Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method
Motivation: Existing methods for estimating copy number variations in array comparative genomic hybridization (aCGH) data are limited to estimations of the gain/loss of chromosome regions for single sample analysis. We propose the linear-median method for estimating shared copy numbers in DNA sequen...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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SAGE Publishing
2010-10-01
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| Series: | Cancer Informatics |
| Online Access: | http://la-press.com/estimating-shared-copy-number-aberrations-for-array-cgh-data-the-linea-a2294 |
| _version_ | 1818231152377331712 |
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| author | K.-A. Do V. Bonato V. Baladandayuthapani Y.-X. Lin |
| author_facet | K.-A. Do V. Bonato V. Baladandayuthapani Y.-X. Lin |
| author_sort | K.-A. Do |
| collection | DOAJ |
| description | Motivation: Existing methods for estimating copy number variations in array comparative genomic hybridization (aCGH) data are limited to estimations of the gain/loss of chromosome regions for single sample analysis. We propose the linear-median method for estimating shared copy numbers in DNA sequences across multiple samples, demonstrate its operating characteristics through simulations and applications to real cancer data, and compare it to two existing methods. Results: Our proposed linear-median method has the power to estimate common changes that appear at isolated single probe positions or very short regions. Such changes are hard to detect by current methods. This new method shows a higher rate of true positives and a lower rate of false positives. The linear-median method is non-parametric and hence is more robust in estimating copy number. Additionally the linear-median method is easily computable for practical aCGH data sets compared to other copy number estimation methods. |
| first_indexed | 2024-12-12T10:45:51Z |
| format | Article |
| id | doaj.art-b174677b24a445cca62e6835108ac4cd |
| institution | Directory Open Access Journal |
| issn | 1176-9351 |
| language | English |
| last_indexed | 2024-12-12T10:45:51Z |
| publishDate | 2010-10-01 |
| publisher | SAGE Publishing |
| record_format | Article |
| series | Cancer Informatics |
| spelling | doaj.art-b174677b24a445cca62e6835108ac4cd2022-12-22T00:26:53ZengSAGE PublishingCancer Informatics1176-93512010-10-0120109229249Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median MethodK.-A. DoV. BonatoV. BaladandayuthapaniY.-X. LinMotivation: Existing methods for estimating copy number variations in array comparative genomic hybridization (aCGH) data are limited to estimations of the gain/loss of chromosome regions for single sample analysis. We propose the linear-median method for estimating shared copy numbers in DNA sequences across multiple samples, demonstrate its operating characteristics through simulations and applications to real cancer data, and compare it to two existing methods. Results: Our proposed linear-median method has the power to estimate common changes that appear at isolated single probe positions or very short regions. Such changes are hard to detect by current methods. This new method shows a higher rate of true positives and a lower rate of false positives. The linear-median method is non-parametric and hence is more robust in estimating copy number. Additionally the linear-median method is easily computable for practical aCGH data sets compared to other copy number estimation methods.http://la-press.com/estimating-shared-copy-number-aberrations-for-array-cgh-data-the-linea-a2294 |
| spellingShingle | K.-A. Do V. Bonato V. Baladandayuthapani Y.-X. Lin Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method Cancer Informatics |
| title | Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method |
| title_full | Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method |
| title_fullStr | Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method |
| title_full_unstemmed | Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method |
| title_short | Estimating Shared Copy Number Aberrations for Array CGH Data: The Linear-Median Method |
| title_sort | estimating shared copy number aberrations for array cgh data the linear median method |
| url | http://la-press.com/estimating-shared-copy-number-aberrations-for-array-cgh-data-the-linea-a2294 |
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