eISSN: 2353-9461
ISSN: 0860-7796
BioTechnologia
Current issue Archive About the journal Editorial board Abstracting and indexing Subscription Contact Instructions for authors Publication charge Ethical standards and procedures
Editorial System
Submit your Manuscript
SCImago Journal & Country Rank
3/2011
vol. 92
 
Share:
Share:
abstract:

RESEARCH PAPER
A stable density approach to probe selection for a custom aCGH design

Tomasz Gambin
,
Paweł Stankiewicz
,
Anna Gambin

BioTechnologia vol. 92(3) C pp. 283-295 C 2011
Online publish date: 2014/10/28
View full text Get citation
 
PlumX metrics:
Usage of the custom aCGH design provides the ability to detect copy number alternations (CNAs) with a very high

resolution in almost every genomic region. Since the detection rate of CNAs greatly depends on the quality of the

design, it is crucial to ensure the optimal probe coverage for the regions of interests. In this paper, we focus on

the problem of finding the best possible probe coverage for a given region and a predefined set of probes.

The lack of available probes at some places is a considerable problem which may lead to the decrease in the detection

rate of CNAs. We propose a new approach towards the generation of coverage with stable probe density.

The developed algorithms attempt to compensate the lack of probes in poorly covered regions by selecting

additional probes from their nearest neighborhood. Here we introduce evaluation measures that reflect density

stabilization along the covered region. Finally, we use these measures to compare our algorithms with other standard

approaches for coverage preparation.
keywords:

custom aCGH design, probe selection, Copy Number Alternations



Stosujemy się do standardu HONcode dla wiarygodnej informacji zdrowotnej This site complies with the HONcode standard for trustworthy health information: verify here