Table 1.

Gold standard CNVs from 13 clinical samples used to assess Atlas-CNV performance

Sample	Gene	Chr	Start	End	Sizea	cSNP sizeb	Class	Number of ES exons in CNV	Exon range of CNV
1–100155	MYH11	16	15797848	15932110	134,262	815,577	hetdel	42	2–42c
2–100159	MYH11	16	15797848	15932110	134,262	735,806	hetdel	42	2–42
3–100161	MYH11	16	15797848	15932110	134,262	2,104,716	hetdel	42	2–42
4–100171	MYH11	16	15797848	15932110	134,262	1,158,489	hetdel	42	2–42
5–100168	RYR2	1	237205822	237995948	790,126	4,170,626	hetdel	104	1–105d
6–100175	DSG2	18	29078215	29118942	40,727	20,632	hetdel	12	1–12
7–100185	BRCA1	17	41242961	41249307	6346	5803	hetdel	4	8–11
8–100196	IL33	9	6241695	6256169	14,474	232,335	hetdel	7	1–7
9–100199	MYH7	14	23882022	23889487	7465	28,302	hetdel	14	27–40
10–100208	MLH1 (LRRFIP2)	3	37089010	37116608	27,598	27,528	hetdel	4 (9)	16–19 (21–29)
11–100184	HNF1B	17	36047375	36104876	57,501	1,351,422	hetdel	9	1–9
12–100189	HNF1B	17	36047336	36104876	57,540	1,375,039	hetdel	9	1–9
13–100209	HNF1B	17	36047336	36104876	57,540	1,375,039	hetdel	9	1–9

All CNVs are heterozygous deletions and were previously identified in ES and Illumina HumanExome-12v array with the exception of sample 13, which has no ES.

CNV copy-number variant, ES exome sequencing.

^aCNV size from clinical ES.

^bCNV size from Illumina HumanExome-12v array.

^cMHY11 exon 42 has 2 targets in ES data.

^dRYR2 exon 91 is absent in ES.