Table 2.

Apparent amplifications and deletions detected prior to amplification through comparison with a reference set of 48 individuals

Sample compared versus Affy48	Genome coordinates of variant (NCBI Build 36/hg18/Mar 2006)	Size (bp)	CN within variant	CN outside variant	SNP count	P-value	Variation locusa
Amplifications
Sample 1	chr7:48424572–48431182	6610	2.88184	2.04848	11	1.99 × 10−8	–
	chr14:19381928–19492423	110495	2.93812	2.03610	28	4.85 × 10−13	Locus 2636
Sample 2	chr2:113809804–113849256	39452	2.28770	2.04023	12	3.70 × 10−7	Locus 0397
	chr17:41569489–41709662	140173	3.07396	2.03694	41	2.31 × 10−12	Locus 3029
Sample 3	chr9:29695281–29706655	11374	2.19958	2.04042	4	<1.00 × 10−16	–
	chr14:19309086–19459561	150475	2.65807	2.03481	25	5.42 × 10−10	Locus 2639
	chr15:19163125–20077554	914429	2.66995	2.04165	72	<1.00 × 10−16	Locus 2748
Deletions
Sample 1	chr7:142030227–142210594	180367	1.54593	2.04848	27	1.61 × 10−10	Locus 1656
	chr14:21451264–22044096	592832	1.51299	2.03610	161	<1.00 × 10−16	Loci 2644 and 2645
	chr22:33661041–33725126	64085	1.75349	2.06794	21	1.65 × 10−9	Locus 3489
Sample 2	chr2:50682535–50865587	183052	1.44974	2.04023	40	<1.00 × 10−16	Locus 0329
	chr14:21792331–22040096	247765	1.38419	2.02893	60	<1.00 × 10−16	Locus 2645
Sample 3	chr14:21800768–21932862	132094	1.53811	2.03481	32	<1.00 × 10−16	Locus 2645

^aFrom the database of genomic variants (http://projects.tcag.ca/variation/).