Supplementary Table e1. Clinical and genetic data on the 37 participants from the WUSM

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1 Supplementary Data Supplementary Table e1. Clinical and genetic data on the 37 participants from the WUSM cohort. Supplementary Table e2. Specificity, sensitivity and unadjusted ORs for glioma in participants with (A) any mutation, (B) nonsense mutations or (C) truncating mutations in the 5' end of the NF1 gene (exons 1-26). Supplementary Table e3. Combined clinical and genetic information from 310 participants (101 glioma and 209 no-glioma participants), comprising individuals from the current study combined with those from the four previously-published datasets (Ars et al., 2003; Sharif et al., 2011, Bolcekova et al., 2013; Hutter et al., 2016). Supplementary Table e4. Calculations tables for adjusted ORs for glioma generated by metaanalyses in participants with (A) any mutation, (B) nonsense or (C) truncation mutations in the 5' end of the NF1 gene. Supplementary Table e5. Specificity, sensitivity, unadjusted ORs and adjusted ORs for optic glioma in participants with (A) any mutation, (B) nonsense mutations or (C) truncating mutations in the 5' end of the NF1 gene (exons 1-26 excluding the RAS-GAP domain). Supplementary Table e6. Specificity, sensitivity, unadjusted ORs and adjusted ORs for glioma in participants with (A) any mutation, (B) nonsense mutations or (C) truncating mutations in the 5' end of the NF1 gene (exons 1-34 including the RAS-GAP domain). Supplementary Table e7. Recurrent NF1 mutations in participants with NF1 that harbor different glioma diagnoses. 1

2 Table e1. Demographic information on participants from the WUSM cohort OPG, optic glioma; CG, cerebellar glioma; BSG, brainstem glioma; TG, temporal lobe glioma; IF indel, in-frame insertion/deletion; FS del, frameshift deletion; FS ins, frameshift insertion. Omission of the three non-optic pathway glioma (OPG) tumors did not change the conclusions of this study. 2

3 Table e2. Specificity, sensitivity and unadjusted odds ratios for glioma in participants with NF1 and glioma P values in bold indicate significance at the p<0.05 level. 3

4 Table e3. Combined clinical and mutation data Diagnosis Family History DNA change Exon Protein change Type Study glioma Y c.98-99delaa 2 p.lys33ser_fs FS del Sharif glioma N c.240_241deltc 3 p.gln83val_fsx23 FS del Bolcekova glioma Y c.291_479del 4 p.gln97val_fsx13 splice Bolcekova glioma N c.483dela 5 p.leu161phe X4 FS del Bolcekova glioma N c.499_502deltgtt 5 p.cys167gln_fsx10 FS del Bolcekova glioma? c.565a>t 5 p.lys189x nonsense Hutter glioma Y c.574c>t 5 p.arg192x nonsense Sharif glioma N c.580delc 5 FS del Ars glioma Y c.725delt 7 p.met242arg_fsx39 FS del Bolcekova glioma? c.731-1g>a i7 p.? splice Hutter glioma? c.889-2a>g i8 p.? splice Hutter glioma N c.910c>t 9 p.arg304x nonsense Bolcekova glioma? c.910c>t 9 p.arg304x nonsense Hutter glioma? c.910c>t 9 p.arg304x nonsense Hutter glioma N c.989insc 9 FS ins Ars glioma N c.989c>t 9 p.ala330val splice Bolcekova glioma Y c.998_999insa 9 p.tyr333x nonsense Bolcekova glioma Y c.998_999insa 9 p.tyr333x nonsense Bolcekova glioma N c.998_999insa 9 p.tyr333x nonsense Ars glioma N c.1011inst 9 FS ins Sharif glioma N c.1012g>a 9 p.asp338asn missense Sharif glioma Y c.1019inst 9 FS ins Ars glioma Y c.1149c>a 10 p.cys383x nonsense WUSM glioma? c.1224t>g 11 p.tyr408x nonsense Hutter glioma? c.1246c>t 11 p.arg416x nonsense Hutter glioma? c.1278g>a 12 p.trp426x nonsense Hutter glioma? c deltc 12 FS del Sharif glioma N c.1381c>t 12 p.arg461x nonsense Sharif glioma? c.1381c>t 12 p.arg461x nonsense Hutter glioma? c.1381c>t 12 p.arg461x nonsense Hutter glioma Y c t>a i12 Splice Ars glioma Y c.1466a>g 13 p.tyr489x nonsense Ars glioma? c.1466a>g 13 p.tyr489x nonsense Hutter glioma Y c.1497_98insa 13 p.ile500asn_fsx11 FS ins Bolcekova glioma Y c.1497_98insa 13 p.ile500asn_fsx11 FS ins Bolcekova glioma? c G>T i13 p.? splice Hutter glioma Y c delag 14 p.gln514arg_fsx43 FS del Ars glioma N c delag 14 p.gln514arg_fsx43 FS del WUSM 4

5 glioma Y c delgg 14 FS del Sharif glioma N c a>g i15 splice Sharif glioma? c a>g i15 p.? splice Hutter glioma? c.1722c>a 16 p.ser574arg missense Sharif glioma? c.1754_1757deltaac 16 p.thr586val_fsx18 FS del Hutter glioma N c.1756_59delacta 16 p.thr586val_fsx18 FS del Ars glioma N c.1756_59delacta 16 p.thr586val_fsx18 FS del Bolcekova glioma N c.1756_59delacta 16 p.thr586val_fsx18 FS del WUSM glioma? c.1782_1783delag 16 p.glu595asn_fsx14 FS del Hutter glioma? c.1842_ delTAA GG 16 p.ala548_lys615del splice Hutter glioma N c.1885g>a 17 p.gly629arg missense WUSM glioma N c.2041c>t 18 p.arg681x nonsense WUSM glioma Y c.2050c>t 18 p.gln684x nonsense WUSM glioma N c.2129dupt 18 p.arg711pro_fsx5 FS ins Bolcekova glioma N c.2173inst 18 FS ins Ars glioma N c g>a i19 p.arg752leu_fsx17 splice Bolcekova glioma N c.2407delc 20 p.gln803_fsx16 FS del WUSM glioma N c.2446c>t 21 p.arg816x nonsense Sharif glioma? c.2446c>t 21 p.arg816x nonsense Hutter glioma Y c.2540t>c 21 p.leu847pro missense Bolcekova glioma N c.2546delg 21 p.gly849glu_fsx29 FS del Bolcekova glioma N c.2559c>t 21 p.gln854x nonsense WUSM glioma N c.2619inst 21 p.lys874x nonsense Bolcekova glioma N c.2984_2988deltggtc 22 p.leu995_fsx22 FS del WUSM glioma? c _ insT i22 p.? splice Hutter glioma? c G>A i23 p.? splice Hutter glioma N c.3449c>a 26 p.ser1150x nonsense WUSM glioma? c.3456_3459delactc 26 p.leu1153met_fsx4 FS del Hutter glioma? c.3456_3459delactc 26 p.leu1153met_fsx4 FS del Hutter glioma? c.3456_3459delactc 26 p.leu1153met_fsx4 FS del Hutter glioma? c.3703c>t 27 p.gln1235x nonsense Hutter glioma N c g>c i27 splice Sharif glioma? c.3721c>t 28 p.arg1241x nonsense Hutter glioma Y c.3892c>t 29 p.gln1298x nonsense Bolcekova glioma Y c.3913deltinsgaa 29 p.leu1305glu_fsx5 FS del ins Bolcekova glioma? c.3916c>t 29 p.arg1306x nonsense Hutter glioma N c.3916c>t 29 p.arg1306x nonsense WUSM glioma N c.3975_4661del675nt p.leu1326_arg1554d el IF deletion Bolcekova glioma N c.4021c>t 30 p.gln1341x nonsense WUSM glioma N c.4111_4772del650nt p.val1372gln_fsx8 IF deletion Bolcekova glioma? c G>T i31 p.? splice Hutter 5

6 glioma? c.4277a>c 32 p.gln1426pro missense Hutter glioma? c.4537c>t 34 p.arg1513x nonsense Hutter glioma? c.4767_4769delacgins CT 35 p.arg1590x nonsense Hutter glioma N c.4922g>a 36 p.trp1641x nonsense WUSM glioma? c.5089_5090delca 36 p.ile1698arg_fsx3 FS del Hutter glioma? c.5113_5114delct 36 p.leu1705thr_fsx30 FS del Hutter glioma N c _5220 deltccaggttggttct ACTGCT i36 p.gly1737ser_fsx4 or p.gly1737leu_fsx3 deletion or splicing FS Bolcekova glioma Y c.5351insc 37 FS ins Ars glioma N c.5242c>t 37 p.arg1748x nonsense WUSM glioma? c.5839c>t 39 p.arg1947x nonsense Hutter glioma? c.5839c>t 39 p.arg1947x nonsense Hutter glioma? c.6524dupga 42 FS ins Sharif glioma Y c.6525_6528deltt 42 p.phe2176cysx44 FS del Bolcekova glioma? c.6787_6790delactt 45 p.tyr2264thr_fsx5 FS del Hutter glioma N c delttac 45 FS del Sharif glioma Y c.7096_7101delaacttt 47 p.2366_67delasnphe IF deletion Bolcekova glioma N c delca 48 FS del Ars glioma? c _ delT AA i49 p.? splice Hutter glioma Y c.7411c>t 50 p.gln2471x nonsense Sharif glioma? c.7528c>t 50 p.gln2510x nonsense Hutter glioma Y c.7702c>t 52 pgln2568x nonsense Ars glioma? c.7881_7882deltg 53 p.phe2629ser_fsx9 FS del Hutter 6

7 Diagnosis Family History DNA change Exon Protein change Type Study no glioma? c.47g>c 1 p.arg16pro missense Bolcekova no glioma? c.55g>t 1 p.glu19x nonsense Hutter no glioma N del13 2 FS del Ars no glioma Y c.204g>c 2 splice WUSM no glioma N c.204+1g/a i2 Splice Ars no glioma? c.204+2t>g i2 p.gln20del48aa splice Bolcekova no glioma? c.263_266delatac 3 p.thr89trp_fsx13 FS del Hutter no glioma N c insG i3 Splice Ars no glioma N c.347dela 4 FS del Ars no glioma Y c.350t>g 4 p.i117s Missense Ars no glioma Y c insct 4 FS ins Ars no glioma N c.446dela 4 FS del Ars no glioma? c.495_498deltgtt 5 p.cys167gln_fsx10 FS del Hutter no glioma N c.495_498deltgtt 5 p.cys167gln_fsx10 FS del WUSM no glioma Y c deltgtt 5 p.cys167gln_fsx10 FS del Ars no glioma N c delat 5 FS del Ars no glioma N c.550dela 5 FS del Ars no glioma Y c G>A i5 Splice Ars no glioma N c.686dela 7 FS del Ars no glioma N c.723insa 7 FS ins Ars no glioma? c.725delt 7 p.met242arg_fsx39 FS del Hutter no glioma N c.717instcccacag 7 FS ins Ars no glioma? c.817_819delctc 8 p.leu273del IF deletion Hutter no glioma N c.878dela 8 FS del Ars no glioma? c.889-2a>g i8 p.? splice Hutter no glioma Y c.889+1g>a i8 Splice Ars no glioma? c.899c>t 9 p.leu300pro missense Hutter no glioma Y c.910c>t 9 p.arg304x nonsense Ars no glioma? c.910c>t 9 p.arg304x nonsense Hutter no glioma? c.910c>t 9 p.arg304x nonsense Hutter no glioma? c.919_926delcttgctgg 9 p.leu307pro_fsx5 FS del Bolcekova no glioma N c.979delc>tt 9 FS del Ars no glioma Y c.999delc 9 FS del Ars no glioma N c delct 9 FS del Ars no glioma N c del11 9 FS del Ars no glioma N c G>A i9 Splice Ars no glioma N c G>A i10 Splice Ars no glioma Y c del15 i10 Splice Ars no glioma N c G>C i11 Splice Ars no glioma? c g>a i11 p.ala422leu_fsx57 splice Bolcekova 7

8 no glioma N c a>c i12 Splice Ars no glioma Y c.1399insa 13 FS ins Ars no glioma N c.1411a>t 13 K469X nonsense Ars no glioma Y c.1414delg 13 FS del Ars no glioma N c del16 13 p.phe477leu_fsx16 FS del WUSM no glioma? c.1440_1441insa 13 p.pro481thr_fsx10 FS ins Hutter no glioma N c.1465inst 13 FS ins Ars no glioma N c.1466a>g 13 p.tyr489x nonsense WUSM no glioma Y c.1466a>g 13 p.tyr489x nonsense WUSM no glioma N c G>A i13 Splice Ars no glioma Y c delAGTA i13 Splice Ars no glioma N c insA i13 Splice Ars no glioma? c.1541_1542delag 14 p.gln514arg_fsx43 FS del Hutter no glioma? c.1541_1542delag 14 p.gln514arg_fsx43 FS del Hutter no glioma N c delag 14 p.gln514arg_fsx43 FS del WUSM no glioma N c a>g i14 Splice Ars no glioma N c.1677delt 15 FS del Ars no glioma Y c a>g i15 Splice Ars no glioma Y c c>g i15 Splice Ars no glioma? c.1756_59delacta 16 p.thr586val_fsx18 FS del Bolcekova no glioma N delTA 16 FS del Ars no glioma? c.1780dela 16 p.thr594gln_fsx11 FS del Hutter no glioma N c.1797g>a 16 W599X nonsense Ars no glioma? c.1808_09delta 16 p.leu604asp_fsx5 FS del Bolcekova no glioma? c.1846c>g 17 p.gln616glu missense Bolcekova no glioma Y c.1885g>a 17 p.gly629arg Splice Ars no glioma? c.1906_1907deltc 17 p.ser636x nonsense Hutter no glioma Y c.2027_2028insc 18 p.ile679arg_fsx22 FS ins WUSM no glioma Y c.2041c>t 18 p.arg681x nonsense Ars no glioma N c.2076instgtac 18 FS ins Ars no glioma N c delat 18 FS del Ars no glioma N c.2125t>c 18 p.cys709arg missense WUSM no glioma N c T>C i18 Splice Ars no glioma N c g>a i19 p.arg752leu_fsx17 splice WUSM no glioma N c deltgcag 19 FS del Ars no glioma N c.2350t>c 20 W784R Missense Ars no glioma Y c inst i20 Splice Ars no glioma Y c a>g i20 Splice Ars no glioma Y c a>g i20 Splice Ars no glioma N c t>g i20 Splice Ars no glioma Y c.2764g>a 21 G922S Splice Ars 8

9 no glioma Y c.2768delt 21 p.leu923gln_fsx2 FS del WUSM no glioma N c g>a i21 Splice Ars no glioma? c G>T i21 p.? splice Hutter no glioma N c delggttt i21 Splice Ars no glioma? c _2851-8delttct i21 p.? splice Hutter no glioma N c.2942insgctctga 22 FS ins Ars no glioma N c delaa 22 FS del Ars no glioma N c delaat 22 IF deletion Ars no glioma N c insT i22 Splice Ars no glioma N c G>A i23 Splice Ars no glioma N c G>T i23 Splice Ars no glioma Y c G>C i23 Splice Ars no glioma? c.3142t>c 24 p.trp1048arg missense Bolcekova no glioma N c G>A i24 Splice Ars no glioma? c a>g i24 p.? splice Hutter no glioma N c del11 25 Splice Ars no glioma N c.3239inst 25 FS ins Ars no glioma N c.3277g>a 25 V1093M Splice Ars no glioma N c delcgtggca 26 FS del Ars no glioma N c deltc 26 FS del Ars no glioma N c.3419c>g 26 S1140X nonsense Ars no glioma N c.3427c>t 26 H1140Y Splice Ars no glioma? c.3455_3456insa 26 p.leu1153thr_fsx42 FS ins Hutter no glioma Y c delactc 26 FS del Ars no glioma? c.3457_60delctca 26 p.leu1153met_fsx4 FS del Bolcekova no glioma N c.3497g>t 27 p.gly1166val missense WUSM no glioma N c.3509dela 27 FS del Ars no glioma Y c.3520c>t 27 p.gln1174x nonsense WUSM no glioma Y c.3525_3526delaa 27 FS del Ars no glioma? c.3525_3526delaa 27 p.arg1176ser_fsx18 FS del Hutter no glioma N c delatggaa+insg 27 FS del Ars no glioma? c.3566a>g 27 p.gln1189arg missense Bolcekova no glioma? c.3591_3594delagaa 27 p.glu1198gln_fsx16 FS del Hutter no glioma N c.3610c>t 27 R1204W Missense Ars no glioma N c deltttg 28 FS del Ars no glioma Y c delctacc 28 FS del Ars no glioma N c delct 28 FS del Ars no glioma? c.3826c>t 28 p.arg1276x nonsense Bolcekova no glioma? c.3827g>a 28 p.arg1276gln missense Bolcekova no glioma N c G>C i28 Splice Ars no glioma? c.3916c>t 29 p.arg1306x nonsense Hutter 9

10 no glioma Y c a>g i29 Splice Ars no glioma N c.3977t>a 30 pleu1326x nonsense WUSM no glioma N c.4084c>t 30 p.arg1362x nonsense WUSM no glioma N c.4084c>t 30 p.arg1362x nonsense WUSM no glioma N c.4084c>t 30 p.arg1362x nonsense WUSM no glioma? c.4076_4077insc 30 p.gln1360ser_fsx20 FS ins Bolcekova no glioma? c.4226_4227delaginst 31 p.lys1409ile_fsx10 FS del ins Bolcekova no glioma N c.4267a>g 31 K1423E Missense Ars no glioma? c.4268a>g 31 p.lys1423arg missense Hutter no glioma Y c.4274t>c 32 L1425P Missense Ars no glioma Y c delgaa 32 IF deletion Ars no glioma? c.4325_29delctttc 32 p.pro1442gln_fsx2 FS del Bolcekova no glioma Y c.4330a>g 32 p.asn1444asp missense WUSM no glioma N c G>A i32 Splice Ars no glioma N c.4426delt 33 FS del Ars no glioma Y c.4493g>a 33 G1498E Missense Ars no glioma Y c.4537c>t 34 p.arg1513x nonsense Ars no glioma? c.4537c>t 34 p.arg1513x nonsense Hutter no glioma N c.4568insc 34 Splice Ars no glioma Y c delgt 34 FS del Ars no glioma? c a>g i34 p.his1555tyr_fsx10 splicing Bolcekova no glioma Y c del9 i35 Splice Ars no glioma? c.4827_29delt 36 p.leu1610x nonsense Bolcekova no glioma N c.4829del15 36 FS del Ars no glioma Y c delag 36 FS del Ars no glioma Y c.5194insa 36 FS ins Ars no glioma Y c g>a i36 Splice Ars no glioma Y c g>a i36 Splice Ars no glioma N c a>g i36 Splice Ars no glioma N c.5242c>t 37 p.arg1748x nonsense Ars no glioma? c.5264c>a 37 p.ser1755x nonsense Bolcekova no glioma N c.5303dela 37 FS del Ars no glioma Y c delac 37 FS del Ars no glioma N c.5482delg 37 p.asp1828met_fsx14 FS del WUSM no glioma N c.5486insc 37 FS ins Ars no glioma N c.5546g>a 37 p.arg1849gln missense WUSM no glioma Y c.5546g>a 37 p.arg1849gln Splice Ars no glioma N c G>A i37 Splice Ars no glioma? c a>t i37 p.? splice Hutter no glioma? c t>g i37 p.? splice Hutter no glioma N c del16 38 FS del Ars 10

11 no glioma Y c.5738insat 38 FS ins Ars no glioma Y c A>G i38 Splice Ars no glioma Y c.5839c>t 39 p.arg1947x nonsense Ars no glioma? c.5839c>t 39 p.arg1947x nonsense Hutter no glioma? c.5839c>t 39 p.arg1947x nonsense Hutter no glioma Y c.5887dela 39 FS del Ars no glioma? c.5904c>a 39 p.tyr1968x nonsense Hutter no glioma? c.6037dupa 40 p.thr2013asn_fsx26 FS ins Hutter no glioma N c.6125_6129_duptatct 41 p.pro2044tyr_fsx9 FS ins WUSM no glioma? c a>t i41 p.? splice Hutter no glioma Y c del10 42 FS del Ars no glioma N c.6483c>g 42 p.tyr2161x nonsense Ars no glioma? c.6483_6484insac 42 p.arg2162thr_fsx18 FS ins Bolcekova no glioma N c insgcat 43 FS ins Ars no glioma Y c.6593inst 43 FS ins Ars no glioma? c g>t i43 p.ala2174ile_fsx6 splice Bolcekova no glioma N c T>A i43 Splice Ars no glioma Y c.6649delt 44 FS del Ars no glioma Y c.6709c>t 44 p.arg2237x nonsense WUSM no glioma N c.6724c>t 44 Q2242X nonsense Ars no glioma N c T>A i44 Splice Ars no glioma Y c A>G i44 Splice Ars no glioma? c a>c i44 p.? splice Hutter no glioma Y c.6792c>a 45 p.tyr2264x nonsense Ars no glioma Y c.6792c>a 45 p.tyr2264x nonsense WUSM no glioma Y c.6792insa 45 p.tyr2264x nonsense Ars no glioma Y c T>G i45 Splice Ars no glioma? c.6878_6878delc 46 p.leu2294ser_fsx4 FS del Hutter no glioma? c.7084_85dela 47 p.asn2362thr_fsx13 FS del Bolcekova no glioma Y c delaacttt 47 p.2366_67delasnphe IF deletion Ars no glioma Y c.7267insa 49 p.thr2423asn_fsx4 FS ins Ars no glioma? c.7267dupa 49 p.thr2423asn_fsx4 FS ins Bolcekova no glioma Y c.7308insa 49 FS ins Ars no glioma Y c.7337delc 49 p.ser2446x nonsense Ars no glioma? c.7337c>g 49 p.ser2446x nonsense Hutter no glioma N c.7372delc 49 FS del Ars no glioma N c.7719insa 52 FS ins Ars no glioma N c.7720dela 52 FS del Ars no glioma N c G>T i52 Splice Ars no glioma Y c C>G i53 Splice Ars no glioma N c _insc 54 p.leu2648phe_fs24 FS ins WUSM 11

12 no glioma Y c.8040delt 54 FS del Ars no glioma Y c.8042insa 54 p.tyr2681x nonsense Ars no glioma Y c.8047c>t 54 p.gln2683x nonsense Ars no glioma Y c delaa 56 FS del Ars no glioma? c.8146_8153delgccttgat 56 p.ala2716x nonsense Bolcekova 12

13 Table e4. Calculations tables for adjusted ORs for glioma generated by meta-analyses 13

14 Table e5. Specificity, sensitivity, unadjusted odds ratios, and weighted odds ratios for optic glioma in participants with NF1 P values in bold indicate significance at the p<0.05 level. OPG: optic glioma 14

15 Table e6. Specificity, sensitivity, unadjusted odds ratios, and weighted odds ratios for glioma in participants with NF1 P values in bold indicate significance at the p<0.05 level. 15

16 Table e7. Recurrent NF1 mutations in participants with NF1 that harbor different glioma diagnoses Subjects with the same germline NF1 gene mutation, but differing glioma diagnoses (presence versus absence of glioma) 16

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