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Table 1 Somatic and germline variants of FCD type II in this study

From: An integrated genetic analysis of epileptogenic brain malformed lesions

ID

Gene

Variant

Method

VAF (%) in validation

Germline/somatic

Reported/novel variant

Detection

Validation

Blood

Brain

FCD type IIA

F53

DEPDC5

c.982C > T p.(Arg328*)

TS

Sanger

NA

NA

Germline

Reported

F72

PIK3CA

c.1035T > A p.(Asn345Lys)

TS

DS

NA

12.8–16.8

Somatic

Reported

FCD type IIB

F04

TUBB3

c.520A > G p.(Lys174Glu)

WES

Sanger

NA

NA

Germline

Novel

F08

MTOR

c.4339_4353del p.(Ala1447_Glu1451del)

WES

DS

0

1.8

Somatic

Novel

F36

TSC2

c.2492C > T p.(Thr831Met)

TS

DS

0.1a

1.4

Somatic

Novel

F38

NPRL3

c.629 + 2_3insT

TS

DS

32.5

32.9

Somatic

Novel

F40

MTOR

c.4447T > C p.(Cys1483Arg)

TS

DS

0

0.6

Somatic

Reported

F41

TSC2

c.5227C > T p.(Arg1743Trp)

TS

DS

0

1

Somatic

Novel

F43

DEPDC5

22q11.23q13.33del and 17q12q25.3dup

WES

CMA

0

20–25

Somatic

Novel

F43

DEPDC5

c.856C > T p.(Arg286*)

TS

DS

0.1a

1.8

Somatic

Reported

F44

TSC2

c.1513C > T p.(Arg505*)

TS

DS

0

1.6

Somatic

Novel

F46

MTOR

c.4376C > A p.(Ala1459Asp)

TS

ddPCR

0

2.56

Somatic

Reported

F49

TSC2

c.5228G > A p.(Arg1743Gln)

TS

DS

0.1a

1.3

Somatic

Reported

F50

MTOR

c.5930C > A p.(Thr1977Lys)

TS

DS

0

2.6

Somatic

Reported

F54

MTOR

c.4379T > C p.(Leu1460Pro)

TS

ddPCR

0

1.84

Somatic

Reported

F57

MTOR

c.6644C > A p.(Ser2215Tyr)

TS

ddPCR

0

3.18

Somatic

Reported

F61

TSC2

c.4375C > T p.(Arg1459*)

TS

DS

0

0.6

Somatic

Novel

F61

TSC2

c.4960G > A p.(Gly1654Ser)

TS

Sanger

NA

NA

Germline

Novel

F64

MTOR

c.4448G > A p.(Cys1483Tyr)

TS

DS

NA

4

Somatic

Reported

F68

TSC2

c.1418_1422del p.(Leu473Hisfs*7)

TS

DS/ASP

0.03–0.4

3.6

Somatic

Novel

  1. ASP allele-specific PCR, CMA chromosomal microarray, ddPCR droplet digital PCR, DS amplicon deep sequencing, NA not available, TS targeted sequencing, VAF variant allele frequency, WES whole-exome sequencing
  2. aThese data were considered false positive due to similar error rates in the short-read sequencer (0.1%) (Additional file 1: Tables S2 and S3). Refseq accession number: DEPDC5 (NM_001242896), MTOR (NM_004958), NPRL3 (NM_001077350), PIK3CA (NM_006218), TSC2 (NM_000548), and TUBB3 (NM_006086)