scholarly journals FACETS: allele-specific copy number and clonal heterogeneity analysis tool for high-throughput DNA sequencing

2016 ◽  
Vol 44 (16) ◽  
pp. e131-e131 ◽  
Author(s):  
Ronglai Shen ◽  
Venkatraman E. Seshan
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Copy Number ◽  
Analysis Tool ◽  
Clonal Heterogeneity ◽  
Allele Specific ◽  
High Throughput Dna Sequencing ◽  
Heterogeneity Analysis

scholarly journals CoDEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing

2017 ◽  
Author(s):  
Yuchao Jiang ◽  
Rujin Wang ◽  
Eugene Urrutia ◽  
Ioannis N. Anastopoulos ◽  
Katherine L. Nathanson ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Copy Number ◽  
Copy Number Variations ◽  
Negative Control ◽  
Sequencing Data ◽  
Full Spectrum ◽  
Number Variation ◽  
High Throughput Dna Sequencing ◽  
Low Sensitivity

AbstractHigh-throughput DNA sequencing enables detection of copy number variations (CNVs) on the genome-wide scale with finer resolution compared to array-based methods, but suffers from biases and artifacts that lead to false discoveries and low sensitivity. We describe CODEX2, a statistical framework for full-spectrum CNV profiling that is sensitive for variants with both common and rare population frequencies and that is applicable to study designs with and without negative control samples. We demonstrate and evaluate CODEX2 on whole-exome and targeted sequencing data, where biases are the most prominent. CODEX2 outperforms existing methods and, in particular, significantly improves sensitivity for common CNVs.

scholarly journals CODEX2: full-spectrum copy number variation detection by high-throughput DNA sequencing

2018 ◽  
Vol 19 (1) ◽  
Author(s):  
Yuchao Jiang ◽  
Rujin Wang ◽  
Eugene Urrutia ◽  
Ioannis N. Anastopoulos ◽  
Katherine L. Nathanson ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Dna Sequencing ◽  
High Throughput ◽  
Copy Number ◽  
Full Spectrum ◽  
Number Variation ◽  
High Throughput Dna Sequencing ◽  
Copy Number Variation Detection

scholarly journals Chemiluminiscence sensor for high-throughput DNA sequencing

2009 ◽  
Vol 1 (1) ◽  
pp. 1091-1094
Author(s):  
A R A Rahman ◽  
Shihui Foo ◽  
Sanket Goel
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
High Throughput Dna Sequencing

scholarly journals Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 16 ◽  
Author(s):  
Michael P Mullen ◽  
Christopher J Creevey ◽  
Donagh P Berry ◽  
Matt S McCabe ◽  
David A Magee ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
Allele Frequency ◽  
High Throughput ◽  
Frequency Estimation ◽  
Allele Frequency Estimation ◽  
Polymorphism Discovery ◽  
Pooled Dna ◽  
High Throughput Dna Sequencing

Application of high-throughput DNA sequencing to score population-specific variants for rare disorders

2019 ◽  
Vol 305 ◽  
pp. S25
Author(s):  
M.C. Ergoren ◽  
E. Manara ◽  
S. Paolacci ◽  
S.G. Temel ◽  
G. Mocan ◽  
...  
Keyword(s):  
Dna Sequencing ◽  
High Throughput ◽  
Rare Disorders ◽  
High Throughput Dna Sequencing
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