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Figure 4 | BMC Bioinformatics

Figure 4

From: A forward-backward fragment assembling algorithm for the identification of genomic amplification and deletion breakpoints using high-density single nucleotide polymorphism (SNP) array

Figure 4

Sample output of the R-package FASeg. The results were obtained using the smoothing span of 50 SNPs and the alpha level of 10-6. (a) Raw copy number (upper panel) and fitted values (lower panel) of chromosome 9 for data from the Mapping 50 K Xba array, generated from an oral squamous cell carcinoma case (CZ T26). (b) Comparison of the copy numbers for chromosome 9 between four samples. Two primary skin fibroblast cell lines: GM03226 (with a known trisomic segment in chromosome 9 [9pter > q11]; red) and GM00870 (with a known single copy deletion segment in chromosome 9 [9pter > p21]; blue). Two previously uncharacterized oral squamous cell carcinoma cases: CZ T26 (green) and CZ T322 (aqua). (c) Color display of the fitted values of the whole genome for all four samples. From top to bottom: GM03226, GM00870, CZ T26 and CZ T322. The gridlines separate chromosomes lined up in numerical order, with the X chromosome being the last. Black: normal; red: higher; green: lower. (d) A section of the condensed table output containing copy number and Cytoband information for samples GM03226, GM00870, CZ T26, and CZ T322.

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BMC Bioinformatics

ISSN: 1471-2105

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