Probe design optimization of HLA microarray - Data cleaning of probe signals from cDNA tiling microarray: Outlier detection, noise reduction, and identification of uninformative probes in HLA typing application

Esma Dilek, Tanya Zlateva, Guang Lan Zhang, Lou Chitkushev, Jae Young Lee, Vladimir Brusic

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

Custom made tiling cDNA microarrays have been developed for high resolution HLA genotyping. The array comprises tens of thousands of sequence-specific oligonucleotide probes (SSOP) that hybridize with HLA sequences. Sophisticated methods for analyzing the multidimensional complex data are needed due to large amounts of data generated from the microarray experiments. Moreover, the inconsistencies, noise, and outliers in the probe signals add additional complexities. We proposed data cleaning methods for the identification of uninformative and misinformative probes to improve the performance of HLA typing process.

Original languageEnglish
Title of host publication2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages680-682
Number of pages3
DOIs
Publication statusPublished - Dec 1 2011
Event2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States
Duration: Nov 12 2011Nov 15 2011

Publication series

Name2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011

Other

Other2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
CountryUnited States
CityAtlanta, GA
Period11/12/1111/15/11

Keywords

  • HLA typing
  • cDNA micorarray
  • noise reduction
  • outlier detection

ASJC Scopus subject areas

  • Biomedical Engineering
  • Health Informatics
  • Health Information Management

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