, tumor purity, sequencing platform (Whole-Genome Sequencing (WGS) versus Whole-Exome Sequencing (WES)), and sequencing coverage. We found that callers greatly determined the pattern of CNV calls. Calling quality was drastically impaired by low purity (<50%) and became variable when WES, FFPE, and medium purity (50%-75%) were applied. Effects of low DNA amount and low coverage were relatively minor. Our analysis demonstrates the limitation of benchmarking somatic CNV callers when the real ground truth is not available. Our comprehensive analysis has further characterized each caller with respect to confounding factors and examined the consistency of CNV calls, thereby providing guidelines for conducting somatic CNV analysis.

scholarly journals Validation of copy number variation analysis for next-generation sequencing diagnostics

2017 ◽  
Vol 25 (6) ◽  
pp. 719-724 ◽  
Author(s):  
Jamie M Ellingford ◽  
Christopher Campbell ◽  
Stephanie Barton ◽  
Sanjeev Bhaskar ◽  
Saurabh Gupta ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variation ◽  
Copy Number ◽  
Variation Analysis ◽  
Next Generation ◽  
Copy Number Variation Analysis ◽  
Number Variation ◽  
Generation Sequencing

scholarly journals 28: Copy Number Variation Detection Using Next-Generation Sequencing

2015 ◽  
Vol 143 (suppl_1) ◽  
pp. A013-A013
Author(s):  
Linda B. Baughn ◽  
Getiria Onsongo ◽  
Matthew Bower ◽  
Christine Henzler ◽  
Kevin A.T. Silverstein ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Copy Number Variation ◽  
Copy Number ◽  
Next Generation ◽  
Number Variation ◽  
Copy Number Variation Detection ◽  
Generation Sequencing
Sign in / Sign up

Export Citation Format

Share Document