Purchase this article with an account.
T. A. Braun, A. P. DeLuca, N. Anand, K. Taylor, J. Bogaard, B. Faga, T. E. Scheetz, T. L. Casavant, V. C. Sheffield, E. M. Stone; Automated Sequence Analysis Pipeline (ASAP) for Genetic Testing. Invest. Ophthalmol. Vis. Sci. 2009;50(13):4133.
Download citation file:
© ARVO (1962-2015); The Authors (2016-present)
To perform accurate, low-cost genetic testing for inherited eye diseases utilizing modular software, commodity SNP detection software, bioinformatics, and heterogeneous molecular assays.
The Automated Sequence Analysis Pipeline (ASAP) is a collection of Java applications, web-based interfaces, bioinformatic annotation software, SNP detection software (PolyPhred), and a relational database.
We have designed and implemented ASAP to support genetic testing for inherited eye diseases. Currently, the Carver Non-profit Genetic Testing Laboratory (CNGTL) offers genetic tests for 17 disorders. ASAP consists of software to support: on-line genetic test requests, the workflow within the molecular lab, the assessment of quality of ABI sequencing, performing mutation detection with PolyPhred, annotating mutations based on the Human Genome Variation Society standard, and providing web-based tracking for electronic feedback to both patients and clinicians. To date, we have used ASAP to process 63,314 sequences from patients for genetic testing and identified 5,373 variations. The design is modular to facilitate integration within a laboratory information management system and to support additional genetic testing assays including SNPlex and next-generation sequencing.
In response to the growing volume of genetic testing in the CNGTL we developed ASAP to augment the manual DNA sequence reading to improve workflow, laboratory information management, and add software-based mutation identification in addition to human sequence reading. ASAP detects mutations with existing bioinformatic software. The result is a significant increase in our capacity to perform genetic testing with a decrease in cost and no loss of accuracy. Additionally patients will receive more timely on-line status updates regarding their tests and observed allelic variation frequencies will be made more widely available to the scientific community.
This PDF is available to Subscribers Only