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| Status |
Public on Aug 12, 2014 |
| Title |
DNA copy number detection from exome sequencing - Exploiting the off-targets (SNP) |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by SNP array
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| Summary |
Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality. Current methods for detection of copy number aberrations (CNA) from whole-exome sequencing (WES) data are based on the read counts of the captured exons only. However, accurate CNA determination is complicated by the non-uniform read depth and uneven distribution of exons. Therefore, we developed ENCODER (ENhanced COpy number Detection from Exome Reads), which eludes these problems. By exploiting the ‘off-target’ sequence reads, it allows for creation of robust copy number profiles from WES. The accuracy of ENCODER compares to approaches specifically designed for copy number detection, and outperforms current exon-based WES methods, particularly in samples of low quality.
DNA copy number profiles generated with a new tool, ENCODER, were compared to DNA copy number profiles from SNP6, NimbleGen and low-coverage Whole Genome Sequencing.
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| Overall design |
DNA copy number profiles of melanoma PDX sample were generated with ENCODER from whole exome sequencing data and compared to results from the SNP6 platform.
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| Contributor(s) |
Kuilman T, Krijgsman O |
| Citation(s) |
25887352 |
| Submission date |
Aug 06, 2014 |
| Last update date |
Nov 27, 2018 |
| Contact name |
Oscar Krijgsman |
| E-mail(s) |
o.krijgsman@nki.nl, oscarkrijgsman@gmail.com
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| Phone |
31205122028
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| Organization name |
Netherlands Cancer Institute
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| Department |
Molecular Oncology and Immunology
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| Lab |
Peeper
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| Street address |
Plesmanlaan 121
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| City |
Amsterdam |
| State/province |
Outside the US or Canada |
| ZIP/Postal code |
1066CX |
| Country |
Netherlands |
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| Platforms (1) |
| GPL6801 |
[GenomeWideSNP_6] Affymetrix Genome-Wide Human SNP 6.0 Array |
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| Samples (6)
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| GSM1466817 |
T98 Cell lines from human melanoma grown in PDX |
| GSM1466818 |
T99 Cell lines from human melanoma grown in PDX |
| GSM1466819 |
T100 Cell lines from human melanoma grown in PDX |
| GSM1466820 |
T101 Cell lines from human melanoma grown in PDX |
| GSM1466821 |
T102 Cell lines from human melanoma grown in PDX |
| GSM1466822 |
T103Cell lines from human melanoma grown in PDX |
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| This SubSeries is part of SuperSeries: |
| GSE60259 |
DNA copy number detection from exome sequencing - Exploiting the off-targets |
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| Relations |
| BioProject |
PRJNA257823 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE60168_RAW.tar |
162.8 Mb |
(http)(custom) |
TAR (of CEL) |
| Processed data included within Sample table |
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