High resolution discovery and confirmation of copy number variants in 90 Yoruba Nigerians

Table 2 Comparison of Yoruba event calls

Study (method)	Common Yoruba	% call agreement	Events compared	Events in study	% study compared	Events in our work	% our work compared
Bentley et al. 2008	1	92.6%	338	4,103	8.2%
(Sequencing)		93.6%	326			792	41.2%
Kidd et al. 2008	4	92.1%	316	944	33.5%
(Seq_Mapping)		93.1%	320			4,680	6.8%
Korbel et al. 2007	1	87.4%	199	732	27.2%
(Seq_Mapping)		87.0%	200			903	22.1%
McCarroll et al. 2008	90	99.7%	5,442	7,752	70.2%
(SNP_Array)		99.6%	5,699			97,745	5.8%
Perry et al. 2008	10	89.5%	1,403	6,695	21.0%
(HiRes_aCGH)		89.9%	1,344			10,951	12.3%
Wang et al. 2007	36	99.3%	814	1,156	70.4%
(SNP_Array_Early)		99.2%	869			40,739	2.1%

Event calls at confirmed CNVs were compared with events reported in six recent studies that included one or more Yoruba individuals. For each Yoruba in common, events were matched based on the longest overlap. Because of differences in resolution among methods, an event at a confirmed CNV could match many reported events, and vice-versa. For each study, the numbers of compared events differ slightly depending on whether our event calls were compared against study events, or vice versa. Agreement was determined by comparing loss versus gain events, and not integer copy numbers. The percentage of events that overlapped reflects the relative degree of missed events in either our work or the previous study.

ISSN: 1474-760X