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  1. NTU Scholars
  2. 醫學院
  3. 醫學系
Please use this identifier to cite or link to this item: https://scholars.lib.ntu.edu.tw/handle/123456789/523738
Title: A probe-density-based analysis method for array CGH data: Simulation, normalization and centralization
Authors: Chen, H.-I.H.
Hsu, F.-H.
Jiang, Y.
Tsai, M.-H.
PAN-CHYR YANG 
Meltzer, P.S.
Chuang, E.Y.
MONG-HSUN TSAI 
Yang, Pan-Chyr 
CHUANG, ERIC YAO-YU 
ERIC YAO-YU CHUANG 
Issue Date: 2008
Journal Volume: 24
Journal Issue: 16
Start page/Pages: 1749-1756
Source: Bioinformatics
Abstract: 
Motivation: Genomic instability is one of the fundamental factors in tumorigenesis and tumor progression. Many studies have shown that copy-number abnormalities at the DNA level are important in the pathogenesis of cancer. Array comparative genomic hybridization (aCGH), developed based on expression microarray technology, can reveal the chromosomal aberrations in segmental copies at a high resolution. However, due to the nature of aCGH, many standard expression data processing tools, such as data normalization, often fail to yield satisfactory results. Results: We demonstrated a novel aCGH normalization algorithm, which provides an accurate aCGH data normalization by utilizing the dependency of neighboring probe measurements in aCGH experiments. To facilitate the study, we have developed a hidden Markov model (HMM) to simulate a series of aCGH experiments with random DNA copy number alterations that are used to validate the performance of our normalization. In addition, we applied the proposed normalization algorithm to an aCGH study of lung cancer cell lines. By using the proposed algorithm, data quality and the reliability of experimental results are significantly improved, and the distinct patterns of DNA copy number alternations are observed among those lung cancer cell lines. ? The Author 2008. Published by Oxford University Press. All rights reserved.
URI: https://www.scopus.com/inward/record.uri?eid=2-s2.0-49549100274&doi=10.1093%2fbioinformatics%2fbtn321&partnerID=40&md5=cacaf79eeb1b352184f85cd002f52700
https://scholars.lib.ntu.edu.tw/handle/123456789/523738
ISSN: 1367-4803
DOI: 10.1093/bioinformatics/btn321
SDG/Keyword: accuracy; algorithm; breast cancer; cancer cell culture; comparative genomic hybridization; conference paper; controlled study; data analysis; DNA replication; hidden Markov model; human; human cell; lung cancer; microarray analysis; numerical chromosome aberration; priority journal; reliability; simulation; statistical analysis; validation process; Base Sequence; Chromosome Mapping; Computer Simulation; DNA Probes; Gene Dosage; Models, Genetic; Molecular Sequence Data; Oligonucleotide Array Sequence Analysis; Sequence Alignment; Sequence Analysis, DNA
[SDGs]SDG3
Appears in Collections:醫學系

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臺大位居世界頂尖大學之列,為永久珍藏及向國際展現本校豐碩的研究成果及學術能量,圖書館整合機構典藏(NTUR)與學術庫(AH)不同功能平台,成為臺大學術典藏NTU scholars。期能整合研究能量、促進交流合作、保存學術產出、推廣研究成果。

To permanently archive and promote researcher profiles and scholarly works, Library integrates the services of “NTU Repository” with “Academic Hub” to form NTU Scholars.

總館學科館員 (Main Library)
醫學圖書館學科館員 (Medical Library)
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開放取用是從使用者角度提升資訊取用性的社會運動,應用在學術研究上是透過將研究著作公開供使用者自由取閱,以促進學術傳播及因應期刊訂購費用逐年攀升。同時可加速研究發展、提升研究影響力,NTU Scholars即為本校的開放取用典藏(OA Archive)平台。(點選深入了解OA)

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