CONDEL: Detecting Copy Number Variation and Genotyping Deletion Zygosity from Single Tumor Samples using Sequence Data

2018 ◽  
pp. 1-1 ◽  
Author(s):  
Xiguo Yuan ◽  
Jun Bai ◽  
Junying Zhang ◽  
Liying Yang ◽  
Junbo Duan ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Sequence Data ◽  
Number Variation ◽  
Single Tumor

scholarly journals Rapid, Paralog-Sensitive CNV Analysis of 2457 Human Genomes Using QuicK-mer2

Genes ◽  
2020 ◽  
Vol 11 (2) ◽  
pp. 141 ◽  
Author(s):  
Feichen Shen ◽  
Jeffrey M. Kidd
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Sequence Data ◽  
Data Sets ◽  
Short Read ◽  
Major Mechanism ◽  
Rapid Construction ◽  
A Genome ◽  
Number Variation ◽  
Short Read Sequence

Gene duplication is a major mechanism for the evolution of gene novelty, and copy-number variation makes a major contribution to inter-individual genetic diversity. However, most approaches for studying copy-number variation rely upon uniquely mapping reads to a genome reference and are unable to distinguish among duplicated sequences. Specialized approaches to interrogate specific paralogs are comparatively slow and have a high degree of computational complexity, limiting their effective application to emerging population-scale data sets. We present QuicK-mer2, a self-contained, mapping-free approach that enables the rapid construction of paralog-specific copy-number maps from short-read sequence data. This approach is based on the tabulation of unique k-mer sequences from short-read data sets, and is able to analyze a 20X coverage human genome in approximately 20 min. We applied our approach to newly released sequence data from the 1000 Genomes Project, constructed paralog-specific copy-number maps from 2457 unrelated individuals, and uncovered copy-number variation of paralogous genes. We identify nine genes where none of the analyzed samples have a copy number of two, 92 genes where the majority of samples have a copy number other than two, and describe rare copy number variation effecting multiple genes at the APOBEC3 locus.

scholarly journals Copy number variation detection and genotyping from exome sequence data

2012 ◽  
Vol 22 (8) ◽  
pp. 1525-1532 ◽  
Author(s):  
N. Krumm ◽  
P. H. Sudmant ◽  
A. Ko ◽  
B. J. O'Roak ◽  
M. Malig ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Copy Number ◽  
Sequence Data ◽  
Exome Sequence Data ◽  
Number Variation ◽  
Copy Number Variation Detection ◽  
Exome Sequence

scholarly journals A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data

2018 ◽  
Vol 102 (1) ◽  
pp. 142-155 ◽  
Author(s):  
Brett Trost ◽  
Susan Walker ◽  
Zhuozhi Wang ◽  
Bhooma Thiruvahindrapuram ◽  
Jeffrey R. MacDonald ◽  
...  
Keyword(s):  
Copy Number Variation ◽  
Genome Sequence ◽  
Copy Number ◽  
Sequence Data ◽  
Read Depth ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Number Variation

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
Sign in / Sign up

Export Citation Format

Share Document