Aspects of coverage in medical DNA sequencing
DNA sequencing is now emerging as an important component inbiomedical studies of diseases like cancer. Short-read,highly parallel sequencing instruments are expectedto be used heavily for such projects, but many designspecifications have yet to be conclusively established.Perhaps the most fundamental of these is the redundancyrequired to detect sequence variations, which bearsdirectly upon genomic coverage and the consequent resolvingpower for discerning somatic mutations.
Results: We address the medical sequencing coverage problem via anextension of the standard mathematical theory of haploidcoverage.
The expected diploid multi-fold coverage, aswell as its generalization for aneuploidy are derived andthese expressions can be readily evaluated for any project.The resulting theory is used as a scaling law to calibrateperformance to that of standard BAC sequencing at 8X to10X redundancy, i.e. for expected coverages that exceed99% of the unique sequence.
A differential strategy isformalized for tumor/normal studies wherein tumor samplesare sequenced more deeply than normal ones. In particular,both tumor alleles should be detected at least twice,while both normal alleles are detected at least once.Our theory predicts these requirements can be met fortumor and normal redundancies of approximately 26X and21X, respectively.
We explain why these values do notdiffer by a factor of 2, as might intuitively be expected.Future technology developments should prompt even deepersequencing of tumors, but the 21X value for normal samplesis essentially a constant.
Conclusions: Given the assumptions of standard coverage theory, ourmodel gives pragmatic estimates for required redundancy.The differential strategy should be an efficient means ofidentifying potential somatic mutations for further study.
Author: Michael C Wendl and Richard K Wilson
Credits/Source: BMC Bioinformatics 2008, 9:239
Published on: 2008-05-16
Limited copyright is granted for you to use and/or republish any story on this site for
any legitimate media purpose as long as you reference 7thSpace and any source mentioned in the story above. Please
make sure to read our disclaimer prior to contacting 7thSpace Interactive. To contact our editors, visit our online helpdesk.
Social Bookmarking
Digg this! | Post to del.icio.us | Post to Furl | Add to Netscape | Add to Yahoo! | Rojo
|
|
