|
| Status |
Public on Oct 04, 2012 |
| Title |
Long Span DNA Paired-End-Tag (DNA-PET) Sequencing Strategy for the Interrogation of Genomic Structural Mutations |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by high throughput sequencing
|
| Summary |
Structural variations (SVs) contribute significantly to the variability of the human genome and extensive genomic rearrangements are a hallmark of cancer. Genomic DNA paired-end-tag (DNA-PET) sequencing is an attractive approach to identify genomic SVs. The current application of PET sequencing with short insert size DNA is insufficient for the comprehensive mapping of SVs in low complexity and repeat-rich genomic regions. We have developed a robust procedure to generate PET sequencing data using large DNA inserts of 10 - 20 kb for the identification of SVs. We compared the characteristics of the large insert libraries with short insert (1 kb) libraries with the same sequencing depths and costs. Although short insert libraries bear an advantage in identifying small deletions, they do not provide a significantly better breakpoint resolution. Large inserts are superior to short inserts in providing higher physical genome coverage and therefore achieve greater sensitivity for the identification of the different types of SVs, including copy number neutral and complex events. Further, large inserts allow the identification of SVs within repetitive sequences which cannot be spanned by short inserts.
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| |
|
| Overall design |
Structural variations of three cancer cell lines using short (1 kb) and long (10 kb and 20 kb) insert size DNA fragments
|
| |
|
| Contributor(s) |
Ruan Y, Yao F, Hillmer AM |
| Citation(s) |
23029419 |
| |
| Submission date |
Oct 06, 2011 |
| Last update date |
May 15, 2019 |
| Contact name |
Axel HILLMER |
| E-mail(s) |
ahillmer@uni-koeln.de
|
| Organization name |
University of Cologne
|
| Department |
Institute of Pathology
|
| Street address |
Kerpener Str. 62
|
| City |
Cologne |
| ZIP/Postal code |
50937 |
| Country |
Germany |
| |
|
| Platforms (2) |
| GPL9115 |
Illumina Genome Analyzer II (Homo sapiens) |
| GPL9138 |
AB SOLiD System 2.0 (Homo sapiens) |
|
| Samples (5)
|
| GSM810995 |
Genomic DNA of the cell line HCT116_IHH021 |
| GSM810996 |
Genomic DNA of the cell line K562_IHK002004_GAII |
| GSM810997 |
Genomic DNA of the cell line K562_IHK002004_SOLiDv2 |
| GSM810998 |
Genomic DNA of the cell line K562_IHK016017_SOLiDv2 |
| GSM810999 |
Genomic DNA of the cell line MCF-7_IHM072 |
|
| Relations |
| SRA |
SRP008983 |
| BioProject |
PRJNA147033 |
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