Skip to main content

Table S1 Summary of germline mutations and loss of heterozygosity (LOH) in NF1-associated tumours

From: Neurofibromatosis type 1-associated tumours: Their somatic mutational spectrum and pathogenesis

Patient ID

Germline mutation

Type of germline mutation

LOH

LOH markers

Predicted extent of LOH

Evidence for genomic deletion? MLPA/CGHarrayCGH/FISH

Probable mechanism

No. samples with LOH

Reference

Dermal neurofibromas

        

T190.2

Exon 2 and 3 deletion

Two exon deletion

Yes

E5 RFLP, I12b,

IVS27A28.4, J1/J2,

EVI20, IVS38GT53.0,

3'NF1, C7CT1/2

(3'UTR), EW206,

EW207, D17S798,

D17S1868

NF1 and 3' flanking region

MLPA

Deletion

5/23

1

T190.6

  

Yes

E5 RFLP, I12b,

IVS27A28.4, J1/J2,

EVI20, IVS38GT53.0,

3'NF1, C7CT1/2

(3'UTR), EW206

NF1 and 3' flanking region

MLPA

Deletion

  

T190.11

  

Yes

E5 RFLP, I12b,

IVS27A28.4, J1/J2,

EVI20, IVS38GT53.0,

3'NF1, C7CT1/2

(3'UTR)

NF1 and 3' flanking region

MLPA

Deletion

  

T190.17

  

Yes

E5 RFLP, I12b,

IVS27A28.4, J1/J2

Intragenic NF1

MLPA

Deletion

  

T190.18ii

  

Yes

E5 RFLP

Intragenic NF1

MLPA

Deletion

  

T206.1

Ex4b:

c.499_502delTGTT;

p.C167GnfsX9

4 bp

deletion

(FS)

 

LOH

 

NIA

  

Unpublished data, Cardiff

T206.2

   

LOH

     

T206.3

   

LOH

     

L002_3

Ex9: c.1246C > T;

p.Arg416X

Nonsense

Yes

rs29001484, rs4583306,

NF1 germline mutation,

rs2055091, rs11869264

NF1

Array CGH

Deletion

6/28

2

L002_5

  

Yes

rs29001484, rs4583306,

NF1 germline mutation,

rs2055091, rs11869264

NF1

Array CGH

Mitotic recombination

  

L002_12

  

Yes

rs29001484, rs4583306,

NF1 germline mutation,

rs2055091, rs11869264

NF1

Array CGH

Mitotic recombination

  

L002 C

  

Yes

NS

 

NIA

 

3/38

3

T473.1A

Ex10b: c.1413-

1414delAG;

p.Lys471AsnfsX4

2 bp

deletion

(FS)

Yes

HHH202, J1J2, IVS27,

EV120, IVS38

NF1

MLPA

Mitotic recombination

22/89

4

T473.1C

  

Yes

HHH202, J1J2, EV120

NF1

MLPA

Mitotic recombination

  

T473.3

  

Yes

J1J2, EV120, IVS38

NF1

MLPA

Mitotic recombination

  

T473.5

  

Yes

HHH202, J1J2, EV120,

IVS38

NF1

MLPA

Mitotic recombination

  

T473.7

  

Yes

J1J2, EV120

NF1

MLPA

Mitotic recombination

  

T473.8

  

Yes

HHH202, J1J2, EV120,

IVS38, 3'NF1, EW207,

D17S949, D17S1822

NF1 and 3'

flanking

region

MLPA

Mitotic recombination

  

T473.10

  

Yes

J1J2, EV120, IVS38

NF1

MLPA

Mitotic recombination

  

T473.14

  

Yes

J1J2, EV120, IVS38,

3'NF1, EW207,

D17S949, D17S1822

NF1 and 3'

flanking

region

MLPA

Mitotic recombination

  

T473.15

  

Yes

J1J2, EV120, IVS38,

3'NF1

NF1

MLPA

Mitotic recombination

  

T473.16

  

Yes

J1J2, EV120, IVS38,

3'NF1, EW207,

D17S949,

D17S1822

NF1 and 3'

flanking

region

MLPA

Mitotic recombination

  

T473.21

  

Yes

J1J2, EV120

NF1

MLPA

Mitotic recombination

  

T473.35

  

Yes

EV120, IVS38

Intragenic NF1

MLPA

Mitotic recombination

  

T473.30

  

Yes

J1J2, EV120, IVS38,

3'NF1, EW207,

D17S949

NF1 and 3'

flanking

region

MLPA

Mitotic recombination

  

T473.32

  

Yes

J1J2, EV120

Intragenic NF1

MLPA

Mitotic recombination

  

T473.34

  

Yes

EV120, IVS38

Intragenic NF1

MLPA

Mitotic recombination

  

T225.1

Ex10b deletion [MLPA]

Single exon deletion

 

LOH

 

NIA

  

Unpublished data, Cardiff

T225.3

   

LOH

     

T68.2

Deletion exons 10b-19b

Partial gene deletion

Yes

UT172 - I38 206,207

Exon 5-3' region

NIA

  

Unpublished data, Cardiff

T68.3

  

Yes

UT172 - I38 206,207

Exon 5-3' region

    

CLJ1N

Ex13: c.2041C > T;

p.Arg681X

Nonsense

Yes

NF1, D17S1800

NF1 and 3' flanking region

NIA

 

32/126

5, 6, 7

CLJ2N

  

Yes

D17S33, D17S1294,

NF1, D17S1800,

D17S798, D17S250,

D17S787, D17S802

Majority of 17q

    

T170.3

Ex13: c.2041C > T;

p.Arg681X

Nonsense

 

LOH

 

NIA

  

Unpublished data, Cardiff

T170.2

   

LOH

     

ABA1N

Ex13: c.2251 + 2T > C

Splice site

Yes

DS17S1824, D17S841,

D17S1294, D17S1863,

NF1, D17S1800,

D17S1880, D17S798,

D17S250, D17S787,

D17S802, D17S784,

D17S928

Majority of 17q

NIA

 

32/126

5, 6, 7

ABA2N

  

Yes

DS17S1824, D17S841,

D17S1294, D17S1863,

NF1, D17S1800,

D17S1880, D17S798,

D17S250, D17S787,

D17S802, D17S784,

D17S928

Majority of 17q

   

5, 6, 7

T436

Ex17: c.2875C > T;

p.Glu959X

Nonsense

Yes

IVS27, EV120, IVS38

Intragenic NF1

MLPA

Mitotic recombination

22/89

4

T439

  

Yes

IVS27, EV120, IVS38

Intragenic NF1

MLPA

Mitotic recombination

  

T440

  

Yes

IVS27, EV120, IVS38

Intragenic NF1

MLPA

Mitotic recombination

  

T444

  

Yes

HHH202, J1J2, IVS27,

EV120, IVS38, 3'NF1

NF1 and flanking regions

MLPA

Mitotic recombination

  

T446

  

Yes

IVS27, EV120, IVS38

Intragenic NF1

MLPA

Mitotic recombination

  

T448

  

Yes

HHH202, J1J2, IVS27,

EV120, IVS38, 3'NF1

NF1 and flanking regions

MLPA

Mitotic recombination

  

T454

  

Yes

IVS27, EV120, IVS38

Intragenic NF1

MLPA

Mitotic recombination

  

EAD1N

Ex20: c.3419C > G;

p.Ser1140X

Nonsense

Yes

NS

 

NIA

 

32/126

5, 6, 7

EAD2N

         

CSG3N

Ex21: c.3525_3526delAA;

p.Arg1176GlufsX17

2 bp deletion (FS)

Yes

D17S1824, D17S1294,

NF1, D17S1800,

D17S1880, D17S798

NF1 and flanking regions

NIA

 

32/126

5, 6, 7

CSG38N

  

Yes

NF1

NF1

    

CSN1N

  

Yes

D17S1294, NF1,

D17S1880, D17S798,

D17S250, D17S787,

D17S784, D17S928

Majority of 17q

    

CSG1N

  

Yes

D17S1294, NF1,

D17S1800, D17S1880,

D17S798, D17S250,

D17S787, D17S802

Majority of 17q

    

CSG2N

  

Yes

DS17S1824, D17S1294,

NF1, D17S1800,

D17S1880, D17S798,

D17S250, D17S787,

D17S802

Majority of 17q

    

CSG4N

  

Yes

DS17S1824, D17S1294,

NF1, D17S1800,

D17S1880, D17S798,

D17S250, D17S787,

D17S802

Majority of 17q

    

CSG5N

  

Yes

DS17S1824, D17S1294,

NF1, D17S1800,

D17S1880, D17S798,

D17S250, D17S787,

D17S802

Majority of 17q

    

CSG21N

  

Yes

DS17S1824, D17S1294,

NF1, D17S1800,

D17S1880, D17S798,

D17S250, D17S787,

D17S802

Majority of 17q

    

CSG25N

  

Yes

D17S1294, NF1,

D17S1800, D17S1880,

D17S798, D17S250,

D17S787, D17S802

Majority

of 17q

    

CSG42N

  

Yes

D17S1294, NF1,

D17S1800, D17S1880,

D17S798, D17S250,

D17S787, D17S802

Majority of 17q

    

CSG51N

  

Yes

DS17S1824, D17S1294,

NF1, D17S1800,

D17S1880, D17S798,

D17S250, D17S787,

D17S802

Majority

of 17q

FISH

Mitotic recombination

  

CSG52N

  

Yes

D17S33, DS17S1824,

D17S1294, NF1,

D17S1800, D17S1880,

D17S798, D17S250,

D17S787, D17S802

Majority

of 17q

NIA

   

CSG62N

  

Yes

NS

     

T177

Ex23.1: c.3916 C > T;

p.Arg1306X

Nonsense

 

LOH

 

NIA

  

Unpublished data, Cardiff

T213

   

LOH

     

NF44

UHG_1

Ex27a: c.4515-2A > T

Splice site

Yes

NF1 germline mutation,

rs9891455

NF1

Array CGH

Deletion

6/28

2

NF44

UHG_41

  

Yes

rs1018190

NF1

Array CGH

Deletion

  

T106.1

Ex37: c.6791dupA;

p.Tyr2264X

1 bp

insertion

(FS)

Yes

IVS38, 3'NF1-1

 

NIA

  

Unpublished data, Cardiff

T106.5

  

Yes

I41 - C3

3' UTR

    

T106.6

  

Yes

J1J2, EVI20, I38, I41,

C3C7, 206, 207

     

T210.2

Ex42: c.7458delC;

p.Tyr2487IlefsX5

1 bp

deletion

(FS)

   

30% WG

  

Unpublished data, Cardiff

T210.4

     

30% WG

   

T210.8

     

30% WG

   

T210.4

     

E8: 30% WG

   

T210.5

     

E8: exon duplication

   

HT1335

Ex4c: c.7237C > T;

p.Gln2413X

Nonsense

   

E16: del

  

Unpublished data, Cardiff

T128.30

Ex6: c.784C > T;

p.Arg262Cys

Missense

Yes

 

3' UTR to

3' region

NIA

  

Unpublished data, Cardiff

T192.4

Deletion of exons 6-27a [MLPA]

Multi-exon deletion

 

LOH: J1J2, EV120,

HHH202,

    

Unpublished data, Cardiff

p062

Ex7: c.910C > T;

p.Arg304X

Nonsense

 

LOH (6 samples)

 

Deletion (2 samples)

  

Unpublished data, Cardiff

p082

Ex7: c.910C > T;

p.Arg304X

Nonsense

 

LOH (5 samples)

 

Deletion(5 samples)

   

ACF1N

Ex7: c.910C > T;

p.Arg304X

Nonsense

Yes

D17S841, D17S1294,

D17S1863, NF1,

D17S1880, D17S798,

D17S250, D17S802,

D17S784

Majority of 17q

FISH

Mitotic recombination

32/126

5, 6, 7

MIGS1N

Ex7: c.910C > T;

p.Arg304X

Nonsense

Yes

D171863, NF1,

D17S1800, D17S1880

NF1 and flanking regions

NIA

 

32/126

 

CAG1N

Ex7: c.979delCinsTT;

p.Leu327PhefsX3

Indel (FS)

Yes

NF1

Intragenic NF1

NIA

 

32/126

 

CAG3N

Ex7: c.979delCinsTT;

p.Leu327PhefsX3

Indel (FS)

Yes

NS

 

NIA

 

32/126

 

T199

Ex7: c.983_984delGT;

p.Cys324X

2 bp

deletion

(FS)

Yes

IVS12, J1J2

 

NIA

  

Unpublished data, Cardiff

NF56-2

Ex9: c.1246C > T;

p.Arg416X

Missense

Yes

Pin 1, RsaI, AluI, Pin 28,

530, NF1 3'UTR, Mfd

15

NF1 and flanking regions

NIA

 

1/6

8

T197A

Ex10a: c.1318C > T

p.Arg440X

Nonsense

 

LOH?

    

Unpublished data, Cardiff

CLT1N

Ex12a:

c.1754_1757delTAAC;

p.Thr586SerfsX19

4 bp deletion (FS)

Yes

D17S841, D17S1863,

NF1, D17S1800,

D17S1880, D17S787,

D17S802

Majority of 17q

  

32/126

 

p022

Ex12a:

c.1756_1759delACTA;

p.Thr586ValfsX18

4 bp deletion (FS)

 

LOH (9 samples)

 

Deletion (2 samples)

  

Unpublished data, Cardiff

p020

Ex13: c.2041C > T;

p.Arg681X

Nonsense

 

LOH (2 samples)

 

Deletion

(0 samples)

   

T141.5

Ex13: c.2233delA;

p.Ser745AlafsX2

1 bp

deletion

(FS)

Yes

202, 12b, IVS27, IVS38,

3'NF1

    

Unpublished data, Cardiff

p103

Ex15: c.2338A > C;

p.Thr780Pro

Missense

 

LOH (10 samples)

 

Deletion(3 samples)

  

Unpublished data, Cardiff

T22

Ex17: c.2851-2A > G

Splice site

Yes

 

3'UTR to 3' flanking regions

   

Unpublished data, Cardiff

NF253-UHG E

Ex17: c.2851-2A > G

Splice site

Yes

Not specific

 

NIA

 

3/38

3

L005 A

Ex18: c.3113 + 1G > A

Splice site

       

319T1

Ex19b: c.3208C > T;

p.Gln1070X

Nonsense

Yes

NF-exon5

Intragenic NF1

  

2/15

9

p023

Ex21: c.3525_3526delAA;

p.Arg1176SerfsX18

2 bp deletion (FS)

 

LOH (14 samples)

 

Deletion (5 samples)

  

Unpublished data, Cardiff

p011

Ex22: c.3826C > T;

p.Arg1276X

Nonsense

 

LOH (5 samples)

 

Deletion (1 sample)

   

MASG2N

Ex22: c.3870 + 1G > T

Splice site

Yes

NF1, D17S1880,

D17S798, D17S250,

D17S787

Majority of 17q

FISH

Mitotic recombination

32/126

5, 6, 7

T171

Ex23.2: c.4084 C > T;

p.Arg1362X

Nonsense

 

LOH

    

Unpublished data, Cardiff

p104

Ex25: c.4309G > T;

p.Glu1436X

Nonsense

 

LOH (3 samples)

 

Deletion

(0 samples)

  

Unpublished data, Cardiff

p078

Ex27a: c.4537C > T;

p.Arg1513X

Nonsense

 

LOH (6 samples)

 

Deletion

(0 samples)

   

p084

Ex27a: c.4572C > G;

p.Tyr1524X

Nonsense

 

LOH (2 samples)

 

Deletion

(0 samples)

   

p102

Ex29: c.5242C > T;

p.Arg1748X

Nonsense

 

LOH (5 samples)

 

Deletion

(2 samples)

   

p055

Ex30: c.5710 G > T;

p.Glu1904X

Nonsense

 

LOH (1 sample)

 

Deletion

(0 samples)

   

EMN1N

Ex30:

c.5749 + 332A > G

Splice site

Yes

NF1, D17S1800

NF1 and 3' flanking region

  

32/126

5, 6, 7

p027

Ex33: c.6226delG;

p.Ala2076GlnfsX13

1 bp deletion (FS)

 

LOH (1 sample)

 

Deletion (0 samples)

  

Unpublished data, Cardiff

p052

Ex37: c.6791_6792dupA;

p.Tyr2264X

1 bp duplication (FS)

 

LOH (1 sample)

 

Deletion (1 sample)

   

T23.6

Ex41:

c.7268_7269delCA;

p.Thr2423SerfsX2

2 bp deletion (FS)

Yes

EVI20, I38, I41, C3

 

NIA

  

Unpublished data, Cardiff

T100

Ex41: c.7267dupA;

p.Thr2426X

1 bp duplication (FS)

Yes

 

I38 to 3'UTR

   

Unpublished data, Cardiff

T164.1

Ex41: c.7285 C > T;

p.Arg2429X

Nonsense

 

LOH

    

Unpublished data, Cardiff

MAR2N

NI

NI

Yes

NF1, D17S1800

NF1 and 3' flanking region

NIA

 

32/126

5, 6, 7

MOPT2N

NI

NI

Yes

D17S1824, D17S1294,

D171863, NF1,

D17S1800, D17S1880

NF1 and flanking regions

    

NGL1N

NI

NI

Yes

D17S841, D17S1294,

NF1, D17S1800,

D17S1880, D17S798,

D17S250, D17S802,

D17S784, D17S928

Majority of 17q

    

JRR2N

NI

NI

Yes

D17S1294, D17S1863,

NF1, D17S1800,

D17S1880, D17S798,

D17S250, D17S787

Majority of 17q

    

SLC1N

NI

NI

Yes

D17S33, DS17S1824,

D17S841, D17S1294,

NF1, D17S1880,

D17S798, D17S250,

D17S784, D17S928

Majority of 17q

    

HT1377.1

NI

NI

Yes

     

Unpublished data, Cardiff

HT1377.2

NI

NI

Yes

  

NIA

   

T109.4

NI

NI

Yes

I38, I41, 206

3' region

    

T167.c

NI

NI

Yes

IVS27, IVS38, 3'NF1

     

T192.1

NI

NI

Yes

202, IVS12, J1J2, IVS27

     

T197

NI

NI

Yes

J1J2

     

T227.2

NI

NI

Yes

IVS12, J1J2

     

T230.2

NI

NI

Yes

202, IVS12, IVS27

     

T232.2

NI

NI

Yes

J1J2

     

T241

NI

NI

Yes

J1J2

     

NF253_32

NI

NI

Yes

rs1018190, rs9891455,

rs8074061

NF1

Array CGH

Mitotic recombination

6/28

2

T224.1

NI

NI

 

LOH

 

NIA

  

Unpublished data, Cardiff

T162

NI

NI

 

LOH

     

T172

NI

NI

 

LOH

     

T179.1

NI

NI

 

LOH

     

T204.2

NI

NI

 

LOH

     

T224.2

NI

NI

 

LOH

     

T173.1

NI

NI

 

LOH

     

T179.2

NI

NI

 

LOH

     

T1281.2

NI

NI

 

LOH

     

T1281.4

NI

NI

 

LOH

     

T220

NI

NI

 

LOH

     

T221

NI

NI

 

LOH

     

T223

NI

NI

 

LOH

     

T258.1

NI

NI

 

LOH

     

T258.2

NI

NI

 

LOH

     

SCs from cutaneous neurofibromas

        

T543.2

Ex4a:

c.373delGinsATGTGT;

p.Arg125HisfsX4

Indel (FS)

Yes

J1J2-3'NF1

    

Unpublished data, Cardiff

T536A

Ex40: c.7127_7258del132

[Exon 40 deletion?]

132 bp deletion (FS)

Yes

J1J2-IVS38

 

NIA

  

Unpublished

data, Cardiff

T541.2

  

Yes

EV120-3'NF1

     

T541.4

  

Yes

EV120-3'NF1

     

T539

90 kb Deletion

Genomic deletion

   

Duplication:

Ex19b-25

  

Unpublished data, Cardiff

PNFs

         

37a

Ex24: c.4268A > G;

p.Lys1423Arg

Missense

Yes

HHH202, E5, I12b,

EVI20,3'NF1-1

Complete gene deletion

(1.4 Mb)

NF1

(1.4 Mb)

MLPA

Genomic deletion

20/29

10

37b

  

Yes

IVS27, EVI20, IVS38,

3'NF1-1 Probable gene

deletion

NF1 and 3' flanking

region

MLPA

Genomic deletion

20/29

10

T210.2

PNF

Ex42: c.7458delC;

p.Tyr2486IlefsX15

1 bp deletion (FS)

Yes

LOH detected in only 30% of cells

  

30% whole gene deletion

 

Unpublished data, Cardiff

T261

PNF

Ex3: c.288 + 1 delG

1 bp deletion at a splice site

LOH IVS38

      

605-1

Ex4a: c.289-2A > G

Splice site

Yes

D17S975, IVS27TG24.8,

IVS27TG28.4,

D17S1166, D17S1880,

D17S907, D17S1788,

D17S1861, D17S1809,

D17S668, D17S928

NF1 and flanking regions

MLPA

Mitotic recombination

13/43

11

47/T411

Ex4a:

c.440_441GC > AA;

p.Cys147X

Nonsense

LOH IVS27,

IVS38,

3'NF1-1

IVS38, 3'NF1-1

NF1 and 3' flanking

region

NIA

 

20/29

10

8/T328

Ex4b: c.480-2A > G

Splice site

LOH:

IVS27, IVS38

IVS27, IVS38

Intragenic NF1

MLPA

Mitotic recombination

20/29

10

335-3

Ex4b: c.528T > A;

p.Asp176Glu

Missense

Yes

D17S2237,

IVS27TG24.8,

D17S1166, D17S1800

NF1

MLPA

Genomic deletion

13/43

11

59

Ex6: c.752dupA;

p.Asp241GlufsX7

Small Insertion (fs)

Yes

intron 38 marker 53.0

Intragenic NF1

NIA

 

1/38

12

T265.2

Ex9: c.1186-13delT

(Pathogenicity?)

1 bp deletion within a splice site

LOH ivs27,

ivs38

      

374-4

Ex10a: c.1318C > T;

p.Arg440X

Nonsense

Yes

IVS27TG24.8,

IVS27TG28.4,

D17S1166, D17S1880,

D17S907, D17S1861

NF1 and 3' flanking region

MLPA

Mitotic

recombination

13/43

11

14a/

T412

Ex13: c.2076C > G;

p.Tyr692X

Nonsense

I12B, 3' NF1

I12B, 3' NF1-1

NF1 and 3' flanking region

MLPA

Mitotic recombination

20/29

10

T263

Ex15: c.2326-2A > T

Splice site

LOH ivs27

[rest hom]

      

22/T394

Ex16: c.2446C > T;

p.Arg816X

Nonsense

IVS27

IVS 27, EVI20

Intragenic NF1

MLPA

Mitotic recombination

20/29

10

T437.2

Ex16: c.2497delT;

p.Ser833ProfsX7

1 bp deletion (FS)

1-6ex

1,2,3,4a,4b,4c,

6 deletion

  

NIA

   

T212

Ex16: c.2705deT;

p.Met902ArgfsX22

1 bp deletion (FS)

    

Ex1-Ex 41

deletion

[variable ?]

  

18/T298

Ex18: c.3113 + 1G > A

Splice site

LOH

:HHH202,

IVS 27

IVS 27

Intragenic

NF1

MLPA

Inconclusive

20/29

10

30/T342

Ex19a: c.3123G > T;

p.Met1041Ile

Missense

Yes

Determined by MLPA

NF1

(1.4 Mb)

MLPA

Genomic

deletion

20/29

10

5

Ex20:

c.345&_3460delCTCA;

p.Leu1153MetfsX3

4 bp

deletion

(FS)

Yes

NF1 gene

NF1

  

1/3

13

23/

T373.2

Ex22: c.3826C > T;

p.Arg1276X

Nonsense

WG deletion

[mixed cell

population]

IVS 27, IVS38

Intragenic

NF1

MLPA

Inconclusive

20/29

10

452T

Ex23.2: c.4084C > T;

p.Arg1362X

Nonsense

Yes

NF-exon5 RFLP, NF-

(GATN)n intron 26, NF-

Alu(AAAT)n(i27b), NF-

EVI2B RFLP(i27b), NF-

EVI2A RFLP(i27b), NF-

IVSAC28.4(i27b), NF-

Evi-20, NF-

IVS38TG53.0, NF intron

41 RFLP, D17S57

(EW206), D17S250,

D17S1301, D17S384

NF1 and

3' flanking

region

NIA

 

4/10

9

27/T301

Ex23.2: c.4095C > A;

p.Cys1365X

Nonsense

Yes

Determined by MLPA

Intragenic

NF1

MLPA

Genomic

deletion

20/29

10

T330

Ex24: c.4267A > G;

p.Lys1423Glu

Missense

IVS27

  

NIA

   

6/T362/

T395

Ex24: c.4268A > G;

p.Lys1423Arg

Missense

Yes

EW206, EW207

Intragenic

NF1

MLPA

Inconclusive

20/29

 

T362

PNF

Ex24: c.4268A > G;

p.Lys1423Arg

Missense

LOH:

HHH202, E5,

I12b, EVI20,

3'NF

  

NIA

   

T395

PNF

Ex24: c.4268A > G;

p.Lys1423Arg

Missense

LOH:IVS27,

EVI20, IVS38,

3'NF1-1

      

317-1

Ex25: c.4270-2A > G

Splice site

Yes

IVS27TG24.8,

IVS27TG28.4,

D17S1166

NF1

MLPA

Genomic

deletion

13/43

11

T393

Ex27a: c.4537C > T;

p.Arg1513X

Nonsense

    

Whole gene

deletion

  

26/T300

Ex29:

c.5227_5229delGTAinsT;

p.Val1743TyrfsX17

Indel (FS)

Yes

Determined by MLPA

NF1

(1.4 Mb)

MLPA

Genomic

deletion

20/29

10

338-2

Ex29: c.5290delG;

p.Ala1764LeufsX8

1 bp

deletion

(FS)

Yes

D17S783, D17S975,

IVS27TG28.4,

D17S1166, D17S1880

NF1 and

flanking

regions

MLPA

Genomic

deletion

13/43

11

952-8

Ex30: c.5749 + 4delA

Splice site

Yes

D17S975, D17S1880,

D17S907, D17S1788,

D17S1861, D17S1809,

D17S668, D17S928

NF1 and

flanking

regions

MLPA

Genomic

deletion

  

34/T392

Ex31:

c.5750_5754dupGTATT;

p.Glu1919ValfsX4

5 bp

duplication

(FS)

Yes

EVI20, IVS38, 3'NF1-1,

NF1 and

3' flanking

region

NIA

 

20/29

10

21/T357

Ex37: c.6791dupA;

p.Tyr2264X

1 bp

duplication

(FS)

LOH: EW206

EW206

Intragenic

NF1

MLPA

Mitotic

recombination

  

T375

Ex40: c.7237C > T;

p.Gln2413X

Nonsense

16Ex 16

deletion,

ex13 & 18

also lower

  

NIA

   

7

Ex41: c.7285C > T;

p.Arg2429X

Nonsense

Yes

HHH202, IVS27

Intragenic

NF1

MLPA

Mitotic

recombination

  

15/T407

Ex46: c.7926dupT;

p.Lys2643X

1 bp

duplication

(FS)

LOH 3'NF1-1,

EW206

3'NF1-1

NF1 and

3' flanking

region

MLPA

Inconclusive

  

c1 UK/

T56

Ex46: c.8035A > T;

p.Thr2679Ser

Missense

LOH IVS27

IVS27

Intragenic

NF1

NIA

   

T408

Segmental NF1 NI

NI

LOH: IVS27,

IVS38,

3'NF1-1

      

T377

Segmental NF1 NI

NI

WG deletion

      

39

Segmental NF1 NI

NI

Yes

Determined by MLPA

NF1

(1.1 Mb)

MLPA

Genomic

deletion

  

43

Segmental NF1 NI

NI

Yes

IVS27, IVS38, 3'NF1-1

NF1 and

3' flanking

region

MLPA

Mitotic

recombination

  

T385.1

NI

NI

Yes

  

NIA

  

Unpublished

data, Cardiff

T385.2

NI

NI

LOH/del

      

T316

NI

NI

Yes

LOH:

HHH202,

E5, I12b,

EVI20,3'NF,

C71/2, EW206

     

76, 45-95

NI

NI

Yes

IVS27AC28.4,

IVS27TG24.8,

IVS38GT53

Intragenic

NF1

NIA

 

8/14

14

x1, 47-95

NI

NI

Yes

IVS27AC28.4, M98509,

IVS38GT53

Intragenic

NF1

    

x1, 27-97

NI

NI

Yes

IVS27AC28.4, M98509,

IVS38GT53

Intragenic

NF1

    

293,

71-97

NI

NI

Yes

M98509, IVS27TG24.8,

IVS38GT53

Intragenic

NF1

    

293,

124-98

NI

NI

Yes

M98509, IVS27TG24.8,

IVS38GT54

Intragenic

NF1

    

290,

83-97

NI

NI

Yes

IVS27AC28.4,

IVS27TG24.8,

IVS38GT53

Intragenic

NF1

    

290,

121-98

NI

NI

Yes

IVS27AC28.4,

IVS27TG24.8,

IVS38GT53

Intragenic

NF1

    

292,

122-98

NI

NI

Yes

IVS27TG24.8,

IVS38GT53

Intragenic

NF1

    

PD-T1

NI

NI

Yes

NF-Alu(AAAT)n(i27b),

D17S1800

Intragenic

NF1

NIA

 

4/10

9

386T

NI

NI

 

NF-Alu(AAAT)

n(i27b), NF-

IVSAC28.4(i27b),

NF-Evi-20, NF-

IVS38TG53.0,

D17S1800

NF1

    

454T-V

NI

NI

Yes

NF-Alu(AAAT)n(i27b),

NF-EVI2B RFLP(i27b),

NF-IVSAC28.4(i27b),

NF-Evi-20, NF intron 41

RFLP, D17S57

(EW206), D17S1301

NF1

    

NF284-1

NI

NI

Yes

Exon 28 14bp

duplication marker

(specific

to germline

lesion found)

Intragenic

NF1

  

1/1

8

2654-97

NI

NI

Yes

Determined by FISH

Whole

chromosome

FISH

Genomic

deletion

1/11

15

385

NI

NI

Yes

D17S975, D17S1880,

D17S907, D17S1788,

D17S1861, D17S1809,

D17S668, D17S928

NF1 and

flanking

regions

MLPA

Mitotic

recombination

13/43

11

389-2

NI

NI

Yes

D17S975, D17S1307,

D17S2237,

IVS27TG28.4,

D17S1800, D17S1880,

D17S907, D17S1861,

D17S1809, D17S668,

D17S928

NF1 and

flanking

regions

MLPA

Mitotic

recombination

  

604-4

NI

NI

Yes

D17S1800, D17S1880,

D17S907, D17S1861,

D17S928

NF1 and

flanking

regions

MLPA

Mitotic

recombination

  

913-5

NI

NI

Yes

D17S2237,

IVS27TG24.8,

D17S1880, D17S1788,

D17S1861

NF1 and

3' flanking

region

MLPA

Genomic

deletion

  

612-1

NI

NI

Yes

D17S1307, D17S2237,

IVS27TG24.8,

D17S1166, D17S1800,

D17S1880

NF1 and

flanking

regions

MLPA

Genomic

deletion

  

337-5

NI

NI

Yes

D17S1307, D17S2237,

IVS27TG24.8,

D17S1166, D17S1800

NF1

MLPA

Genomic

deletion

  

390

NI

NI

Yes

IVS27TG24.8,

IVS27TG28.4,

D17S1166, D17S1800

NF1

MLPA

Genomic

deletion

  

49

NI

NI

Yes

HHH202, E5, I12b,

EVI20, 3'NF1-1, C71/2,

EW206

NF1

MLPA

Inconclusive

20/29

10

Spinal neurofibromas

         

1

Ex7: c.899T > C;

p.Leu300Pro

Missense

Yes

EVI20, IVS38

Intragenic

NF1

MLPA

Mitotic

recombination

8/22

16

7

Ex9: c.1186-13delT

(Pathogenicity?)

1 bp

deletion

(FS)

Yes

IVS27, IVS38

Intragenic

NF1

MLPA

Mitotic

recombination

  

3

Ex16: c.2410-2A > T

Splice site

Yes

IVS27

Intragenic

NF1

MLPA

Mitotic

recombination

  

11.1

Ex22: c.3827G > A;

p.Arg1276Glu

Missense

Yes

IVS38

Intragenic

NF1

MLPA

Mitotic

recombination

  

11.2

  

Yes

Deletion of exons

13 > 16

Intragenic

NF1

MLPA

Deletion

  

2

Ex23.2: c.4066G > A;

p.Glu1356Lys

Missense

Yes

27, 3'NF1

NF1

MLPA

Mitotic

recombination

  

10

Ex29: c.5242C > T;

p.Arg1748X

Nonsense

Yes

I12B, Alu1, J1J2 and

EVI20

Intragenic

NF1

MLPA

Mitotic

recombination

  

MPNSTs

         

T196.20

Deletion exons 2 and 3

Two exon

deletion

Yes

I12b, IVS27AC28.4,

EVI20(IVS27B),

IVS38GT53.0 (IVS38),

3'-NF1, C7/CT1/2

(3'-UTR), EW206

(3extragenic), EW207

(3'extragenic), D17S798

NF1 and

3' flanking

region

MLPA

Mitotic

recombination

2/11

1

T196.24

  

Yes

NF1 exon 5, I12b,

IVS27AC28.4,

EVI20(IVS27B),

IVS38GT53.0 (IVS38),

3'-NF1, C7/CT1/2

(3'-UTR), EW206

(3'extragenic), EW207

(3'extragenic)

NF1 and

3' flanking

region

MLPA

Genomic

deletion

2/11

1

13

Deletion exons 2 and 3

Two exon

deletion

Yes

Ex5, I12b, IVS27, EVI20,

IVS38,C7CT, EW206,

EW207,3'NF1

NF1 and

3' flanking

region

MLPA/CGH

array

Genomic

deletion

31/34

17

7

Ex4c: c.654 + 1G > T

Splice site

Yes

UT172, HH202, J1/J2,

EVI20

NF1

MLPA/CGH

array

Genomic

deletion

  

27

Ex8:

c.1133_1136delACTG;

p.Asp378AlafsX7

4 bp

deletion

(FS)

Yes

Ex5, J1J2,3'NF1

NF1 and

3' flanking

region

NIA

   

9

Ex11: c.1713G > A;

p.Trp571X

Nonsense

Yes

D17S182, I12b, J1/J2

Intragenic

NF1

    

10

  

Yes

UT172, HH202, J1/J2,

EVI20, > 2.2Mb

NF1

MLPA/CGH

array

Genomic

deletion

  

23

Ex12a: c.1318C > T;

p.Arg440X

Nonsense

Yes

HHH202, EVI20. IVS38

Intragenic

NF1

NIA

   

14

Ex12a:

c.1754_1757delTAAC;

p.Thr586ValfsX19

4 bp

deletion

(FS)

Yes

IVS27, 3'NF1

NF1 and

3' flanking

region

MLPA/CGH

array

Mitotic

recombination

  

12

Ex13: c.2002-14C > G

Splice site

Yes

I12b, IVS27, EVI20,

IVS38, 3'NF

NF1 and

3' flanking

region

MLPA/CGH

array

Genomic

deletion

  

43

Ex13: c.2041C > T;

p.Arg681X

Nonsense

Yes

Determined by MLPA

NF1

MLPA

Duplication

mitotic

recombination

6/25

18

15

Ex16: c.2497delT;

p.Ser833ProfsX7

1 bp

deletion

(FS)

 

Intragenic Deletion

(Exons 1-6) MLPA

Intragenic

NF1

MLPA/CGH

array

Genomic

deletion

31/34

17

25

Ex16: c.2705delT;

p.Met902ArgfsX22

1 bp

deletion

(FS)

Yes

Intragenic deletion

(exons1-41) MLPA

Intragenic

NF1

MLPA/CGH

array

Genomic

deletion

  

17

Ex20:

c.3457_3460delCTCA;

p.Leu1153MetfsX3

4 bp

deletion

(FS)

   

NIA

   

18

  

Yes

3'NF1

Intragenic

NF1

MLPA/CGH

array

Genomic

deletion

  

459T1

Ex21: c.3684delC;

p.Asn1229MetfsX11

1 bp

deletion

(FS)

Yes

TP53(INTRON1),

TP53(INTRON6), NF-

(GATN)n INTRON26,

NF-IVSAC28.4(i27b),

D17S57, D17S250,

D17S1301, D17S784

Whole

chromosome

NIA

 

3/5

9

8

Ex22: c.3732delT;

p.Thr1245Leufsx21

1 bp

deletion

(FS)

Yes

Int12, J1J2

Intragenic

NF1

  

31/34

17

64

Ex23.1: c.3368 + 1delG

1 bp

deletion at

a splice site

Yes

Determined by MLPA

NF1

MLPA

Genomic

deletion

6/25

18

56

Ex25: c.4276C > A;

p.Gln1426Lys

Missense

Yes

Determined by MLPA

NF1

MLPA

Duplication

mitotic

recombination

  

4

Ex27a: c.4537C > T;

p.Arg1513X

Nonsense

Yes

IVS27b

Intragenic

NF1

MLPA/CGH

array

Genomic

deletion

31/34

17

6

Ex28: c.5003insTG;

p.Tyr1668LeufsX7

2 bp

insertion

(FS)

Yes

I4b, J1J2, EVI20

NF1

MLPA/CGH

array

Genomic

deletion

  

21

Ex29: c.5234C > G;

p.Ser1745X

Nonsense

Yes

Partial gene deletion

Intragenic

NF1

MLPA/CGH

array

Genomic

deletion

  

19

Ex37: c.6792C > A;

p.Tyr2264X

Nonsense

Yes

I12b, IVS27, J1J2, EVI20,

IVS38, C7CT

NF1

MLPA/CGH

array

Genomic

deletion

  

24

Ex38: c.6961insC;

p.Leu2321ProfsX5

1 bp

duplication

(FS)

Yes

Determined by MLPA

NF1

MLPA

Genomic

deletion

6/25

18

1

Ex41:

c.7268_7269delCA;

p.Thr2423SerfsX2

2 bp

deletion

(FS)

Yes

Intron 41-30

Intragenic

NF1

MLPA/CGH

array

Genomic

deletion

31/34

17

58

NI

NI

Yes

HHH202, NF1, EW206

Intragenic

NF1

 

Genomic

deletion

6/11

19

52

NI

NI

Yes

HHH202, NF1, EW206,

EW207

Intragenic

NF1

 

Genomic

deletion

  

22

NI

NI

Yes

HHH202

Intragenic

NF1

 

Genomic

deletion

  

8

NI

NI

Yes

EW206, EW207

Intragenic

NF1

 

Genomic

deletion

  

2

NI

NI

Yes

p144D6, pYNZ22.1,

pYNH37.3, EW503

NF1 region

and some

17p

 

Genomic

deletion

5/6

20

3

NI

NI

Yes

EW503, EW301 (B),

EW301 (T)

Intragenic

NF1

 

Genomic

deletion

  

4

NI

NI

Yes

p144D6, pYNZ22.1,

pYNH37.3, EW503,

EW301 (T), pHHH202,

EW207 (B), pTHH59

Whole

chromosome

 

Genomic

deletion

  

5

NI

NI

Yes

p144D6, pYNZ22.1,

pYNH37.3, EW503,

EW301 (B), EW301 (T),

pHHH202, EW207

(B)

Whole

chromosome

 

Genomic

deletion

  

10

NI

NI

Yes

p144D6, pYNZ22.1,

NF1 region

and some

17p

 

Genomic

deletion

  

88-3/14

NI

NI

Yes

D17S30, TP53, D17S71,

D17S8, D17S57

Whole

chromosome

G-banded

chromosome

17

duplication

Genomic

duplication

3/9

21

88-8

NI

NI

Yes

D17S30, D17S71

NF1

NIA

   

88-18

NI

NI

Yes

D17S30, D17S71,

D17S21, D17S33,

EVI2B, D17S82

Whole

chromosome

    

1

NI

NI

Yes

DI7S5, DI7SI, DI7SI37,

CRYBI, NF1, DI7S146

NF1 and

flanking

regions

NIA

 

2/5

22

4

NI

NI

Yes

DI7S34, DI7S5, DI7S146

NF1 and

flanking

regions

    

1

NI

NI

Yes

 

NF1

 

Genomic

deletion

1/1

23

1

NI

NI

Yes

NF1 alu, TP53 BHP53

Whole

chromosome

NIA

 

3/7

24

7

NI

NI

Yes

CRYB1, NF1 alu, TP53

BHP53

Whole

chromosome

    

8

NI

NI

Yes

D17S4, D17S74, NF1

e.31, NF1 alu

NF1

    

441T

NI

NI

Yes

TP53(INTRON6),

D17S1863,

D17twbch = S33, NF-

IVSAC28.4(i27b),

NF-Evi-20,

NF-IVS38TG53.0,

D17S1800, D17S73,

D17S1301

Whole

chromosome

NIA

 

3/5

9

396T4

NI

NI

Yes

NF-IVSAC28.4(i27b,

NF-IVS38TG53.0,

D17S57, D17S250,

D17S1301

NF1 and 3' flanking

region

    

2

NI

NI

Yes

NF1, P16, TP53

Whole

chromosome

NIA

 

5/8

13

5a

NI

NI

Yes

NF1, P16, TP53

Whole

chromosome

    

5b

NI

NI

Yes

NF1, P16, TP53

Whole

chromosome

    

6a

NI

NI

Yes

NF1, P16, TP53

Whole

chromosome

    

6b

NI

NI

Yes

NF1, P16, TP53

Whole

chromosome

    

2

NI

NI

Yes

Total gene deletion

NF1

MLPA/CGH

array

Genomic

deletion

31/34

17

5

NI

NI

Yes

Total gene deletion

NF1

MLPA/CGH

array

Genomic

deletion

  

24

NI

NI

Yes

EVI20, IVS27, IVS38

Intragenic

NF1

MLPA/CGH

array

Genomic

deletion

  

26

NI

NI

Yes

NF1 gene deletion

NF1

MLPA/CGH

array

Genomic

deletion

  

48

NI

NI

Yes

Determined by MLPA

NF1

MLPA

Genomic

deletion

6/25

18

86

NI

NI

Yes

Determined by MLPA

NF1

MLPA

Genomic

deletion

  

ACs

         

T65.1

Ex24: c.4267A > G;

p.Lys1423Glu

Missense

Yes

NS

NF1 3' flanking

region

NIA

 

1/1

25

57

NI

NI

Yes

EW206

Intragenic

NF1

NIA

 

1/1

19

58

NI

NI

Yes

D17S1849, D17S1863,

D17S1880

NF1 and 3'

flanking

region

NIA

 

2/4

26

76

NI

NI

Yes

D17S1863, D17S1880

NF1 and 3'

flanking

region

    

182

NI

NI

Yes

IVS27TG24.8

Intragenic

NF1

NIA

 

11/12

27

185

NI

NI

Yes

IVS27AC28.4,

IVS38GT53, D17S804

NF1 region

and some

17p

    

187

NI

NI

Yes

IVS27AC28.4,

IVS38GT53, D17S796

NF1 region

and some

17p

    

309

NI

NI

Yes

IVS38GT53, D17S796

NF1 region

and some

17p

    

330

NI

NI

Yes

IVS27AC28.4,

IVS38GT53, D17S520,

D17S796, D17S804

NF1 region

and some

17p

    

502

NI

NI

Yes

IVS27AC28.4, D17S520,

D17S796

NF1 region

and some

17p

    

519

NI

NI

Yes

IVS27TG28.4, M98509,

IVS27TG24.8,

IVS38GT53

Intragenic

NF1

    

297

NI

NI

Yes

IVS27TG28.4, M98509,

IVS38GT53

Intragenic

NF1

    

609

NI

NI

Yes

IVS27TG28.4, M98509

Intragenic

NF1

    

20954

NI

NI

Yes

IVS27TG24.8,

IVS38GT53

Intragenic

NF1

    

20962

NI

NI

Yes

IVS27AC28.4, M98509,

IVS38GT53

Intragenic

NF1

    

1

NI

NI

Yes

Homozygous

 

FISH

Unknown

3/4

28

9

NI

NI

Yes

Homozygous

 

FISH

Genomic

deletion

  

10

NI

NI

Yes

Homozygous

 

FISH

Genomic

deletion

  

Gastric carcinoid tumours

         

1

Ex37: c.6841C > T;

p.Gln2281X

Nonsense

Yes

IVS27TG24, D17S250

Intragenic

NF1

NIA

 

1/1

29

GISTs

         

1

Ex27a: c.4537C > T;

p.Arg1513X

Nonsense

Yes

D17S841, Alu, IVS27GT,

IVS27CAGT, IVS38,

3'NF1-1, 3'NF1-2

NF1 and 3'

flanking

region

MLPA

Mitotic

recombination

1/1

30

NF1-3

Ex45: c.7807delG;

p.Aal2603LeufsX3

1 bp

deletion

(FS)

Yes

Alu, IVS27AC33.1,

IVS38GT53.0,

IVS27TG24.8

Intragenic

NF1

Array CGH

Genomic

deletion

1/7

3

JMML

         

D102

Ex4b: c.574C > T;

p.Arg192X

Nonsense

Yes

D17S925, D17S1800,

D17S1880, D17S855,

D17S1827, D17S787,

D17S948, D17S784

Majority

of 17q

SNP array

Mitotic

recombination-

UPD

4/5

31

D115

Ex13: c.2066delT;

p.Val689GlyfsX59

1 bp

deletion

(FS)

Yes

D17S925, D17S1800,

D17S1880, D17S855,

D17S1827, D17S787,

D17S948, D17S784

Majority

of 17q

SNP array

Mitotic

recombination-

UPD

  

D003

Ex22: c.3861_3862delCT;

p.Cys1288ValfsX21

2 bp

deletion

(FS)

Yes

D17S925, D17S1800,

D17S1880, D17S855,

D17S1827, D17S787,

D17S948, D17S784

Majority

of 17q

SNP array

Mitotic

recombination-

UPD

  

D126

Ex44: c.7699C > T;

p.Gln2567X

Nonsense

Yes

D17S925, D17S1800,

D17S1880, D17S855,

D17S1827, D17S787,

D17S948, D17S784

Majority

of 17q

SNP array

Mitotic

recombination-

UPD

  

1

NI

NI

Yes

D17S1975, D17S1294,

UT172, NF1,

D17S1800, D17S250,

D17S801, D17S939,

D17S836, D17S1806,

D17S1822, D17S1830

Majority

of 17q

FISH

Mitotic

recombination-

interstitial

isodisomy

(paternal)

10/10

32

2

NI

NI

Yes

D17S1975, D17S1294,

UT172, NF1,

D17S1800, D17S250,

D17S801, D17S939,

D17S836, D17S1806,

D17S1822, D17S1830

Majority

of 17q

FISH

Mitotic

recombination-

interstitial

isodisomy

(paternal)

  

3

NI

NI

Yes

D17S1294, UT172,

NF1, D17S1800,

D17S250, D17S801,

D17S939, D17S836,

D17S1806, D17S1822,

D17S1830

Majority

of 17q

FISH

Mitotic

recombination

interstitial

isodisomy

(paternal)

  

4

NI

NI

Yes

D17S1975, D17S1294,

UT172, NF1,

D17S1800, D17S250,

D17S801, D17S939,

D17S836, D17S1806,

D17S1822, D17S1830

Majority

of 17q

FISH

Mitotic

recombination-

interstitial

isodisomy

(maternal)

  

5

NI

NI

Yes

D17S1975, D17S1294,

UT172, NF1,

D17S1800, D17S250,

D17S801, D17S939,

D17S836, D17S1806,

D17S1822

Majority of

17q

FISH

Mitotic

recombination-

interstitial

isodisomy

(maternal)

  

6

NI

NI

Yes

D17S1878, D17S33,

D17S1975, D17S1294,

UT172, NF1,

D17S1800, D17S250,

D17S801, D17S939,

D17S836, D17S1806,

D17S1822, D17S1830

Majority of

17q

FISH

Mitotic

recombination-

interstitial

isodisomy

(maternal)

  

7

NI

NI

Yes

D17S1294, UT172,

NF1, D17S1800,

D17S250, D17S801,

D17S939, D17S836,

D17S1806, D17S1822,

D17S1830, D17S928

Majority of

17q

FISH

Mitotic

recombination-

interstitial

isodisomy

(maternal)

  

8

NI

NI

Yes

D17S1975, D17S1294,

UT172, NF1,

D17S1800, D17S250,

D17S801, D17S939,

D17S836, D17S1806,

D17S1822, D17S1830,

D17S928

Majority of

17q

FISH

Mitotic

recombination-

interstitial

isodisomy

(paternal)

  

9

NI

NI

Yes

NF1, D17S1800

Intragenic

NF1

FISH

Genomic

deletion

  

10

NI

NI

Yes

NF1, D17S1800

Intragenic

NF1

FISH

Genomic

deletion

  

D419

NI

NI

Yes

D17S925, D17S1841,

D17S1294, D17S1863,

D17S1849, D17S1166,

D17S1800, D17S1880,

D17S1818, D17S855,

D17S1827, D17S787,

D17S948, D17S785,

D17S784

Majority of

17q

MLPA

Mitotic

recombination-

UPD

5/10

33

D561

NI

NI

Yes

D17S1294, D17S1863,

D17S1849, D17S1166,

D17S1800, D17S1880,

D17S1818, D17S855,

D17S1827, D17S787,

D17S948, D17S785,

D17S784

Majority of

17q

MLPA

Mitotic

recombination-

UPD

  

D378

NI

NI

Yes

D17S1294, D17S1863,

D17S1849, D17S1166,

D17S1800, D17S1880,

D17S1818, D17S855,

D17S785

Majority of

17q

Array CGH

Mitotic

recombination-

UPD

  

D341

NI

NI

Yes

D17S1849, D17S1166,

D17S1800, D17S1880

NF1 and

flanking

regions

Array CGH

Genomic

deletion

  

D566

NI

NI

Yes

D17S1849, D17S1166,

D17S1800, D17S784

NF1 and

flanking

regions

Array CGH

Genomic

deletion

  

PCs

         

1

NI

NI

Yes

DI7S34, DI7S137,

CRYBI, NF1, DI7S4

Whole

chromosome

NIA

 

7/7

22

2

NI

NI

Yes

CRYBI, DI7S33, NF1,

DI7S55, DI7S4

NF1

    

3

NI

NI

Yes

DI7S5, DI7S134,

DI7S58, DI7S33

Whole

chromosome

    

4

NI

NI

Yes

DI7S33, NF1

Intragenic

NF1

    

5

NI

NI

Yes

DI7S71, NF1, DI7S226

Whole

chromosome

    

6L

NI

NI

Yes

DI7S5, NF1, DI7S145,

DI7S226

Whole

chromosome

    

6R

NI

NI

Yes

DI7S5, NF1, DI7S145,

DI7S226

Whole

chromosome

    

1

NI

NI

Yes

TP53-BAM, TP53 AccII,

NF1-AE25 (BgIII) SNP,

THH59-TaqI,

THH59-PvuII

Majority of

17

NIA

 

2/7

34

1

NI

NI

Yes

NF1-AE25 (BgIII) SNP,

THH59-TaqI, THH59-

PvuII-adrenal corticoid

tumour

NF1 and 3'

flanking

region

    

NS

NI

NI

Yes

    

14/21

35

Glomus tumours

         

NF1-G2

Ex42: c.7395_7404del10;

p.Thr2466SerfsX33

10 bp

deletion

(FS)

Yes

Introns 27-38

Intragenic

NF1

Array CGH

Mitotic

recombination

1/7

36

  1. CGH, comparative genomic hybridisation; array CGH, high resolution CGH; FS, frame shift; NI, not informative; WG, whole gene; NA, not available; UPD, uniparental disomy; MLPA, multiplex ligation-dependent probe amplification; FISH, fluorescent in situ hybridisation.
  2. Supplementary Table References
  3. 1. Spurlock, G., Griffiths, S., Uff, J. and Upadhyaya, M. (2007), 'Somatic alterations of the NF1 gene in an NF1 individual with multiple benign tumours (internal and external) and malignant tumour types', Fam. Cancer Vol. 6, pp. 463-471.
  4. 2. De Raedt, T., Maertens, O., Chmara, M., Brems, H. et al. (2006), 'Somatic loss of wild type NF1 allele in neurofibromas: Comparison of NF1 microdeletion and non-microdeletion patients', Genes Chromosomes Cancer Vol. 45, pp. 893-904.
  5. 3. Maertens, O., Brems, H., Vandesompele, J., De Raedt, T. et al. (2006), 'Comprehensive NF1 screening on cultured Schwann cells from neurofi-bromas', Hum. Mutat. Vol. 27, pp. 1030-1040.
  6. 4. Thomas, L., Kluwe, L., Chuzhanova, N., Mautner, V. et al. (2010), 'Analysis of NF1 somatic mutations in cutaneous neurofibromas from patients with high tumor burden', Neurogenetics Vol. 11, pp. 391-400.
  7. 5. Serra, E., Puig, S., Otero, D., Gaona, A. et al. (1997), 'Confirmation of a double-hit model for the NF1 gene in benign neurofibromas', Am. J. Hum. Genet. Vol. 61, pp. 512-519.
  8. 6. Serra, E., Ars, E., Ravella, A., Sánchez, A. et al. (2001), 'Somatic NF1 mutational spectrum in benign neurofibromas: mRNA splice defects are common among point mutations', Hum. Genet. Vol. 108, pp. 416-429.
  9. 7. Serra, E., Rosenbaum, T., Nadal, M., Winner, U. et al. (2001), 'Mitotic recombination effects homozygosity for NF1 germline mutations in neu-rofibromas', Nat. Genet. Vol. 28, pp. 294-296.
  10. 8. Eisenbarth, I., Beyer, K., Krone, W. and Assum, G. (2000), 'Toward a survey of somatic mutation of the NF1 gene in benign neurofibromas of patients with neurofibromatosis type 1', Am. J. Hum. Genet. Vol. 66, pp. 393-401.
  11. 9. Rasmussen, S., Overman, J., Thomson, S., Colman, S. et al. (2000), 'Chromosome 17 loss-of-heterozygosity studies in benign and malignant tumors in neurofibromatosis type 1', Genes Chromosomes Cancer Vol. 28, pp. 425-431.
  12. 10. Upadhyaya, M., Spurlock, G., Monem, B., Thomas, N. et al. (2008), 'Germline and somatic NF1 gene mutations in plexiform neurofibromas', Hum. Mutat. Vol. 29, pp. E103-E111.
  13. 11. Steinmann, K., Kluwe, L., Friedrich, R., Mautner, V. et al. (2009), 'Mechanisms of loss of heterozygosity in neurofibromatosis type 1-associated plexiform neurofibromas', J. Invest. Dermatol. Vol. 129, pp. 615-621.
  14. 12. Däschner, K., Assum, G., Eisenbarth, I., Krone, W. et al. (1997), 'Clonal origin of tumor cells in a plexiform neurofibroma with LOH in NF1 intron 38 and in dermal neurofibromas without LOH of the NF1 gene', Biochem. Biophys. Res. Commun. Vol. 234, pp. 346-350.
  15. 13. Frahm, S., Mautner, V., Brems, H., Legius, E. et al. (2004), 'Genetic and phenotypic characterization of tumor cells derived from malignant peripheral nerve sheath tumors of neurofibromatosis type 1 patients', Neurobiol. Dis. Vol. 16, pp. 85-91.
  16. 14. Kluwe, L., Friedrich, R. and Mautner, V. (1999), 'Allelic loss of the NF1 gene in NF1-associated plexiform neurofibromas', Cancer Genet. Cytogenet. Vol. 113, pp. 65-69.
  17. 15. De Luca, A., Buccino, A., Gianni, D., Mangino, M. et al. (2003), 'NF1 gene analysis based on DHPLC', Hum. Mutat. Vol. 21, pp. 171-172.
  18. 16. Upadhyaya, M., Spurlock, G., Kluwe, L., Chuzhanova, N. et al. (2009), 'The spectrum of somatic and germline NF1 mutations in NF1 patients with spinal neurofibromas', Neurogenetics Vol. 10, pp. 251-263.
  19. 17. Upadhyaya, M., Kluwe, L., Spurlock, G., Monem, B. et al. (2008), 'Germline and somatic NF1 gene mutation spectrum in NF1-associated malignant peripheral nerve sheath tumors (MPNSTs)', Hum. Mutat. Vol. 29, pp. 74-82.
  20. 18. Bottillo, I., Ahlquist, T., Brekke, H., Danielsen, S. et al. (2009), 'Germline and somatic NF1 mutations in sporadic and NF1-associated malignant peripheral nerve sheath tumours', J. Pathol. Vol. 217, pp. 693-701.
  21. 19. Skuse, G., Kosciolek, B. and Rowley, P. (1989), 'Molecular genetic analysis of tumors in von Recklinghausen neurofibromatosis: Loss of het-erozygosity for chromosome 17', Genes Chromosomes Cancer Vol. 1, pp. 36-41.
  22. 20. Menon, A., Anderson, K., Riccardi, V., Chung, R. et al. (1990), 'Chromosome 17p deletions and p53 gene mutations associated with the formation of malignant neurofibrosarcomas in von Recklinghausen neu-rofibromatosis', Proc. Natl. Acad. Sci. USA Vol. 87, pp. 5435-5439.
  23. 21. Glover, T., Stein, C., Legius, E., Andersen, L. et al. (1991), 'Molecular and cytogenetic analysis of tumors in von Recklinghausen neurofibroma-tosis', Genes Chromosomes Cancer Vol. 3, pp. 62-70.
  24. 22. Xu, W., Mulligan, L.M., Ponder, M.A., Liu, L. et al. (1992), 'Loss of NF1 alleles in phaeochromocytomas from patients with type I neurofi-bromatosis', Genes Chromosomes Cancer Vol. 4, pp. 337-342.
  25. 23. Legius, E., Marchuk, D., Collins, F. and Glover, T. (1993), 'Somatic deletion of the neurofibromatosis type 1 gene in a neurofibrosarcoma supports a tumour suppressor gene hypothesis', Nat. Genet. Vol. 3, pp. 122-126.
  26. 24. Lothe, R., Slettan, A., Saeter, G., Brøgger, A. et al. (1995), 'Alterations at chromosome 17 loci in peripheral nerve sheath tumors', J. Neuropathol. Exp. Neurol. Vol. 54, pp. 65-73.
  27. 25. Upadhyaya, M., Han, S., Consoli, C., Majounie, E. et al. (2004), 'Characterization of the somatic mutational spectrum of the neurofibro-matosis type 1 (NF1) gene in neurofibromatosis patients with benign and malignant tumors', Hum. Mutat. Vol. 23, pp. 134-146.
  28. 26. Gutmann, D., Donahoe, J., Brown, T., James, C. et al. (2000), 'Loss of neurofibromatosis 1 (NF1) gene expression in NF1-associated pilocytic astrocytomas', Neuropathol. Appl. Neurobiol. Vol. 26, pp. 361-367.
  29. 27. Kluwe, L., Hagel, C., Tatagiba, M., Thomas, S. et al. (2001), 'Loss of NF1 alleles distinguish sporadic from NF1-associated pilocytic astrocyto-mas', J. Neuropathol. Exp. Neurol. Vol. 60, pp. 917-920.
  30. 28. Gutmann, D., James, C., Poyhonen, M., Louis, D. et al. (2003), 'Molecular analysis of astrocytomas presenting after age 10 in individuals with NF1', Neurology Vol. 61, pp. 1397-1400.
  31. 29. Stewart, W., Traynor, J.P., Cooke, A., Griffiths, S. et al. (2007), 'Gastric carcinoid: Germline and somatic mutation of the neurofibromatosis type 1 Gene', Fam. Cancer Vol. 6, pp. 147-152.
  32. 30. Stewart, D., Corless, C., Rubin, B., Heinrich, M. et al. (2007), 'Mitotic recombination as evidence of alternative pathogenesis of gastrointestinal stromal tumours in neurofibromatosis type 1', J. Med. Genet. Vol. 44, p. e61.
  33. 31. Flotho, C., Steinemann, D., Mullighan, C., Neale, G. et al. (2007), 'Genome-wide single-nucleotide polymorphism analysis in juvenile mye-lomonocytic leukemia identifies uniparental disomy surrounding the NF1 locus in cases associated with neurofibromatosis but not in cases with mutant RAS or PTPN11', Oncogene Vol. 26, pp. 5816-5821.
  34. 32. Stephens, K., Weaver, M., Leppig, K., Maruyama, K. et al. (2006), 'Interstitial uniparental isodisomy at clustered breakpoint intervals is a frequent mechanism of NF1 inactivation in myeloid malignancies', Blood Vol. 108, pp. 1684-1689.
  35. 33. Steinemann, D., Arning, L., Praulich, I., Stuhrmann, M. et al. (2010), 'Mitotic recombination and compound-heterozygous mutations are predominant NF1-inactivating mechanisms in children with juvenile myelomonocytic leukemia and neurofibromatosis type 1', Haematologica Vol. 95, pp. 320-323.
  36. 34. Gutmann, D.H., Cole, J.L., Stone, W.J., Ponder, B.A. et al. (1994), 'Loss of neurofibromin in adrenal gland tumors from patients with neurofibro-matosis type I', Genes Chromosomes Cancer Vol. 10, pp. 55-58.
  37. 35. Bausch, B., Borozdin, W., Mautner, V.F., Hoffmann, M.M. et al. (2007), 'Germline NF1 mutational spectra and loss-of-heterozygosity analyses in patients with pheochromocytoma and neurofibromatosis type 1', J. Clin. Endocrinol. Metab. Vol. 92, pp. 2784-2792.
  38. 36. Brems, H., Park, C., Maertens, O., Pemov, A. et al. (2009), 'Glomus tumors in neurofibromatosis type 1: Genetic, functional, and clinical evidence of a novel association', Cancer Res. Vol. 69, pp. 7393-7401.
  39. 37. Wiest, V., Eisenbarth, I., Schmegner, C., Krone, W. et al. (2003), 'Somatic NF1 mutation spectra in a family with neurofibromatosis type 1: Toward a theory of genetic modifiers', Hum. Mutat. Vol. 22, pp. 423-427.
  40. 38. Sawada, S., Florell, S., Purandare, S., Ota, M. et al. (1996), 'Identification of NF1 mutations in both alleles of a dermal neurofibroma', Nat. Genet. Vol. 14, pp. 110-112.
  41. 39. John, A., Ruggieri, M., Ferner, R. and Upadhyaya, M. (2000), 'A search for evidence of somatic mutations in the NF1 gene', J. Med. Genet. Vol. 37, pp. 44-49.