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174634 1 Supp 3807641 Kj8n Supplementary Table S2 Page 1 Supplementary Table S2: List of somatic mutations identified in the cohort of 35 metaplastic breast cancers and list of primers used for validation with Sanger sequencing of selected mutations. Lower bound Upper bound Kandoth et al Lawrence et of 95% of 95% Validated Mutant Cancer 127 Probability Cancer Sample Chromo- Reference Alternate Mutation al Haplo- confidence confidence using Gene Mutation Effect Position allele Depth FATHMM CHASM Provean Gene significantly LOH Pathogenicity of mutation cell Clonal Forward primer for Sanger sequencing Reverse primer for Sanger sequencing name some allele allele Taster Cancer5000- insufficient interval for interval for Sanger fraction Census mutated being clonal fraction S genes cancer cell cancer cell sequencing genes fraction fraction META31 MMEL1 p.Val141Ile missense_variant 1 2541142 C T 32.00% 25 N PASSENGER/OTHER Passenger . Likely passenger 0.4224 46.20% 100.00% 97% Subclonal META31 PRDM16 p.Asp36Asp synonymous_variant 1 3102759 C T 31.43% 35 . true . 0.4396 51.33% 100.00% 95% Subclonal META31 CEP104 p.Gly392Gly synonymous_variant 1 3753200 C T 7.59% 79 . 0.0000 10.32% 46.65% 23% Subclonal META31 ENO1 p.Arg50Arg synonymous_variant 1 8931981 C A 5.15% 97 . 0.0000 6.35% 34.25% 16% Subclonal META31 SPEN p.Asn870fs frameshift_variant 1 16255339 GA G 16.79% 131 A . true Likely pathogenic 0.0001 33.84% 72.39% 51% Subclonal META31 HSPG2 p.Arg92His missense_variant 1 22217157 C T 36.96% 92 N PASSENGER/OTHER Passenger . Likely passenger 0.7019 75.58% 100.00% 100% Clonal META31 ZBTB40 p.Lys803dup disruptive_inframe_insertion 1 22838560 C CAAG 17.78% 45 P . Neutral . Likely passenger 0.0414 27.68% 90.42% 54% Subclonal META31 ARID1A p.Pro1349fs frameshift_variant 1 27100330 AC A 22.22% 99 A . true true true Likely pathogenic 0.0464 45.26% 92.34% 67% Subclonal META31 ZMYM4 p.Ser18fs frameshift_variant 1 35790967 C CA 20.00% 40 A . Indeterminate 0.0954 31.16% 94.77% 60% Subclonal META31 NRD1 p.Thr207Ala missense_variant 1 52305909 T C 39.34% 61 N PASSENGER/OTHER Passenger . Likely passenger 0.6828 72.70% 100.00% 100% Clonal META31 TMEM59 p.Asp174Asp synonymous_variant 1 54509067 G A 20.00% 30 . 0.1263 28.05% 95.88% 60% Subclonal META31 C1orf87 p.Gly129Arg missense_variant 1 60506761 C T 18.18% 44 D PASSENGER/OTHER Passenger . Indeterminate 0.0495 28.32% 91.44% 55% Subclonal META31 USP33 p.Arg277* stop_gained 1 78194379 G A 33.78% 74 A . Indeterminate 0.5890 67.47% 100.00% 100% Clonal META31 SH3GLB1 p.Leu179Leu synonymous_variant 1 87190055 A T 20.83% 24 . 0.1652 27.00% 96.85% 63% Subclonal META31 PKN2 p.Arg917fs frameshift_variant 1 89298831 A AT 22.50% 40 D . Indeterminate 0.1627 36.32% 96.86% 68% Subclonal META31 NBPF6 p.Pro648Pro synonymous_variant 1 109010269 G A 6.33% 79 . 0.0000 7.97% 41.73% 19% Subclonal META31 KCNA10 p.Ala370Val missense_variant 1 111060301 G A 5.95% 84 D PASSENGER/OTHER Passenger . Indeterminate 0.0000 7.42% 39.35% 18% Subclonal META31 KCNA10 p.Val88Ala missense_variant 1 111061147 A G 9.33% 75 D PASSENGER/OTHER Passenger . Indeterminate 0.0000 13.53% 54.02% 28% Subclonal META31 NOTCH2 p.Asp1481Asp synonymous_variant 1 120467996 A G 3.48% 374 . true . 0.0006 24.20% 69.85% 42% Subclonal META31 PDE4DIP p.Ala347Thr missense_variant 1 144921990 C T 3.63% 689 D PASSENGER/OTHER Passenger true . Likely pathogenic 0.0000 19.33% 42.01% 29% Subclonal META31 TXNIP p.Tyr279Tyr synonymous_variant 1 145440637 T C 7.33% 150 . 0.0027 24.60% 75.55% 44% Subclonal META31 CA14 c.863-2A>G splice_acceptor_variant 1 150236191 A G 16.81% 357 D . Indeterminate 0.6593 76.21% 100.00% 100% Clonal META31 FLG p.Gly387Cys missense_variant 1 152286203 C A 10.78% 306 N PASSENGER/OTHER Passenger . true Likely passenger 0.0144 46.38% 87.92% 65% Subclonal META31 NUP210L p.Thr864Ala missense_variant 1 154034115 T C 5.68% 88 D PASSENGER/OTHER Passenger . true Likely pathogenic 0.0053 14.61% 74.89% 34% Subclonal META31 UBAP2L p.Pro875Pro synonymous_variant 1 154233414 G A 5.94% 101 . 0.0037 16.36% 73.59% 36% Subclonal META31 CLK2 p.Arg45Cys missense_variant 1 155240636 G A 7.89% 152 D PASSENGER/OTHER Passenger . Indeterminate 0.0053 27.19% 79.23% 48% Subclonal META31 RUSC1 p.Leu771Gln missense_variant 1 155296821 T A 10.23% 88 N PASSENGER/OTHER Passenger . Likely passenger 0.1151 32.40% 95.60% 62% Subclonal META31 IGSF8 p.Cys544Tyr missense_variant 1 160062167 C T 15.52% 58 D PASSENGER/OTHER Passenger . Indeterminate 0.3987 45.47% 100.00% 93% Subclonal META31 CD84 p.Arg84Trp missense_variant 1 160535332 G A 10.00% 230 N PASSENGER/OTHER Passenger . Likely passenger 0.0138 40.24% 86.59% 60% Subclonal META31 SH2D1B p.Ser105Ile missense_variant 1 162368762 C A 5.69% 123 N PASSENGER/OTHER Passenger . Likely passenger 0.0009 16.49% 67.38% 34% Subclonal META31 F5 p.Thr206Thr synonymous_variant 1 169528503 C T 12.10% 124 . 0.1937 44.07% 97.46% 73% Subclonal META31 SELL p.Thr121Thr synonymous_variant 1 169677706 A G 12.11% 190 . 0.1434 48.73% 96.61% 73% Subclonal META31 METTL11B p.Ala56Ala synonymous_variant 1 170129672 T G 3.60% 222 . 0.0000 10.68% 41.32% 22% Subclonal META31 TNN p.Thr994Thr synonymous_variant 1 175096158 G A 14.17% 127 . 0.3589 53.04% 98.85% 85% Subclonal META31 RNASEL p.Ser591Ile missense_variant 1 182551188 C A 5.70% 228 N PASSENGER/OTHER Passenger . Likely passenger 0.0000 19.85% 56.76% 34% Subclonal META31 RNASEL p.Pro242Thr missense_variant 1 182555218 G T 20.88% 91 N CANCER Passenger . Likely passenger 0.6381 67.85% 100.00% 100% Clonal META31 LAMC1 p.Val503Ile missense_variant 1 183085981 G A 5.51% 127 D PASSENGER/OTHER Passenger . Indeterminate 0.0006 15.98% 65.34% 33% Subclonal META31 ARPC5 p.Gln59His missense_variant 1 183602265 C A 8.00% 125 D . Passenger . Indeterminate 0.0128 26.20% 83.38% 48% Subclonal META31 ZBTB41 p.Gly627Gly synonymous_variant 1 197144244 A G 20.83% 120 . 0.6748 72.42% 100.00% 100% Clonal META31 CSRP1 p.Gly78Gly synonymous_variant 1 201459351 G A 23.21% 56 . 0.6319 63.26% 100.00% 100% Clonal META31 IPO9 p.His475Tyr missense_variant 1 201828077 C T 17.24% 58 D CANCER Passenger . Likely pathogenic 0.4654 50.44% 100.00% 100% Subclonal META31 LGR6 p.Arg844His missense_variant 1 202287962 G A 12.86% 70 N PASSENGER/OTHER Passenger . Likely passenger 0.2765 39.67% 98.33% 77% Subclonal META31 FMOD p.Arg274Trp missense_variant 1 203316579 G A 14.63% 123 D PASSENGER/OTHER Passenger . Indeterminate 0.3936 54.39% 100.00% 88% Subclonal META31 CR1 p.Asp2254Val missense_variant 1 207790019 A T 7.82% 371 N PASSENGER/OTHER Passenger . Likely passenger 0.0000 32.63% 65.75% 47% Subclonal META31 PLXNA2 p.Pro1822Pro synonymous_variant 1 208201477 T C 7.41% 81 . 0.0284 20.51% 87.29% 45% Subclonal META31 USH2A p.Ser1741Tyr missense_variant 1 216256874 G T 5.43% 184 D PASSENGER/OTHER Passenger . Indeterminate 0.0000 17.57% 57.97% 33% Subclonal META31 MIA3 p.Ala87Val missense_variant 1 222794627 C T 11.96% 92 D PASSENGER/OTHER Passenger . Indeterminate 0.2101 39.90% 97.66% 72% Subclonal META31 URB2 p.Ser558Asn missense_variant 1 229772033 G A 8.99% 89 N PASSENGER/OTHER Passenger . Likely passenger 0.0617 27.50% 92.53% 54% Subclonal META31 URB2 p.Arg567Gln missense_variant 1 229772060 G A 9.30% 129 D PASSENGER/OTHER Passenger . Indeterminate 0.0367 32.15% 90.04% 56% Subclonal META31 EXOC8 p.Ala308Thr missense_variant 1 231472570 C T 19.08% 131 D . Passenger . Indeterminate 0.6425 69.73% 100.00% 100% Clonal META31 PCNXL2 p.Lys619fs frameshift_variant 1 233388512 CT C 13.24% 136 A . Indeterminate 0.2792 50.07% 98.37% 80% Subclonal META31 LYST p.Asp2130Gly missense_variant 1 235922764 T C 14.17% 120 D PASSENGER/OTHER Passenger . Indeterminate 0.3579 52.23% 98.84% 85% Subclonal META31 EDARADD p.Leu185Phe missense_variant 1 236645854 C T 6.10% 82 D PASSENGER/OTHER Passenger . Indeterminate 0.0102 15.72% 79.44% 37% Subclonal META31 CHRM3 p.Lys567fs frameshift_variant 1 240072443 CA C 15.13% 119 D . Indeterminate 0.4273 55.77% 100.00% 91% Subclonal META31 FH p.Thr277Thr synonymous_variant 1 241669376 A G 8.74% 103 . true . 0.0401 27.76% 90.14% 53% Subclonal META31 CHML p.Thr373Ala missense_variant 1 241797952 T C 5.67% 141 D PASSENGER/OTHER Passenger . Indeterminate 0.0004 17.18% 64.49% 34% Subclonal META31 WDR64 p.His748Arg missense_variant 1 241934982 A G 7.04% 71 D PASSENGER/OTHER Passenger . Indeterminate 0.0309 18.21% 87.58% 42% Subclonal META31 HNRNPU p.Ala588Val missense_variant 1 245019908 G A 9.77% 174 D PASSENGER/OTHER Passenger . Indeterminate 0.0259 36.85% 88.80% 59% Subclonal META31 OR2M2 p.Ser21Arg missense_variant 1 248343348 A C 6.10% 328 N PASSENGER/OTHER Passenger . Likely passenger 0.0000 23.52% 55.07% 37% Subclonal META31 OR14C36 p.Phe105fs frameshift_variant 1 248512383 GT G 11.76% 85 D . Indeterminate 0.2042 38.15% 97.58% 71% Subclonal META31 TEX261 p.Ala116fs frameshift_variant 2 71216905 C CA 22.22% 45 D . Indeterminate 0.1417 37.13% 96.41% 67% Subclonal META31 NAT8B p.Ala50fs frameshift_variant 2 73928284 GC G 14.29% 49 . Indeterminate 0.0074 21.14% 79.66% 43% Subclonal META31 MTHFD2 p.Met207Val missense_variant 2 74437125 A G 50.00% 12 D PASSENGER/OTHER Passenger . Indeterminate 0.5856 50.40% 100.00% 100% Clonal META31 HK2 p.Tyr461Cys missense_variant 2 75107508 A G 20.00% 35 D PASSENGER/OTHER Passenger .
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