Bayesian estimation of genomic copy number with single nucleotide polymorphism genotyping arrays

BMC Research Notes

Table 1 Misclassification rates from simulation study.

CN	# SNP	Scenario 1 .05/7.3/0	Scenario 2 .15/2.4/0
3	5	0	16
1	10	0	2
3	20	0	5
3	40	0	1
CN	# SNP	Scenario 3 .2/1.8/0	Scenario 4 .2/1.5/20
3	5	51	50
1	10	11	37
3	20	9	11
3	40	6	6
CN	# SNP	Scenario 5 .05/7.3/0	Scenario 6 .15/2.4/0
4	5	6	87
3	10	0	14
0	20	0	0
3	40	0	9
CN	# SNP	Scenario 7 .2/1.8/0	Scenario 8 .2/1.5/20
4	5	77	98
3	10	31	31
0	20	0	0
3	40	17	4

The entry is the misclassification rate, expressed as a percentage, over 50 replicates of one chromosome. Eight scenarios were simulated and defined by the given combination of true CN, number SNPs within the region of aberration, and SD/SNR/percent contamination. The SD and SNR are given on the log2 ratio scale under a true CN of 3. The true CN profile for Scenarios 1-4 is CN(#SNPs): 2(10), 3(5), 2(50), 1(10), 2(50), 3(20), 2(50), 3(40), 2(10). The true CN profile for Scenarios 5-8 is CN(#SNPs):2(10), 4(5), 2(50), 3(10), 2(50), 0(20), 2(50), 3(40), 2(10).

ISSN: 1756-0500