Smoothing waves in array CGH tumor profiles Export

@article{citeulike:4186552, abstract = {Motivation: Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult. Results: An efficient and highly effective algorithm that largely removes the wave bias from tumor profiles by regressing the tumor profile data on data of profiles from the clinical genetics practice. Results are illustrated on two independent datasets. The algorithm is shown to be robust against the presence of true copy number aberrations. Moreover, the smoothed profiles are able to recapitulate the aberration location and signal for simulated tumor profiles. Availability: Easy-to-use R scripts, user instructions and data are available from http://www.few.vu.nl/\~{}mavdwiel/nowaves.html. Contact: mark.vdwiel@vumc.nl Supplementary information: Supplementary information are available at Bioinformatics online. 10.1093/bioinformatics/btp132}, author = {van de Wiel, Mark A. and Brosens, Rebecca and Eilers, Paul H. C. and Kumps, Candy and Meijer, Gerrit A. and Menten, Bjorn and Sistermans, Erik and Speleman, Frank and Timmerman, Marieke E. and Ylstra, Bauke}, citeulike-article-id = {4186552}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp132}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/25/9/1099.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/25/9/1099.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/9/1099?etoc}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19276148}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19276148}, day = {1}, doi = {10.1093/bioinformatics/btp132}, journal = {Bioinformatics}, keywords = {array-cgh, segmentation, software}, month = {May}, number = {9}, pages = {1099--1104}, posted-at = {2009-11-03 17:17:48}, priority = {2}, title = {Smoothing waves in array CGH tumor profiles}, url = {http://dx.doi.org/10.1093/bioinformatics/btp132}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:4186552 L3 - citeulike-article-id:4186552 N2 - Motivation: Many high-resolution array comparative genomic hybridization tumor profiles contain a wave bias, which makes accurate detection of breakpoints in such profiles more difficult. Results: An efficient and highly effective algorithm that largely removes the wave bias from tumor profiles by regressing the tumor profile data on data of profiles from the clinical genetics practice. Results are illustrated on two independent datasets. The algorithm is shown to be robust against the presence of true copy number aberrations. Moreover, the smoothed profiles are able to recapitulate the aberration location and signal for simulated tumor profiles. Availability: Easy-to-use R scripts, user instructions and data are available from http://www.few.vu.nl/~mavdwiel/nowaves.html. Contact: mark.vdwiel@vumc.nl Supplementary information: Supplementary information are available at Bioinformatics online. 10.1093/bioinformatics/btp132 IS - 9 JF - Bioinformatics EP - 1104 TI - Smoothing waves in array CGH tumor profiles VL - 25 SP - 1099 KW - array-cgh KW - segmentation KW - software AU - van de Wiel, Mark AU - Brosens, Rebecca AU - Eilers, Paul AU - Kumps, Candy AU - Meijer, Gerrit AU - Menten, Bjorn AU - Sistermans, Erik AU - Speleman, Frank AU - Timmerman, Marieke AU - Ylstra, Bauke PY - 2009/05/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp132 ER -