Transcript annotation prioritization and screening system (TrAPSS) for mutation screening.
When searching for disease-causing mutations with polymerase chain reaction (PCR)-based methods, candidate genes are usually screened in their entirety, exon by exon. Genomic resources (i.e. www.ncbi.nih.gov, www.ensembl.org, and genome.ucsc.edu) largely support this paradigm for mutation screening by making it easy to view and access sequence data associated with genes in their genomic context. However, the administrative burden of conducting mutation screening in potentially hundreds of genes and thousands of exons in thousands of patients is significant, even with the use of public genome resources. For example, the manual design of oligonucleotide primers for all exons of the 10 Leber's congenital amaurosis (LCA) genes (149 exons) represents a significant information management challenge. The Transcript Annotation Prioritization and Screening System (TrAPSS) is designed to accelerate mutation screening by (1) providing a gene-based local cache of candidate disease genes in a genomic context, (2) automating tasks associated with optimizing candidate disease gene screening and information management, and (3) providing the implementation of an algorithmic technique to utilize large amounts of heterogeneous genome annotation (e.g. conserved protein functional domains) so as to prioritize candidate genes.
O'Leary
Brian M
BM
Coordinated Laboratory for Computational Genomics, University of Iowa, Iowa City, IA 52242, USA. boleary@eng.uiowa.edu
Davis
Steven G
SG
Smith
Michael F
MF
Brown
Bartley
B
Kemp
Mathew B
MB
Almabrazi
Hakeem
H
Grundstad
Jason A
JA
Burns
Thomas
T
Leontiev
Vladimir
V
Andorf
Jeaneen
J
Clark
Abbot F
AF
Sheffield
Val C
VC
Casavant
Thomas L
TL
Scheetz
Todd E
TE
Stone
Edwin M
EM
Braun
Terry A
TA
D000465:Algorithms; D019295:Computational Biology; D003628:Database Management Systems; D030541:Databases, Genetic; D023281:Genomics / Q000706:statistics & numerical data; D006801:Humans; D009154:Mutation; D012984:Software; D014584:User-Computer Interface