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| Status |
Public on Apr 02, 2010 |
| Title |
DNA copy number, including telomeres and mitochondria, assayed using next-generation sequencing |
| Organism |
Homo sapiens |
| Experiment type |
Genome variation profiling by high throughput sequencing
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| Summary |
DNA copy number variations occur within populations and aberrations can cause disease. We sought to develop an improved lab-automatable, cost-efficient, accurate platform to profile DNA copy number. We developed a sequencing-based assay of nuclear, mitochondrial, and telomeric DNA copy number that draws on the unbiased nature of next-generation sequencing and incorporates techniques developed for RNA expression profiling. To demonstrate this platform, we assayed UMC-11 cells using 5 million 33 nt reads and found tremendous copy number variation, including regions of single and homogeneous deletions and amplifications to 29 copies; 5 times more mitochondria and 4 times less telomeric sequence than a pool of non-diseased, blood-derived DNA; and that UMC-11 was derived from a male individual. The described assay outputs absolute copy number, outputs an error estimate (p-value), and is more accurate than array-based platforms at high copy number. The platform enables profiling of mitochondrial levels and telomeric length. The assay is lab-automatable and has a genomic resolution and cost that are tunable based on the number of sequence reads.
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| Overall design |
DNA genome sequencing at roughly 0.03 coverage to identify genomic copy number variations
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| Contributor(s) |
Castle JC, Chen R |
| Citation(s) |
20398377 |
| Submission date |
Mar 31, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
John Castle |
| E-mail(s) |
castle@uni-mainz.de
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| Organization name |
Institute for Translational Oncology and Immunology
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| Department |
Genomics
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| Street address |
Langenbeckstr. 1
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| City |
Mainz |
| ZIP/Postal code |
55131 |
| Country |
Germany |
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| Platforms (1) |
| GPL9052 |
Illumina Genome Analyzer (Homo sapiens) |
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| Samples (3) |
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| Relations |
| SRA |
SRP002238 |
| BioProject |
PRJNA126609 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE21159_RAW.tar |
147.1 Mb |
(http)(custom) |
TAR (of TXT) |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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