Supplementary table 6. Summary of mutation frequency and significance per microsatellite and per gene in exome sequencing of 24 and MiSeq sequencing of 93 MSI CRCs Summary of mutation frequency and significance per gene in exome sequencing of 24 and MiSeq sequencing of 93 MSI CRCs Gene MiSeq_MutFreq MiSeq_MutFreqCI95High MiSeq_MutFreqCI95Low MiSeq_MutatedTumors MiSeq_NAF MiSeq_P MiSeq_Q WXS_MutFreq WXS_MutatedTumors WXS_P WXS_Q CASP5 0.989247312 1.006838564 0.97165606 92 0.666666667 1.70E-89 4.83E-88 0.791666667 19 2.12E-17 1.33E-14 TGFBR2 0.967741935 0.997877874 0.937605997 90 0.883484163 1.48E-96 6.99E-95 0.833333333 20 4.39E-19 4.13E-16 SLC9A8 0.935483871 0.977386193 0.893581549 87 0.655034325 1.70E-89 4.83E-88 0.458333333 11 5.71E-07 5.25E-05 MIS18BP1 0.913978495 0.961803749 0.86615324 85 0.488888889 7.02E-61 9.07E-60 0.708333333 17 1.51E-08 1.97E-06 ACVR2A 0.892473118 0.945310572 0.839635665 83 0.80625 4.77E-128 6.77E-126 1 24 5.63E-36 2.12E-32 CDH26 0.88172043 0.936801974 0.826638886 82 0.55 4.12E-79 7.31E-78 0.416666667 10 5.46E-06 0.000331959 TFAM 0.88172043 0.936801974 0.826638886 82 0.620192308 4.12E-79 7.31E-78 0.583333333 14 2.52E-10 4.75E-08 ATR 0.860215054 0.919360254 0.801069854 80 0.632996633 2.72E-75 4.30E-74 0.583333333 14 3.89E-09 5.86E-07 AASDH 0.838709677 0.901442635 0.77597672 78 0.832712022 1.27E-71 1.80E-70 0.416666667 10 5.46E-06 0.000331959 USF3 0.806451613 0.873837619 0.739065607 75 0.771428571 5.39E-50 4.25E-49 0.5 12 0.002548628 0.01890901 SLC35F5 0.76344086 0.83592506 0.69095666 71 0.607908352 8.90E-60 1.05E-58 0.541666667 13 3.89E-09 5.86E-07 RPL22 0.752688172 0.826277658 0.679098686 70 0.342342342 1.28E-99 9.09E-98 0.666666667 16 2.60E-22 4.90E-19 CCDC178 0.709677419 0.787098046 0.632256792 66 0.587554722 4.15E-52 3.69E-51 0.541666667 13 5.71E-07 5.25E-05 LARP7 0.709677419 0.787098046 0.632256792 66 0.363095238 1.20E-43 7.38E-43 0.5 12 5.71E-07 5.25E-05 COBLL1 0.612903226 0.695982274 0.529824178 57 0.584440228 6.56E-55 6.65E-54 0.333333333 8 3.21E-06 0.000227932 TRIM59 0.602150538 0.685633473 0.518667603 56 0.538690476 1 1 0.416666667 10 5.46E-06 0.000331959 CLOCK 0.559139785 0.643822824 0.474456746 52 0.458333333 2.99E-47 1.93E-46 0.541666667 13 1.45E-12 3.03E-10 SEC31A 0.559139785 0.643822824 0.474456746 52 0.371710526 2.99E-47 1.93E-46 0.416666667 10 2.40E-07 2.82E-05 MSH3 0.52688172 0.612040065 0.441723376 49 0.46875 2.67E-58 2.91E-57 0.416666667 10 1.19E-11 2.35E-09 TTK 0.516129032 0.601366337 0.430891727 48 0.426406926 5.56E-36 2.82E-35 0.625 15 4.80E-14 1.65E-11 LMAN1 0.494623656 0.579900413 0.409346898 46 0.379807692 1.10E-38 5.99E-38 0.375 9 2.40E-07 2.82E-05 KIAA1919 0.494623656 0.579900413 0.409346898 46 0.498834499 1.10E-38 5.99E-38 0.625 15 1.35E-15 6.37E-13 DDX27 0.494623656 0.579900413 0.409346898 46 0.333333333 4.17E-53 3.95E-52 0.458333333 11 2.97E-13 7.48E-11 TNFAIP6 0.483870968 0.569108273 0.398633663 45 0.866666667 1.22E-09 3.10E-09 0.5 12 0.004740766 0.0237755 UBR5 0.47311828 0.558276624 0.387959935 44 0.435612083 9.77E-50 7.30E-49 0.541666667 13 2.97E-13 7.48E-11 SLC35G2 0.451612903 0.53649431 0.366731497 42 0.473684211 2.37E-33 1.12E-32 0.541666667 13 1.45E-12 3.03E-10 TCF7L2 0.451612903 0.53649431 0.366731497 42 0.516196447 2.37E-33 1.12E-32 0.541666667 13 1.45E-12 3.03E-10 TBC1D23 0.440860215 0.525543254 0.356177176 41 0.5 4.59E-32 2.10E-31 0.5 12 8.12E-10 1.33E-07 RBM27 0.430107527 0.514551909 0.345663144 40 0.362820513 8.51E-31 3.78E-30 0.583333333 14 4.80E-14 1.65E-11 TEAD2 0.430107527 0.514551909 0.345663144 40 0.393548387 1.68E-15 5.06E-15 0.458333333 11 2.12E-05 0.001094051 RBM43 0.397849462 0.481332397 0.314366527 37 0.48 3.99E-15 1.18E-14 0.416666667 10 0.000306039 0.008719925 SLAMF1 0.35483871 0.436447216 0.273230203 33 0.47826087 1.83E-22 7.04E-22 0.333333333 8 3.21E-06 0.000227932 BMPR2 0.344086022 0.425115443 0.2630566 32 0.441176471 1.16E-49 8.26E-49 0.458333333 11 1.15E-19 1.44E-16 TTC3 0.322580645 0.402312843 0.242848447 30 0.389805097 2.67E-28 1.15E-27 0.375 9 1.15E-08 1.54E-06 XPOT 0.322580645 0.402312843 0.242848447 30 0.46875 3.42E-19 1.22E-18 0.333333333 8 3.21E-06 0.000227932 SERPINB10 0.301075269 0.379317014 0.222833524 28 0.414444444 4.07E-17 1.31E-16 0.333333333 8 3.21E-06 0.000227932 CKAP2 0.301075269 0.379317014 0.222833524 28 0.271113831 1.46E-25 5.94E-25 0.458333333 11 2.97E-13 7.48E-11 TCERG1 0.290322581 0.367743208 0.212901954 27 0.25 6.85E-18 2.26E-17 0.708333333 17 1.16E-16 6.22E-14 COIL 0.290322581 0.367743208 0.212901954 27 0.258661888 6.85E-18 2.26E-17 0.291666667 7 2.74E-07 2.87E-05 OR6C75 0.279569892 0.356116669 0.203023116 26 0.282608696 6.85E-18 2.26E-17 0.416666667 10 4.01E-10 7.20E-08 GRB14 0.268817204 0.344435571 0.193198837 25 0.421052632 3.60E-14 1.04E-13 0.333333333 8 3.21E-06 0.000227932 SPAG9 0.247311828 0.320901314 0.173722342 23 0.441176471 2.54E-12 7.08E-12 0.333333333 8 3.21E-06 0.000227932 SACS 0.247311828 0.320901314 0.173722342 23 0.324324324 0.000108087 0.000247555 0.5 12 3.21E-06 0.000227932 C6orf89 0.225806452 0.297121097 0.154491806 21 0.21875 0.001198711 0.002540552 0.458333333 11 2.12E-05 0.001094051 ADNP 0.215053763 0.28513137 0.144976157 20 0.430871212 1.57E-15 4.84E-15 0.333333333 8 1.15E-08 1.54E-06 ASH1L 0.215053763 0.28513137 0.144976157 20 0.367307692 9.81E-10 2.53E-09 0.375 9 2.40E-07 2.82E-05 CCDC30 0.204301075 0.273070516 0.135531634 19 0.405405405 3.55E-50 2.97E-49 0.166666667 4 1.95E-13 6.11E-11 AKAP7 0.193548387 0.260934393 0.126162381 18 0.333333333 2.79E-13 7.93E-13 0.291666667 7 2.74E-07 2.87E-05 NRIP1 0.193548387 0.260934393 0.126162381 18 0.320276498 3.38E-12 9.22E-12 0.333333333 8 2.74E-07 2.87E-05 KCNMA1 0.182795699 0.248718263 0.116873135 17 0.717948718 2.17E-07 5.13E-07 0.333333333 8 3.21E-06 0.000227932 GUF1 0.172043011 0.236416669 0.107669353 16 0.281650641 3.80E-11 1.02E-10 0.333333333 8 2.74E-07 2.87E-05 FAM111B 0.139784946 0.198930146 0.080639746 13 0.457142857 0.05542131 0.08284027 0.708333333 17 2.52E-14 1.06E-11 SRPR 0.086021505 0.13384676 0.038196251 8 0.138366627 0.002341289 0.004682578 0.333333333 8 1.15E-08 1.54E-06 ALPK2 0.075268817 0.120267632 0.030270002 7 0.315789474 8.74E-22 3.27E-21 0.25 6 2.91E-18 2.19E-15 MTF1 0.021505376 0.046247589 -0.003236836 2 0.439236111 0.0049755 0.009547581 0.125 3 2.75E-06 0.000227932 SLC26A7 0.021505376 0.046247589 -0.003236836 2 0.258152174 0.0049755 0.009547581 0.166666667 4 2.75E-06 0.000227932 ACIN1 0.010752688 0.02834394 -0.006838564 1 0.131578947 0.04243032 0.06409687 0.25 6 3.77E-07 3.74E-05 UBB 0 0 0 0 1 1 0.083333333 2 3.77E-07 3.74E-05 AIM2 0 0 0 0 1 1 0.083333333 2 0.5651895 0.57823 OR7E24 0 0 0 0 1 1 0.083333333 2 0.7980995 0.8057961 MUC15 0 0 0 0 1 1 0.333333333 8 3.21E-06 0.000227932 AC016725.4 0 0 0 0 1 1 0.166666667 4 4.97E-10 8.52E-08 LTN1 0 0 0 0 1 1 0.25 6 0.113731 0.1356065 SEC63 0 0 0 0 1 1 0.208333333 5 0.01551875 0.04624436 SRP54 0 0 0 0 1 1 0.083333333 2 1.19E-06 0.000106364 SREK1IP1 0 0 0 0 1 1 0.208333333 5 0.03424939 0.05933783 SMAP1 0 0 0 0 1 1 0.291666667 7 0.006453261 0.0237755 SLC22A9 0 0 0 0 1 1 0.208333333 5 0.1493177 0.1754483 OR7C1 0 0 0 0 1 1 0.416666667 10 0.000235801 0.007728108 ASTE1 0 0 0 0 1 1 0.166666667 4 0.02644399 0.05301457 CCDC150 0 0 0 0 1 1 0.041666667 1 0.9525364 0.9532952 Summary of mutation frequency and significance per microsatellite in exome sequencing of 24 and MiSeq sequencing of 93 MSI CRCs Gene Chrom Pos MicrosatelliteContext MicrosatelliteBase MicrosatelliteLen NumSamples_wxs MutFreq_wxs CIlow_wxs CIhigh_wxs p_wxs q_wxs NAF_wxs BCTypes_wxs ACTypes_wxs NumSamples_miseq MutFreq_miseq CIlow_miseq CIhigh_miseq p_miseq q_miseq NAF_miseq BCTypes_miseq ACTypes_miseq ACVR2A 2 148683686 A8 A/T 8 22 0.916666667 0.913128943 0.920204391 5.63E-36 2.12E-32 0.908557626 INS->A:1,DEL->A:21 Fshift1:22 82 0.88172043 0.879620556 0.883820305 4.77E-128 6.77E-126 0.846153846 DEL->A:81,DEL->AA:2 Fshift1 p.435:81,Fshift2 p.435:2 RPL22 1 6257785 T8 A/T 8 16 0.666666667 0.660632704 0.672700629 2.60E-22 4.90E-19 0.521974402 DEL->T:15,INS->T:1 Fshift1:16 70 0.752688172 0.749882719 0.755493625 1.28E-99 9.09E-98 0.342342342 DEL->T:66,DEL->TT:1,INS- >T:3 Fshift2 p.15:1,Fshift1 p.15:69 TGFBR2 3 30691872 A10 A/T 10 20 0.833333333 0.828563067 0.8381036 4.39E-19 4.13E-16 0.767241379 INS->A:1,DEL->A:16,DEL->AA:3 Fshift1:17,Fshift2:3 90 0.967741935 0.966593063 0.968890808 1.48E-96 6.99E-95 0.883484163 INS->A:1,DEL->A:75,DEL->AA:20 Fshift2 p.150:20,Fshift1 p.150:76 CASP5 11 104878041 T10 A/T 10 19 0.791666667 0.78646839 0.796864944 2.12E-17 1.33E-14 0.628198052 DEL->T:18,DEL->TT:1 Fshift1:18,Fshift2:1 87 0.935483871 0.933886428 0.937081314 1.70E-89 4.83E-88 0.714237517 DEL->T:82,DEL->TT:8 Fshift1 p.81:82,Fshift2 p.81:8 SLC9A8 20 48467301 T10 A/T 10 11 0.458333333 0.45195561 0.464711056 5.71E-07 5.25E-05 0.75409632 DEL->T:11 Fshift1:11 87 0.935483871 0.933886428 0.937081314 1.70E-89 4.83E-88 0.655034325 DEL->T:78,DEL->TT:6,INS- >T:4 Fshift1 p.179:82,Fshift2 p.179:6 CASP5 11 104879687 T10 A/T 10 3 0.125 0.120766809 0.129233191 0.2839761 0.328819 NA DEL->TT:3 Fshift2:3 83 0.892473118 0.890458795 0.894487441 4.38E-81 1.04E-79 0.59375 DEL->T:67,DEL->TT:18 Fshift1 p.23:67,Fshift2 p.23:18 TFAM 10 60148570 A10 A/T 10 14 0.583333333 0.577022864 0.589643802 2.52E-10 4.75E-08 0.525700935 DEL->A:10,DEL->AA:4 Fshift1:10,Fshift2:4 82 0.88172043 0.879620556 0.883820305 4.12E-79 7.31E-78 0.620192308 DEL->A:75,DEL->AA:7 Fshift1 p.144:75,Fshift2 p.144:7 CDH26 20 58587784 A10 A/T 10 10 0.416666667 0.410356198 0.422977136 5.46E-06 0.000331959 0.584210245 DEL->A:9,DEL->AA:1 Fshift1:9,Fshift2:1 82 0.88172043 0.879620556 0.883820305 4.12E-79