Aspects of coverage in medical DNA sequencing
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Implication
Mathematical modeling demonstrates optimal coverage redundancies of 26x in tumors and 21x in normal samples, indicating an efficient differential strategy to detect somatic mutations.
Key Points
- To establish a mathematical model extending haploid coverage theory to diploid and aneuploid genomes for determining the sequencing redundancy necessary to detect somatic mutations.
- Extended standard mathematical theories of haploid coverage to derive expected diploid multi-fold coverage and generalized formulas for aneuploid genomes.
- Calibrated model parameters against bacterial artificial chromosome (BAC) sequencing standards operating at 8x to 10x redundancy to achieve greater than 99% unique sequence coverage.
- Evaluated a tumor-normal differential sequencing strategy defined by detecting both tumor alleles at least twice and both normal alleles at least once.
- Derived required sequence redundancies of approximately 26x for tumor samples and 21x for normal samples to satisfy coverage criteria.
- Demonstrated that the required sequencing depths between tumor and normal pairs do not differ by an intuitive factor of two due to non-linear coverage statistics.
- Identified that normal sample sequencing requirements remain essentially constant at 21x, whereas tumor sequencing can scale deeper as sequencing capacity grows.
Cite This Study
Wendl et al. (2008) studied this question.