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Cluster Analysis of Comparative Genomic Hybridization (CGH) Data Using Self-Organizing Maps: Application to Prostate Carcinomas

Comparative genomic hybridization (CGH) is a modern genetic method which enables a genome‐wide survey of chromosomal imbalances. For each chromosome region, one obtains the information whether there is a loss or gain of genetic material, or whether there is no change at that region. Usually it is no...

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Autores principales: Mattfeldt, Torsten, Wolter, Hubertus, Kemmerling, Ralf, Gottfried, Hans‐Werner, Kestler, Hans A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: IOS Press 2001
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617519/
https://www.ncbi.nlm.nih.gov/pubmed/11790857
http://dx.doi.org/10.1155/2001/852674
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author Mattfeldt, Torsten
Wolter, Hubertus
Kemmerling, Ralf
Gottfried, Hans‐Werner
Kestler, Hans A.
author_facet Mattfeldt, Torsten
Wolter, Hubertus
Kemmerling, Ralf
Gottfried, Hans‐Werner
Kestler, Hans A.
author_sort Mattfeldt, Torsten
collection PubMed
description Comparative genomic hybridization (CGH) is a modern genetic method which enables a genome‐wide survey of chromosomal imbalances. For each chromosome region, one obtains the information whether there is a loss or gain of genetic material, or whether there is no change at that region. Usually it is not possible to evaluate all 46 chromosomes of a metaphase, therefore several (up to 20 or more) metaphases are analyzed per individual, and expressed as average. Mostly one does not study one individual alone but groups of 20–30 individuals. Therefore, large amounts of data quickly accumulate which must be put into a logical order. In this paper we present the application of a self‐organizing map (Genecluster) as a tool for cluster analysis of data from pT2N0 prostate cancer cases studied by CGH. Self‐organizing maps are artificial neural networks with the capability to form clusters on the basis of an unsupervised learning rule, i.e., in our examples it gets the CGH data as only information (no clinical data). We studied a group of 40 recent cases without follow‐up, an older group of 20 cases with follow‐up, and the data set obtained by pooling both groups. In all groups good clusterings were found in the sense that clinically similar cases were placed into the same clusters on the basis of the genetic information only. The data indicate that losses on chromosome arms 6q, 8p and 13q are all frequent in pT2N0 prostatic cancer, but the loss on 8p has probably the largest prognostic importance.
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spelling pubmed-46175192016-01-12 Cluster Analysis of Comparative Genomic Hybridization (CGH) Data Using Self-Organizing Maps: Application to Prostate Carcinomas Mattfeldt, Torsten Wolter, Hubertus Kemmerling, Ralf Gottfried, Hans‐Werner Kestler, Hans A. Anal Cell Pathol Other Comparative genomic hybridization (CGH) is a modern genetic method which enables a genome‐wide survey of chromosomal imbalances. For each chromosome region, one obtains the information whether there is a loss or gain of genetic material, or whether there is no change at that region. Usually it is not possible to evaluate all 46 chromosomes of a metaphase, therefore several (up to 20 or more) metaphases are analyzed per individual, and expressed as average. Mostly one does not study one individual alone but groups of 20–30 individuals. Therefore, large amounts of data quickly accumulate which must be put into a logical order. In this paper we present the application of a self‐organizing map (Genecluster) as a tool for cluster analysis of data from pT2N0 prostate cancer cases studied by CGH. Self‐organizing maps are artificial neural networks with the capability to form clusters on the basis of an unsupervised learning rule, i.e., in our examples it gets the CGH data as only information (no clinical data). We studied a group of 40 recent cases without follow‐up, an older group of 20 cases with follow‐up, and the data set obtained by pooling both groups. In all groups good clusterings were found in the sense that clinically similar cases were placed into the same clusters on the basis of the genetic information only. The data indicate that losses on chromosome arms 6q, 8p and 13q are all frequent in pT2N0 prostatic cancer, but the loss on 8p has probably the largest prognostic importance. IOS Press 2001 2001-01-01 /pmc/articles/PMC4617519/ /pubmed/11790857 http://dx.doi.org/10.1155/2001/852674 Text en Copyright © 2001 Hindawi Publishing Corporation.
spellingShingle Other
Mattfeldt, Torsten
Wolter, Hubertus
Kemmerling, Ralf
Gottfried, Hans‐Werner
Kestler, Hans A.
Cluster Analysis of Comparative Genomic Hybridization (CGH) Data Using Self-Organizing Maps: Application to Prostate Carcinomas
title Cluster Analysis of Comparative Genomic Hybridization (CGH) Data Using Self-Organizing Maps: Application to Prostate Carcinomas
title_full Cluster Analysis of Comparative Genomic Hybridization (CGH) Data Using Self-Organizing Maps: Application to Prostate Carcinomas
title_fullStr Cluster Analysis of Comparative Genomic Hybridization (CGH) Data Using Self-Organizing Maps: Application to Prostate Carcinomas
title_full_unstemmed Cluster Analysis of Comparative Genomic Hybridization (CGH) Data Using Self-Organizing Maps: Application to Prostate Carcinomas
title_short Cluster Analysis of Comparative Genomic Hybridization (CGH) Data Using Self-Organizing Maps: Application to Prostate Carcinomas
title_sort cluster analysis of comparative genomic hybridization (cgh) data using self-organizing maps: application to prostate carcinomas
topic Other
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4617519/
https://www.ncbi.nlm.nih.gov/pubmed/11790857
http://dx.doi.org/10.1155/2001/852674
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