Accurate confidence aware clustering of array CGH tumor profiles Export

@article{citeulike:5984054, abstract = {Motivation: Chromosomal aberrations tend to be characteristic for given (sub)types of cancer. Such aberrations can be detected with array comparative genomic hybridization (aCGH). Clustering aCGH tumor profiles aids in identifying chromosomal regions of interest and provides useful diagnostic information on the cancer type. An important issue here is to what extent individual aCGH tumor profiles can be reliably assigned to clusters associated with a given cancer type. Results: We introduce a novel evolutionary fuzzy clustering (EFC) algorithm, which is able to deal with overlapping clusterings. Our method assesses these overlaps by using cluster membership degrees, which we use here as a confidence measure for individual samples to be assigned to a given tumor type. We first demonstrate the usefulness of our method using a synthetic aCGH dataset and subsequently show that EFC outperforms existing methods on four real datasets of aCGH tumor profiles involving four different cancer types. We also show that in general best performance is obtained using 1- Pearson correlation coefficient as a distance measure and that extra preprocessing steps, such as segmentation and calling, lead to decreased clustering performance. Availability: The source code of the program is available from http://ibi.vu.nl/programs/efcwww Contact: heringa@few.vu.nl Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btp603}, author = {van Houte, Bart P. P. and Heringa, Jaap}, citeulike-article-id = {5984054}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp603}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/btp603v1/.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/btp603v1/.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/26/1/6}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19846437}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19846437}, day = {1}, doi = {10.1093/bioinformatics/btp603}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {arraycgh, cancer, clustering, confidence-measure, fuzzy}, month = {January}, number = {1}, pages = {6--14}, posted-at = {2009-10-22 08:03:39}, priority = {2}, title = {Accurate confidence aware clustering of array CGH tumor profiles}, url = {http://dx.doi.org/10.1093/bioinformatics/btp603}, volume = {26}, year = {2010} }

TY - JOUR ID - citeulike:5984054 L3 - citeulike-article-id:5984054 N2 - Motivation: Chromosomal aberrations tend to be characteristic for given (sub)types of cancer. Such aberrations can be detected with array comparative genomic hybridization (aCGH). Clustering aCGH tumor profiles aids in identifying chromosomal regions of interest and provides useful diagnostic information on the cancer type. An important issue here is to what extent individual aCGH tumor profiles can be reliably assigned to clusters associated with a given cancer type. Results: We introduce a novel evolutionary fuzzy clustering (EFC) algorithm, which is able to deal with overlapping clusterings. Our method assesses these overlaps by using cluster membership degrees, which we use here as a confidence measure for individual samples to be assigned to a given tumor type. We first demonstrate the usefulness of our method using a synthetic aCGH dataset and subsequently show that EFC outperforms existing methods on four real datasets of aCGH tumor profiles involving four different cancer types. We also show that in general best performance is obtained using 1- Pearson correlation coefficient as a distance measure and that extra preprocessing steps, such as segmentation and calling, lead to decreased clustering performance. Availability: The source code of the program is available from http://ibi.vu.nl/programs/efcwww Contact: heringa@few.vu.nl Supplementary information: Supplementary data are available at Bioinformatics online. 10.1093/bioinformatics/btp603 IS - 1 JF - Bioinformatics SN - 1460-2059 EP - 14 TI - Accurate confidence aware clustering of array CGH tumor profiles VL - 26 SP - 6 KW - arraycgh KW - cancer KW - clustering KW - confidence-measure KW - fuzzy AU - van Houte, Bart AU - Heringa, Jaap PY - 2010/01/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp603 ER -