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Table 1 Statistics on sequence capture based resequencing

From: Molecular evidence for the bi-clonal origin of neuroendocrine tumor derived metastases

A)

 

p-TU

P-STS -P41

H-STS -P42

L-STS -P49

Total number of reads

272,728

270,044

256,619

268,969

Numb. of mapped reads

262,773 (96.35%)

259,781 (96.20%)

247,300 (96.37%)

258,908 (96.26%)

NumUniqueInRegions (reads within target region

184,206 (72.08%)

200,711 (78.60%)

192,918 (79.38%)

160,272 (63.75%)

Average coverage

~29.3-fold

~31.9-fold

~30.7-FOLD

~25.5-FOLD

% target bases covered ≥ 5-fold

>89%

>86%

>81%

>82%

B)

 

p-TU

P-STS -P41

H-STS -P42

L-STS -P49

HC Diffs (total)

4489

3756

3541

4631

HC Diffs (known)

3961

3372

3163

3907

HC DIffs (within cds)

280

251

206

213

novel or pathogenic (in coding seq.)

27

26

6

7

non-synonymous

24

19

5

6

synonymous

3

7

1

1

knowing (in coding seq.)

253

225

200

206

non-synonymous

97

80

77

77

synonymous

156

145

123

129

C)

GeneID

Status

Mut. type

Nucleotide

AA

Refseq ID

Chr.

Position

BRCA2

unknown

missense

c.C1783T

H595Y

NM_000059.3

13q

31805398

ERCC5

unknown

missense

c.T266C

V89A

NM_000123.2

13q

102304109

KIT

unknown

missense

c.A1606C

M536L

NM_000222.1

4q

55288206

MLL

unknown

missense

c.C11305T

H3769V

NM_005933.2

11q

117895710

ROS1

unknown

missense

c.G625A

D209N

NM_002944.2

6q

117824925

SMAD4

unknown

missense

c.G290A

R97H

NM_005359.5

18q

46829094

SDHB

unknown

missense

cC98T

A33L

Nm_003000.2

1p

17243945

HNF1A

unknown

frameshift

c.872_873insC

p.G292fs*25

NM_000545.4

12q

119916507

RB1

known

missense

c.211_213insAG

p.A74fs*3

NM_000321.2

13q

47779500

TP53

known

missense

c.C817T

R273C

NM_000546.4

17q

7517846

TP53

rs1042522

missense

c.C215G

R72P

NM_000546.4

17q

7520197

HNF1A

rs56348580

synon.

cG864C

G288G

NM_000545.4

12q

119916500

KIAA1549

rs59985563

missense

cA1090G

T364A

NM_001164665.1

7q

138253822

KIAA1549

rs61734132

missense

cC1940G

S647C

NM_00164665.1

7q

138252972

  1. Sequencing statistics (A) and target region related detection of High Confidence Differences (B). C: Selected sequence variants (known mutations, unknown variants and SNPs) further pursued by complementary methods. Chromosomal positions according to Ensembl database release 54 from May 2009.