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Table 2 Clinical features and variants detected by NGS in patients with somatic APC mosaicism

From: Next-generation sequencing with comprehensive bioinformatics analysis facilitates somatic mosaic APC gene mutation detection in patients with familial adenomatous polyposis

ID

Age at onset

Number of polyps

Colorectal carcinoma

Family history

Specimen

Mutation detected

Variant callers (variants allele frequency)

Median depth

Confirmation test

HC

MuTect2

VarScan2

Pindel

P1

40~49

100 s

No

None

leukocyte

c.3295_3296del

p.Val1099PhefsTer19

ND

0.077

ND

0.068

2668

MEMO-PCR

P1

 

polyp

c.3295_3296del

p.Val1099PhefsTer19

0.206

0.206

0.228

0.197

790

 

P2

40~49

100 s

Adenocarcinoma

None

leukocyte

c.3860_3861dup

p.Gly1288Ter

ND

0.035

0.094

0.032

2497

MEMO-PCR

P3

30~39

200 s

No

None

leukocyte

c.3577_3578del

p.Gln1193ValfsTer14

ND

0.003

ND

0.003

4076

Tissue

P4

50~59

50–70

Adenocarcinoma

None

leukocyte

c.1754delT

p.Leu585ProfsTer5

ND

0.018

ND

0.020

2960

 

P5

40~49

30–50

No

Maternal rectal cancer at the age of 70

leukocyte

c.694C > T

p.Arg232Ter

ND

0.034

ND

ND

2185

Tissue

P6

40~49

20–30

No

None

leukocyte

c.3566C > G

p.Ser1189Ter

0.114

0.114

0.114

ND

3624

Sanger sequencing

P7

30~39

300 s

Adenoma

None

leukocyte

c.3211_3238dup

p.Glu1080AlafsTer10

0.195

0.275

ND

0.174

1310

Sanger sequencing

  1. HC HaplotypeCaller, MEMO Mutant enrichment with 3′-modified oligonucleotides, ND Not detected