Copy number variation genotyping using family information

BMC Bioinformatics

Table 4 Confusion matrix for copy number estimates using qPCR and GMM from Agilent CGH arrays

		Agilent CGH arrays GMM results Region 1 (chr19:62166726-62167416)
			2	3	4
	2	Unadjusted	11	6	0
		Family adjusted	(12)	(5)	(0)
	3	Unadjusted	0	26	11
		Family adjusted	(0)	(34)	(3)
qPCR results	4	Unadjusted	0	4	13
		Family adjusted	(0)	(8)	(9)
		Region 2 (chr4:43446373-43446839)
			0	1	2
	0	Unadjusted	14	9	1
		Family adjusted	(15)	(9)	0
	1	Unadjusted	0	26	10
		Family adjusted	(0)	(34)	(2)
qPCR results	2	Unadjusted	0	0	11
		Family adjusted	(0)	(2)	(9)

The numbers in parenthesis show the estimates after family adjustments. The qPCR estimates are rounded off the nearest integer and shifted to correspond to the CGH array estimates, which designate the cluster closest to zero as the two copy group. The overall accuracy goes from 70% to 77% for region 1 (chr19:62166726-62167416) and from 72% to 82% for region 2 (chr4:43446373-43446839).

ISSN: 1471-2105