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

doi:10.1109/BIBMW.2011.6112452

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/Conference proceeding › Conference contribution › peer-review

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 language	English
Title of host publication	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Pages	680-682
Number of pages	3
DOIs	https://doi.org/10.1109/BIBMW.2011.6112452
Publication status	Published - 2011
Externally published	Yes
Event	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 - Atlanta, GA, United States Duration: 12 Nov 2011 → 15 Nov 2011

Publication series

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

Conference

Conference	2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011
Country/Territory	United States
City	Atlanta, GA
Period	12/11/11 → 15/11/11

Keywords

HLA typing
cDNA micorarray
noise reduction
outlier detection

ASJC Scopus subject areas

Biomedical Engineering
Health Informatics
Health Information Management

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10.1109/BIBMW.2011.6112452

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Dilek, E., Zlateva, T., Zhang, G. L., Chitkushev, L., Lee, J. Y., & Brusic, V. (2011). 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. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 (pp. 680-682). Article 6112452 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). https://doi.org/10.1109/BIBMW.2011.6112452

Dilek, Esma ; Zlateva, Tanya ; Zhang, Guang Lan et al. / 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. 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. pp. 680-682 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

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title = "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",

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.",

keywords = "HLA typing, cDNA micorarray, noise reduction, outlier detection",

author = "Esma Dilek and Tanya Zlateva and Zhang, {Guang Lan} and Lou Chitkushev and Lee, {Jae Young} and Vladimir Brusic",

note = "Copyright: Copyright 2012 Elsevier B.V., All rights reserved.; 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011 ; Conference date: 12-11-2011 Through 15-11-2011",

year = "2011",

doi = "10.1109/BIBMW.2011.6112452",

language = "English",

isbn = "9781457716133",

series = "2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011",

pages = "680--682",

booktitle = "2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011",

}

Dilek, E, Zlateva, T, Zhang, GL, Chitkushev, L, Lee, JY & Brusic, V 2011, 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. in 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011., 6112452, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, pp. 680-682, 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011, Atlanta, GA, United States, 12/11/11. https://doi.org/10.1109/BIBMW.2011.6112452

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. / Dilek, Esma; Zlateva, Tanya; Zhang, Guang Lan et al.
2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 680-682 6112452 (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011).

Research output: Chapter in Book/Conference proceeding › Conference contribution › peer-review

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AU - Brusic, Vladimir

PY - 2011

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AB - 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.

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Dilek E, Zlateva T, Zhang GL, Chitkushev L, Lee JY, Brusic V. 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. In 2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011. 2011. p. 680-682. 6112452. (2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops, BIBMW 2011). doi: 10.1109/BIBMW.2011.6112452

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

Abstract

Publication series

Conference

Keywords

ASJC Scopus subject areas

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