Table 2.

Candidate single-exon CNVs from 29 eMERGESeq samples selected for MLPA confirmation

Sample	Site	Gene-Transcript_Exon	Class	CNV exons in sample	CNV genes in sample	Exon size	Target size	Mappability	C-score	EStDev	SampleQC	Distance of probe(s) to exon	MLPA
1	Columbia	BRCA1–005_8	hetdel	6	6	46	99	1.00	−7.20	0.10	0.15		No
2	NU-CGM	BRCA1–005_7	hetdel	2	2	106	105	1.00	−14.17	0.06	0.10		Yes
3	Mayo	BRCA1–005_2	hetdel	1	1	99	99	0.97	−11.67	0.09	0.08		Yes
4	Mayo	LDLR-003_5	hetdel	2	2	123	122	1.00	−10.33	0.09	0.10		Yes
5	NU-CGM	MLH1–001_13	hetdel	1	1	149	148	1.00	−22.40	0.05	0.09		Yes
6	Vanderbilt	PKP2–002_1	hetdel	1	1	248	222	0.95	−11.88	0.08	0.08		Yes
7	CHOP	PKP2–002_4	hetdel	1	1	136	135	0.97	−10.91	0.11	0.10		Yes
8	Vanderbilt	DSP-001_24	hetdel	1	1	4076	3236	1.00	−42.50	0.02	0.10		Yes
9	Vanderbilt	DSP-001_24	hetdel	1	1	4076	3236	1.00	−29.33	0.03	0.09		Yes
10	Mayo	CFTR-001_2	hetdel	1	1	111	110	1.00	−18.00	0.07	0.16		Yes
11	Mayo	TGFBR2–002_3	dup	1	1	169	168	1.00	9.33	0.06	0.08		Yes
12	CHOP	TCF4–004_3	hetdel	2	2	92	99	1.00	−8.75	0.08	0.14		No
13	CHOP	PTEN-001_2	hetdel	6	5	85	99	0.78	−8.10	0.10	0.15		No
14	Columbia	PTEN-001_2	hetdel	37	17	85	99	0.78	−8.00	0.09	0.20		No
15	Mayo	TCF4–004_2	hetdel	1	1	91	99	0.79	−10.64	0.11	0.09	315	Yes
16	NU-CGM	PTEN-001_3	hetdel	14	8	45	99	0.96	−8.86	0.07	0.17	145,28,226	Inconclusive
17	NU-CGM	PTEN-001_4	hetdel	3	3	44	99	1.00	−7.00	0.09	0.15	14,61	Inconclusive
18	Vanderbilt	CACNA1A-001_47	hetdel	2	2	1612	740	0.99	−12.33	0.06	0.12	Flanking 5’	Inconclusive
19	Mayo	CACNA1A-001_47	hetdel	2	2	1612	740	0.99	−8.86	0.07	0.13	Flanking 5’	Inconclusive
20	Mayo	CACNA1A-001_47	hetdel	3	3	1612	740	0.99	−8.25	0.08	0.15	Flanking 5’	Inconclusive
21	Vanderbilt	CACNA1A-001_47	hetdel	1	1	1612	740	0.99	−8.00	0.08	0.13	Flanking 5’	Inconclusive
22	NU-CGM	MYH7–001_27	hetdel	3	3	390	389	0.53	−11.00	0.09	0.11	63	Inconclusive
23	CHOP	MYH7–001_27	hetdel	1	1	390	389	0.53	−9.88	0.08	0.09	63	Inconclusive
24	Columbia	MYH7–001_27	hetdel	1	1	390	389	0.53	−9.44	0.09	0.09	63	Inconclusive
25	Vanderbilt	CHEK2–003_15	hetdel	1	1	81	99	0.26	−13.83	0.06	0.08	207	Inconclusive
26	Mayo	CHEK2–003_14	hetdel	1	1	86	99	0.54	−8.92	0.12	0.10	54	Inconclusive
27	Mayo	CHEK2–003_15	hetdel	1	1	81	99	0.26	−8.57	0.14	0.10	207	Inconclusive
28	Vanderbilt	SDHC-001_1	hetdel	3	3	169	99	1.00	−9.25	0.08	0.13	382,132	Inconclusive
29	Vanderbilt	SDHC-001_1	hetdel	1	1	169	99	1.00	−8.56	0.09	0.09	382,132	Inconclusive

Twenty-three high confidence CNVs (C-score ≥8 and E_StDev ≤ 0.1) and 6 borderline CNVs were tested despite over half (15/29) not having exact MLPA probes on the exon of interest (see probe distance to exon). High CNV genes per sample, exon size <50 bp, or mappability <0.8 may be factors that account for some of the negative and inconclusive cases (see values in bold). For candidates with C-score >8 and having CNV genes per sample <3, MLPA tests confirmed 90.9% (10/11) of single-exon CNVs.

CHOP, CNV copy-number variant, MLPA, NU-CGM.