April 2009
Volume 50, Issue 13
Free
ARVO Annual Meeting Abstract  |   April 2009
Automated Sequence Analysis Pipeline (ASAP) for Genetic Testing
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
Author Affiliations & Notes
  • T. A. Braun
    Ophthalmology,
    Biomedical Engineering,
    University of Iowa, Iowa City, Iowa
  • A. P. DeLuca
    Biomedical Engineering,
    Center for Bioinformatics and Computational Biology,
    University of Iowa, Iowa City, Iowa
  • N. Anand
    Biomedical Engineering,
    Center for Bioinformatics and Computational Biology,
    University of Iowa, Iowa City, Iowa
  • K. Taylor
    Center for Bioinformatics and Computational Biology,
    University of Iowa, Iowa City, Iowa
  • J. Bogaard
    Biomedical Engineering,
    Center for Bioinformatics and Computational Biology,
    University of Iowa, Iowa City, Iowa
  • B. Faga
    Center for Bioinformatics and Computational Biology,
    University of Iowa, Iowa City, Iowa
  • T. E. Scheetz
    Ophthalmology,
    Center for Bioinformatics and Computational Biology,
    University of Iowa, Iowa City, Iowa
  • T. L. Casavant
    Biomedical Engineering,
    Center for Bioinformatics and Computational Biology,
    University of Iowa, Iowa City, Iowa
  • V. C. Sheffield
    Pediatrics,
    Howard Hughes Medical Institute,
    University of Iowa, Iowa City, Iowa
  • E. M. Stone
    Ophthalmology,
    Howard Hughes Medical Institute,
    University of Iowa, Iowa City, Iowa
  • Footnotes
    Commercial Relationships  T.A. Braun, None; A.P. DeLuca, None; N. Anand, None; K. Taylor, None; J. Bogaard, None; B. Faga, None; T.E. Scheetz, None; T.L. Casavant, None; V.C. Sheffield, None; E.M. Stone, None.
  • Footnotes
    Support  None.
Investigative Ophthalmology & Visual Science April 2009, Vol.50, 4133. doi:
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      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.

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Abstract

Purpose: : To perform accurate, low-cost genetic testing for inherited eye diseases utilizing modular software, commodity SNP detection software, bioinformatics, and heterogeneous molecular assays.

Methods: : 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.

Results: : 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.

Conclusions: : 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.

Keywords: mutations • gene screening • genetics 
© 2009, The Association for Research in Vision and Ophthalmology, Inc., all rights reserved. Permission to republish any abstract or part of an abstract in any form must be obtained in writing from the ARVO Office prior to publication.
Copyright © 2025 Association for Research in Vision and Ophthalmology.
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