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

Table 4 Summary of events at CNV regions discovered by sequencing

	Confirmed CNVs	Confirmed < 1 kb	Levy + Wheeler	Levy_only	Wheeler_only
Reported CNVs			221	1,753	957
with YRI events	6,368	1,107	172	1,651	740
% with events			77.8%	94.2%	77.3%
Median length	4,380 bp	490 bp	193 bp	190 bp	240 bp
25th percentile	1,519 bp	290 bp	110 bp	120 bp	120 bp
75th percentile	13,230 bp	735 bp	849 bp	380 bp	974 bp
Events	97,953	27,718	4056	40,968	13,968
Events per region	15.4	25.0	23.6	24.8	18.9
Homozygous loss (0)	5,792	2,177	321	1,004	1,092
One copy loss (1)	55,593	14,335	1,792	20,353	6,882
One copy gain (3)	31,198	9,082	1,415	16,926	4,879
Multiple gains (4+)	5,370	2,124	528	2,685	1,115
Loss:gain	1.7	1.5	1.1	1.1	1.3

Regions are from the Levy et al. [18] and Wheeler et al. [19] whole-genome sequencing studies. Levy+Wheeler refers to regions common to both studies, while Levy_only and Wheeler_only are regions reported only in either study. Regions that overlap any of the putative CNVs from the genome-scan were not included in these three sets. Reported refers to the numbers of CNVs discovered in the studies. 'With events' is the tally of reported regions having at least one observed event on the CNV-typing array, and 'events' is the tally from all 90 Yoruba at all regions. The events are broken down by tallies of integer copy number calls, where 0 is homozygous loss, 1 and 3 are heterozygous loss and gain, and 4+ is the tally of multiple gains. 'Loss:gain' is the ratio of loss and gain event tallies.

ISSN: 1474-760X