Abstract
Background
The ability to accurately detect DNA copy number variation in both a sensitive and quantitative manner is important in many research areas. However, genome-wide DNA copy number analyses are complicated by variations in detection signal.
Results
While GC content has been used to correct for this, here we show that coverage biases are tissue-specific and independent of the detection method as demonstrated by next-generation sequencing and array CGH. Moreover, we show that DNA isolation stringency affects the degree of equimolar coverage and that the observed biases coincide with chromatin characteristics like gene expression, genomic isochores, and replication timing.
Conclusion
These results indicate that chromatin organization is a main determinant for differential DNA retrieval. These findings are highly relevant for germline and somatic DNA copy number variation analyses. Show more
Permanent link
https://doi.org/10.3929/ethz-b-000096130Publication status
publishedExternal links
Journal / series
Genome BiologyVolume
Pages / Article No.
Publisher
BioMed CentralSubject
Copy number variation; DNA isolation; Technological bias; Tissue specificityOrganisational unit
09490 - Stadler, Tanja / Stadler, Tanja
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