Table 2 Open in new tab Summary of...

Variant	Gene	Function	Sample	Tissue	S2N	CADD	WES-Blood	WES-Brain	P-value	Panel-Blood	Panel-Brain	P-value
chr1:11073909: G/A	TARDBP	Nonsyn	SD14	MTG	9.8	20	87	0	0.000	765	10	0.013	0.6	5126	0	0.000	18719	271	0.014	9 × 10⁻²⁹
chr1:11073909: C/T	TARDBP	Nonsyn	SD10	DG	NA	28	138	0	0.000	1037	0	0.000	1	9349	4	0.000	7533	152	0.020	3 × 10⁻⁴⁷
chr9:130928555: T/G	CIZ1	Nonsyn	SD11	DG	20.8	16	39	0	0.000	323	54	0.143	0.005	134	0	0.000	346	35	0.092	3 × 10⁻⁵
chr17:4883215: A/G	CAMTA2	Nonsyn	SD09	DG	11.1	18	58	1	0.017	420	42	0.091	0.07	146	1	0.007	1058	24	0.022	0.4
chr17:34192311: T/G	HEATR9	Nonsyn	SD11	DG	7.6	13	72	0	0.000	278	21	0.070	0.02	3232	24	0.007	18031	329	0.018	3 × 10⁻⁶
chr17:70119726: C/A	SOX9	Nonsyn	SD14	DG	9.0	20	56	1	0.018	405	15	0.036	0.7	1676	5	0.003	1133	76	0.063	9 × 10⁻²⁴
chr19:51133405: A/G	SYT3	Nonsyn	SD11	DG	8.5	14	14	0	0.000	227	25	0.099	0.4	103	0	0.000	1593	29	0.018	0.4
chr19:51133405: A/G	SYT3	Nonsyn	SD09	DG	12.4	14	21	0	0.000	236	40	0.145	0.09	289	1	0.003	1829	29	0.016	0.2

Variant

Gene

Function

Sample

Tissue

S2N

MAF

CADD

WES-Blood

WES-Brain

P-value

Panel-Blood

Panel-Brain

P-value

REF

ALT

VAF

REF

ALT

VAF

REF

ALT

VAF

REF

ALT

VAF

chr1:11073909: G/A

TARDBP

Nonsyn

SD14

MTG

9.8

0.000

765

0.013

0.6

5126

0.000

18719

271

0.014

9 × 10⁻²⁹

chr1:11073909: C/T

TARDBP

Nonsyn

SD10

138

0.000

1037

0.000

9349

0.000

7533

152

0.020

3 × 10⁻⁴⁷

chr9:130928555: T/G

CIZ1

Nonsyn

SD11

20.8

0.000

323

0.143

0.005

134

0.000

346

0.092

3 × 10⁻⁵

chr17:4883215: A/G

CAMTA2

Nonsyn

SD09

11.1

0.017

420

0.091

0.07

146

0.007

1058

0.022

0.4

chr17:34192311: T/G

HEATR9

Nonsyn

SD11

7.6

0.000

278

0.070

0.02

3232

0.007

18031

329

0.018

3 × 10⁻⁶

chr17:70119726: C/A

SOX9

Nonsyn

SD14

9.0

0.018

405

0.036

0.7

1676

0.003

1133

0.063

9 × 10⁻²⁴

chr19:51133405: A/G

SYT3

Nonsyn

SD11

8.5

0.000

227

0.099

0.4

103

0.000

1593

0.018

0.4

chr19:51133405: A/G

SYT3

Nonsyn

SD09

12.4

0.000

236

0.145

0.09

289

0.003

1829

0.016

0.2

Variant	Gene	Function	Sample	Tissue	S2N	CADD	WES-Blood	WES-Brain	P-value	Panel-Blood	Panel-Brain	P-value
chr1:11073909: G/A	TARDBP	Nonsyn	SD14	MTG	9.8	20	87	0	0.000	765	10	0.013	0.6	5126	0	0.000	18719	271	0.014	9 × 10⁻²⁹
chr1:11073909: C/T	TARDBP	Nonsyn	SD10	DG	NA	28	138	0	0.000	1037	0	0.000	1	9349	4	0.000	7533	152	0.020	3 × 10⁻⁴⁷
chr9:130928555: T/G	CIZ1	Nonsyn	SD11	DG	20.8	16	39	0	0.000	323	54	0.143	0.005	134	0	0.000	346	35	0.092	3 × 10⁻⁵
chr17:4883215: A/G	CAMTA2	Nonsyn	SD09	DG	11.1	18	58	1	0.017	420	42	0.091	0.07	146	1	0.007	1058	24	0.022	0.4
chr17:34192311: T/G	HEATR9	Nonsyn	SD11	DG	7.6	13	72	0	0.000	278	21	0.070	0.02	3232	24	0.007	18031	329	0.018	3 × 10⁻⁶
chr17:70119726: C/A	SOX9	Nonsyn	SD14	DG	9.0	20	56	1	0.018	405	15	0.036	0.7	1676	5	0.003	1133	76	0.063	9 × 10⁻²⁴
chr19:51133405: A/G	SYT3	Nonsyn	SD11	DG	8.5	14	14	0	0.000	227	25	0.099	0.4	103	0	0.000	1593	29	0.018	0.4
chr19:51133405: A/G	SYT3	Nonsyn	SD09	DG	12.4	14	21	0	0.000	236	40	0.145	0.09	289	1	0.003	1829	29	0.016	0.2

Table 2

Open in new tab

Summary of results of eight validated somatic variants

Variant	Gene	Function	Sample	Tissue	S2N	MAF	CADD	WES-Blood			WES-Brain			P-value	Panel-Blood			Panel-Brain			P-value
Variant	Gene	Function	Sample	Tissue	S2N	MAF	CADD	REF	ALT	VAF	REF	ALT	VAF	P-value	REF	ALT	VAF	REF	ALT	VAF	P-value
chr1:11073909: G/A	TARDBP	Nonsyn	SD14	MTG	9.8	0	20	87	0	0.000	765	10	0.013	0.6	5126	0	0.000	18719	271	0.014	9 × 10⁻²⁹
chr1:11073909: C/T	TARDBP	Nonsyn	SD10	DG	NA	0	28	138	0	0.000	1037	0	0.000	1	9349	4	0.000	7533	152	0.020	3 × 10⁻⁴⁷
chr9:130928555: T/G	CIZ1	Nonsyn	SD11	DG	20.8	0	16	39	0	0.000	323	54	0.143	0.005	134	0	0.000	346	35	0.092	3 × 10⁻⁵
chr17:4883215: A/G	CAMTA2	Nonsyn	SD09	DG	11.1	0	18	58	1	0.017	420	42	0.091	0.07	146	1	0.007	1058	24	0.022	0.4
chr17:34192311: T/G	HEATR9	Nonsyn	SD11	DG	7.6	0	13	72	0	0.000	278	21	0.070	0.02	3232	24	0.007	18031	329	0.018	3 × 10⁻⁶
chr17:70119726: C/A	SOX9	Nonsyn	SD14	DG	9.0	0	20	56	1	0.018	405	15	0.036	0.7	1676	5	0.003	1133	76	0.063	9 × 10⁻²⁴
chr19:51133405: A/G	SYT3	Nonsyn	SD11	DG	8.5	0	14	14	0	0.000	227	25	0.099	0.4	103	0	0.000	1593	29	0.018	0.4
chr19:51133405: A/G	SYT3	Nonsyn	SD09	DG	12.4	0	14	21	0	0.000	236	40	0.145	0.09	289	1	0.003	1829	29	0.016	0.2

Variant	Gene	Function	Sample	Tissue	S2N	MAF	CADD	WES-Blood			WES-Brain			P-value	Panel-Blood			Panel-Brain			P-value
Variant	Gene	Function	Sample	Tissue	S2N	MAF	CADD	REF	ALT	VAF	REF	ALT	VAF	P-value	REF	ALT	VAF	REF	ALT	VAF	P-value
chr1:11073909: G/A	TARDBP	Nonsyn	SD14	MTG	9.8	0	20	87	0	0.000	765	10	0.013	0.6	5126	0	0.000	18719	271	0.014	9 × 10⁻²⁹
chr1:11073909: C/T	TARDBP	Nonsyn	SD10	DG	NA	0	28	138	0	0.000	1037	0	0.000	1	9349	4	0.000	7533	152	0.020	3 × 10⁻⁴⁷
chr9:130928555: T/G	CIZ1	Nonsyn	SD11	DG	20.8	0	16	39	0	0.000	323	54	0.143	0.005	134	0	0.000	346	35	0.092	3 × 10⁻⁵
chr17:4883215: A/G	CAMTA2	Nonsyn	SD09	DG	11.1	0	18	58	1	0.017	420	42	0.091	0.07	146	1	0.007	1058	24	0.022	0.4
chr17:34192311: T/G	HEATR9	Nonsyn	SD11	DG	7.6	0	13	72	0	0.000	278	21	0.070	0.02	3232	24	0.007	18031	329	0.018	3 × 10⁻⁶
chr17:70119726: C/A	SOX9	Nonsyn	SD14	DG	9.0	0	20	56	1	0.018	405	15	0.036	0.7	1676	5	0.003	1133	76	0.063	9 × 10⁻²⁴
chr19:51133405: A/G	SYT3	Nonsyn	SD11	DG	8.5	0	14	14	0	0.000	227	25	0.099	0.4	103	0	0.000	1593	29	0.018	0.4
chr19:51133405: A/G	SYT3	Nonsyn	SD09	DG	12.4	0	14	21	0	0.000	236	40	0.145	0.09	289	1	0.003	1829	29	0.016	0.2

All eight variants passed the validation criteria. WES-Blood/WES-Brain shows the read counts for variant and wild-type from exome sequencing. Panel-Blood/Panel-Brain shows the counts for the amplicon panel. ALT = number of reads carrying the alternative allele; MAF = minor allele frequency; Nonsyn = non-synonymous; REF = number of reads carrying the reference allele; S2N = signal to noise; VAF = variant allele frequency. P-values were obtained by Fisher’s exact tests of the counts between blood and brain.

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