Sequencing and disease variation detection tools and techniques

Adam P. DeLuca, Alex H. Wagner, Kyle R. Taylor, Ben Faga, David Thole, Val C. Sheffield, Edwin M. Stone, Thomas L. Casavant, Todd E. Scheetz, Terry A. Braun

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

Next-generation sequencing technology provides greater sequencing capacity to identify disease-causing variations. Currently there are many alignment tools and variation detection techniques, multiple SNP data sets used to filter out benign polymorphisms with the intent of enriching for disease-causing variations, and many tools and websites for annotating variations and performing pathogenicity prediction of variations. There is no consensus or standard with regards to which tools and corresponding parameter settings for each tool is appropriate for the different application of next-generation sequencing technologies for disease-causing variation identification. We have implemented an annotation pipeline that can easily use the output from different alignment tools (BLAT, BWA, BFAST, Bowtie) typically used to align sequence from next-generation sequencing and Sanger sequencing experiments. The Automated Sequence Analysis Pipeline (ASAP) reports variations using the HGVS standardized nomenclature[1] to facilitate comparison across tools and publications. To date, we have annotated the sequence from 13 exomes in an effort to identify disease-causing mutations.

Original languageEnglish
Title of host publicationProceedings of the 2011 9th IEEE/ACS International Conference on Computer Systems and Applications, AICCSA 2011
Pages80-83
Number of pages4
DOIs
StatePublished - 2011
Externally publishedYes
Event9th ACS/IEEE International Conference on Computer Systems and Applications, AICCSA 2011 - Sharm El-Sheikh, Egypt
Duration: Dec 27 2011Dec 30 2011

Publication series

NameProceedings of IEEE/ACS International Conference on Computer Systems and Applications, AICCSA
ISSN (Print)2161-5322
ISSN (Electronic)2161-5330

Conference

Conference9th ACS/IEEE International Conference on Computer Systems and Applications, AICCSA 2011
Country/TerritoryEgypt
CitySharm El-Sheikh
Period12/27/1112/30/11

Fingerprint

Dive into the research topics of 'Sequencing and disease variation detection tools and techniques'. Together they form a unique fingerprint.

Cite this