Supplementary Material

A segmental maximum a posteriori approach to genome-wide copy number profiling

Robin Andersson, Carl E.G. Bruder, Arkadiusz Piotrowski, Uwe Menzel, Helena Nord, Johanna Sandgren, Torgeir R. Hvidsten, Teresita Diaz de Ståhl, Jan P. Dumanski, Jan Komorowski

Bioinformatics 2008 24(6): 751-758. Epub 2008 Jan 19. DOI: 10.1093/bioinformatics/btn003

RESULTS

Array design and protocols [PDF (1 page, 13 KB)]

Design of DOP-PCR 32K BAC-based human genome array, hybridization, scanning and data analysis

Parameter settings [PDF (2 pages, 35 KB)]

The parameter settings used for the GBM and synthetic data with a general discussion

Evaluation of aberration detection in synthetic data

Genome plots of the synthetic data predictions [PDF (500 pages, 98 MB)]

Genome plots of the predictions made by SMAP with eight different configurations (see manuscript for details), DNAcopy and BioHMM on the synthetic data set

Copy number profiling of glioblastoma multiforme

Genome plots of the GBM predictions [PDF (30 pages, 6 MB)]

Genome plots of the predictions made by SMAP with eight different configurations (see manuscript for details), DNAcopy and BioHMM on the GBM data set

Chromosome plots of the GBM predictions [PDF (69 pages, 21 MB)]

Chromosome plots of the predictions made by SMAP with eight different configurations (see manuscript for details), DNAcopy and BioHMM on the GBM data set

Raw data

G20856 [tab-delimited raw data (9 MB)],

G20972 [tab-delimited raw data (9 MB)],

G24460 [tab-delimited raw data (9 MB)]