Simple binary segmentation frameworks for identifying variation in DNA copy number

BMC Bioinformatics

Table 2 Summarized results of applying the proposed framework to nine cell lines

Cell line	Chromosome (exact location)	Aneuploidy type	Our method
GM03563	3 (3q12-3qter)	Trisomy	O
	9 (9pter-9p24)	Monosomy	O
GM05296	10 (10q21-10q24)	Trisomy	O
	11 (11p12-11p13)	Monosomy	O
GM01750	9 (9pter-9p24)	Trisomy	O
	14 (14pter-14q21)	Trisomy	O
GM03134	8 (8q13-8q22)	Monosomy	O
GM13330	1 (1q25-1qter)	Trisomy	O
	4 (4q35-4qter)	Monosomy	O
GM01535	5 (5q33-5qter)	Trismoy	O
	12 (12q24-12qter)	Monosomy	X
GM07081	7 (7pter-7q11.2)	Trisomy	O
	15 (15pter-15q11.2)	Monosomy	X
GM13031	17 (17q21.3-17q23)	Monosomy	O
GM01524	6 (6q15-6q25)	Trisomy	O

Of the 15 altered regions found by spectral karyotyping, 13 were identified by our method. The symbol O indicates that our method correctly identified the known alterations found by spectral karyotyping, whereas the symbol × indicates that it did not identify the region. Two unidentified regions appear in chromosome 12 on GM01535 and chromosome 15 on GM07081. For GM01535, the region is represented by only one probe, and single altered probes were not found. For GM07081, our result is consistent with that of Snijders et al.[5], in that no evidence of an alteration was seen in the GM07081 data.

ISSN: 1471-2105