Software Helps Resolve Complex DNA Sequence Data

(HealthDay News) – A new software program can help resolve complex DNA sequencing data more quickly and easily than other methods, according to a study published online Feb. 10 in The Journal of Molecular Diagnostics.

Guoli Chen, MD, PhD, from the Johns Hopkins University School of Medicine in Baltimore, and colleagues validated a free software program called Pyromaker that simulates pyrograms, or traces of DNA sequence, based on user inputs. Validation was performed by comparing the programs with actual programs for common KRAS mutations and mutations in BRAF, GNAS, and p53.

The researchers found that all single-base mutations within codon 12 and 13 of KRAS generated unique pyrosequencing traces. All reported complex mutations produced unique pyrograms. For complicated pyrograms, two models were used: hypothesis-based simulated programs were pattern-matched to actual pyrograms or the Pyromaker was used to identify the mutation by iterative reconstruction. Both strategies identified complex mutations, which were confirmed and sequenced. Pyrosequencing with the Pyromaker was found to be the most efficient approach for unambiguous mutation identification.

“In summary, although pyrosequencing and Sanger sequencing are both powerful tools to resolve most mutations, for certain complex cases, neither of them alone is enough to provide a definitive interpretation,” Chen and colleagues write. “Iterative Pyromaker analysis is the least expensive and the fastest method for resolving these cases.”

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