01.12.2017 | Research article | Ausgabe 1/2017 Open Access

The germline variants in DNA repair genes in pediatric medulloblastoma: a challenge for current therapeutic strategies
- Zeitschrift:
- BMC Cancer > Ausgabe 1/2017
Electronic supplementary material
Background
Methods
Patients and controls
Medulloblastoma patients
|
Number of patients
|
|
---|---|---|
Age at diagnosis (years)
|
≤ 3
|
14
|
3-13
|
88
|
|
Gender
|
Male
|
66
|
Female
|
36
|
|
Histologic type
|
Classic
|
69
|
LCA
|
16
|
|
D/N
|
6
|
|
MBEN
|
6
|
|
MBL
|
5
|
|
Metastasis
|
NO
|
70
|
YES
|
31
|
|
NA
|
1
|
|
Molecular tumor subtype
|
WNT
|
11
|
SHH
|
9
|
|
Non-WNT/SHH
|
25
|
|
Group 3
|
7
|
|
Group 4
|
24
|
|
NA
|
26
|
|
Treatment protocol
|
HR
|
60
|
SR
|
29
|
|
<3 yrs
|
13
|
|
TOTAL
|
102
|
Methods
Targeted gene panel sequencing
Whole exome sequencing
Selection and validation of candidate variants
Variant validation
Determination of molecular subgroups in medulloblastoma patients
Treatment complications assessment
Results
MSH2 and RAD50 analysis
Variant
|
Gene
|
Effect on gene function
|
Wild type nucleotide
|
Altered nucleotide
|
Frequency in matched control group
|
Frequency in 1000 Genomes Database
|
Frequency in ExAC Database
|
“In silico” analysis of pathogenicity
a
|
High conserved nucleotide
|
Protein domain
|
ClinVar
|
|||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
PolyPhen-2
|
SIFT
|
FATHMM
|
Mutation Taster
|
|||||||||||
Missense, nonsense mutation and deletion
|
||||||||||||||
p.V606I
|
MSH2
|
missense
|
G
|
A
|
0
|
0
|
0
|
P score 0.868
|
T score 0.09
|
D score − 2.61
|
D score 0.9999
|
yes phyloP: 0.91
|
1.DNA mismatch repair protein MutS,
2.DNA mismatch repair protein MSH2
|
no data
|
p.A733T
|
MSH2
|
missense
|
G
|
A
|
0
|
0
|
0.000005
|
D score 0.985
|
D score 0
|
D score − 2.3
|
D score 0.9999
|
yes phyloP: 0.91
|
1.DNA mismatch repair protein MutS
2.P-loop containing nucleotide triphosphate hydrolase
3.DNA mismatch repair protein MSH2
|
no data
|
p.I171V
|
NBN
|
missense
|
A
|
G
|
0
|
0.001
|
0.00013
|
D score 1.000
|
D score 0
|
T score 1
|
D score 0.9999
|
yes phyloP: 0.96
|
1.BRCT domain
2.nibrin
|
RCV000007360.2
RCV000007361.2
RCV000115797.5
|
p.L219Afs
|
NBN
|
deletion
|
ACAAA
|
0
|
0
|
0
|
0.000019
|
-
|
-
|
-
|
D score 0.9999
|
-
|
1.nibrin
|
RCV000133576.3
RCV000007353.2
|
p.R695C
|
ERCC2
|
missense
|
G
|
A
|
0
|
0
|
0.000000012
|
D score 0.995
|
D score 0
|
D score − 3.00
|
D score 0.9999
|
yes phyloP: 0.91
|
1.Helicase C terminal domain
|
RCV000120773.1
|
p.R1093*
|
RAD50
|
stopgain
|
C
|
T
|
0
|
0
|
0.000001
|
-
|
-
|
-
|
D score 0.9999
|
yes phyloP: 0.84
|
1.DNA repair prtoien Rad50
2.P-loop containing nucleoside triphosphate hydrolase
|
RCV000006230.1
|
p.L694*
|
FANCM
|
stopgain
|
T
|
G
|
0
|
0
|
0
|
-
|
-
|
-
|
D score 0.9999
|
yes phyloP: 0.99
|
1.ERCC4, restriction endonuclease type II-like,
|
no data
|
Splice site mutation
|
||||||||||||||
Human Splicing Finder
|
MaxEntScan
|
Splice Site Finder-like
|
Mutation Taster
|
|||||||||||
p.V738L
|
EXO1
|
splice site
|
G
|
C
|
0
|
0
|
0.00000086
|
D score 93.10
|
D score 8.44
|
D score 91.77
|
D score 0.9999
|
yes phyloP: 0.89
|
-
|
no data
|
NBN c.511A>G and c.657_661del5 variants analysis
Whole exome sequencing analysis
Characteristics of patients and tumors with molecular variants in DNA repair genes
Patient ID
|
Identified variant/gene
|
Metastases
|
Histologic subtype
|
Molecular subgroup
|
Treatment Protocol
|
Status
a
|
Rare adverse events grade 4 on chemotherapy
|
Drug in the regimen during the incidence of rare adverse events grade 4
|
The course of chemotherapy
|
---|---|---|---|---|---|---|---|---|---|
1.
|
p.V606I/
MSH2
|
YES
|
classic
|
4
|
HR
|
ADF
|
NO
|
-
|
-
|
2.
|
p.A733T/
MSH2
|
YES
|
LCA
|
Non-WNT/SHH (3 or 4)
|
For relapse
|
DoD
|
Pneumonia
|
Irinotecan, Dacarbazine
|
pre-irradiation chemotherapy
|
3.
|
p.R1093* /
RAD50
|
NO
|
classic
|
3
|
HR
|
ADF
|
Central nervous system toxicity
|
Etoposide, Ifosphamide, Cisplatin
|
pre-irradiation fourth course of chemotherapy
|
4.
|
p.Lys219fs*19/
NBN
|
YES
|
classic
|
4
|
HR
|
ADF
|
no data
|
-
|
-
|
5.
b
|
p.Lys219fs*19/
NBN
|
NO
|
classic
|
WNT
|
HR
|
ADF
|
NO
|
-
|
-
|
6.
b
|
p.Lys219fs*19/
NBN
|
YES
|
classic
|
no data
|
<3 yrs
|
DoD
|
Pneumonia
|
Vincristin, Etoposide, Cisplatin
|
first course of chemotherapy
|
7.
|
p.Lys219fs*19/
NBN
|
YES
|
LCA
|
4
|
HR
|
DoD
|
NO but secondary AML M5 4 yrs. after diagnosis
|
-
|
-
|
8.
b
|
p.Lys219fs*19/
NBN
|
NO
|
classic
|
Non-WNT/SHH (3 or 4)
|
SR
|
ADF
|
NO
|
-
|
-
|
9.
|
p.Lys219fs*19/
NBN
|
NO
|
classic
|
4
|
HR
|
DoD
|
NO
|
-
|
-
|
10.
|
p.I171V/
NBN
|
YES
|
classic
|
4
|
HR
|
ADF
|
NO
|
-
|
-
|
11.
|
p.I171V/
NBN
|
NO
|
classic
|
no data
|
<3 yrs
|
DoD
|
Central nervous system toxicity
|
Vincristin, Etoposide, Endoksane, Cisplatin
|
after two courses of chemotherapy
|
12.
b
|
p.I171V/
NBN
|
YES
|
classic
|
no data
|
HR
|
DoD
|
Colitis with gastrointestinal bleeding/
|
Vincristin, Etoposide, Carboplatin
|
pre-irradiation first course of chemotherapy
|
13.
|
p.I171V/
NBN
|
NO
|
classic
|
4
|
HR
|
ADF
|
NO
|
-
|
-
|
14.
|
p.L694*/
FANCM
|
YES
|
LCA
|
4
|
HR
|
ADF
|
Central nervous system toxicity
|
Vincristine, Cisplatin, Lomustin
|
post radiation chemotherapy
|
15.
|
p.R695C/
ERCC2
|
NO
|
classic
|
Non-WNT/SHH (3 or 4)
|
SR
|
ADF
|
Colitis with gastrointestinal bleeding/
|
Vincristine, Etoposide, Carboplatin
|
pre-irradiation first course of chemotherapy
|
16
|
p.V738L/
EXO1
|
NO
|
classic
|
4
|
SR
|
ADF
|
Enterocolitis
|
Vincristine, Etoposide, Carboplatin
|
pre-irradiation first course of chemotherapy
|