Gene Panel Analysis Report
Stephen Kelly
March 17, 2017
1 Analysis Information
Analysis ID:
ExampleIonTorrentRun123
Run ID:
ExampleRunID
| Sample.Name | Barcode | |
|---|---|---|
| 1 | SC | IonXpress_001 |
| 2 | Sample2 | IonXpress_002 |
| 3 | Sample3 | IonXpress_003 |
| 4 | Sample4 | IonXpress_004 |
| 5 | Sample5 | IonXpress_005 |
| 6 | Sample1 | IonXpress_006 |
| 7 | Sample6 | IonXpress_007 |
| 8 | NC | IonXpress_008 |
2 Variant Table
2.1 Non-SC Samples
The following variants are detected:
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode | |
|---|---|---|---|---|---|---|---|
| 1 | PIK3CA | c.A3140G | p.H1047R | 0.176 | US | Sample2 | IonXpress_002 |
| 2 | KRAS | c.G34T | p.G12C | 0.342 | KS | Sample2 | IonXpress_002 |
| 3 | TP53 | c.G1015T | p.E339X | 0.165 | US | Sample2 | IonXpress_002 |
| 4 | TP53 | c.C742T | p.R248W | 0.560 | US | Sample1 | IonXpress_006 |
| 5 | BRAF | c.T1799A | p.V600E | 0.168 | KS | Sample4 | IonXpress_004 |
| 6 | APC | c.3932dupT | p.I1311fs | 0.151 | US | Sample5 | IonXpress_005 |
| 7 | JAK3 | c.G2164A | p.V722I | 0.556 | US | Sample5 | IonXpress_005 |
| 8 | CTNNB1 | c.T97C | p.S33P | 0.214 | US | Sample3 | IonXpress_003 |
| 9 | PTEN | c.A43T | p.R15X | 0.340 | US | Sample6 | IonXpress_007 |
| 10 | TP53 | c.C586T | p.R196X | 0.303 | US | Sample6 | IonXpress_007 |
2.2 SC Sample
The following variants were detected in the SC control sample:
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode | |
|---|---|---|---|---|---|---|---|
| 1 | MPL | c.G1514A | p.S505N | 0.108 | US | SC | IonXpress_001 |
| 2 | MPL | c.G1544T | p.W515L | 0.104 | US | SC | IonXpress_001 |
| 3 | MPL | c.G1555A | p.A519T | 0.099 | US | SC | IonXpress_001 |
| 4 | NRAS | c.A182G | p.Q61R | 0.062 | KS | SC | IonXpress_001 |
| 5 | NRAS | c.G52A | p.A18T | 0.082 | KS | SC | IonXpress_001 |
| 6 | NRAS | c.G35A | p.G12D | 0.078 | KS | SC | IonXpress_001 |
| 7 | NRAS | c.G29A | p.G10E | 0.076 | KS | SC | IonXpress_001 |
| 8 | ALK | c.G3824A | p.R1275Q | 0.104 | US | SC | IonXpress_001 |
| 9 | ALK | c.C3522A | p.F1174L | 0.090 | US | SC | IonXpress_001 |
| 10 | IDH1 | c.G395A | p.R132H | 0.087 | KS | SC | IonXpress_001 |
| 11 | IDH1 | c.A388G | p.I130V | 0.085 | KS | SC | IonXpress_001 |
| 12 | IDH1 | c.G367A | p.G123R | 0.089 | KS | SC | IonXpress_001 |
| 13 | ERBB4 | c.G2791T | p.D931Y | 0.092 | US | SC | IonXpress_001 |
| 14 | ERBB4 | c.G2782T | p.E928X | 0.092 | US | SC | IonXpress_001 |
| 15 | ERBB4 | c.G1835A | p.R612Q | 0.090 | US | SC | IonXpress_001 |
| 16 | ERBB4 | c.C1828A | p.P610T | 0.088 | US | SC | IonXpress_001 |
| 17 | ERBB4 | c.A1784G | p.D595G | 0.096 | US | SC | IonXpress_001 |
| 18 | ERBB4 | c.C1022T | p.S341L | 0.094 | US | SC | IonXpress_001 |
| 19 | ERBB4 | c.G1003T | p.D335Y | 0.102 | US | SC | IonXpress_001 |
| 20 | ERBB4 | c.T885G | p.H295Q | 0.101 | US | SC | IonXpress_001 |
| 21 | ERBB4 | c.C829A | p.H277N | 0.099 | US | SC | IonXpress_001 |
| 22 | ERBB4 | c.C804A | p.Y268X | 0.097 | US | SC | IonXpress_001 |
| 23 | ERBB4 | c.A730G | p.T244A | 0.099 | US | SC | IonXpress_001 |
| 24 | ERBB4 | c.C704T | p.A235V | 0.099 | US | SC | IonXpress_001 |
| 25 | ERBB4 | c.A542G | p.N181S | 0.097 | US | SC | IonXpress_001 |
| 26 | ERBB4 | c.C515G | p.P172R | 0.092 | US | SC | IonXpress_001 |
| 27 | VHL | c.T266A | p.L89H | 0.082 | US | SC | IonXpress_001 |
| 28 | VHL | c.G277C | p.G93R | 0.081 | US | SC | IonXpress_001 |
| 29 | VHL | c.C286T | p.Q96X | 0.080 | US | SC | IonXpress_001 |
| 30 | VHL | c.C343A | p.H115N | 0.093 | US | SC | IonXpress_001 |
| 31 | VHL | c.T353C | p.L118P | 0.095 | US | SC | IonXpress_001 |
| 32 | VHL | c.G388C | p.V130L | 0.103 | US | SC | IonXpress_001 |
| 33 | VHL | c.C472G | p.L158V | 0.108 | US | SC | IonXpress_001 |
| 34 | VHL | c.C481T | p.R161X | 0.109 | US | SC | IonXpress_001 |
| 35 | VHL | c.C499T | p.R167W | 0.108 | US | SC | IonXpress_001 |
| 36 | VHL | c.T506C | p.L169P | 0.106 | US | SC | IonXpress_001 |
| 37 | MLH1 | c.T1151A | p.V384D | 0.096 | US | SC | IonXpress_001 |
| 38 | CTNNB1 | c.C98G | p.S33C | 0.085 | US | SC | IonXpress_001 |
| 39 | CTNNB1 | c.C110T | p.S37F | 0.084 | US | SC | IonXpress_001 |
| 40 | CTNNB1 | c.A121G | p.T41A | 0.085 | US | SC | IonXpress_001 |
| 41 | CTNNB1 | c.C134T | p.S45F | 0.088 | US | SC | IonXpress_001 |
| 42 | PIK3CA | c.G323A | p.R108H | 0.105 | US | SC | IonXpress_001 |
| 43 | PIK3CA | c.A331G | p.K111E | 0.103 | US | SC | IonXpress_001 |
| 44 | PIK3CA | c.G344T | p.R115L | 0.106 | US | SC | IonXpress_001 |
| 45 | PIK3CA | c.C971T | p.T324I | 0.103 | US | SC | IonXpress_001 |
| 46 | PIK3CA | c.T1035A | p.N345K | 0.088 | US | SC | IonXpress_001 |
| 47 | PIK3CA | c.T1213C | p.S405P | 0.090 | US | SC | IonXpress_001 |
| 48 | PIK3CA | c.T1258C | p.C420R | 0.118 | US | SC | IonXpress_001 |
| 49 | PIK3CA | c.A1370G | p.N457S | 0.098 | US | SC | IonXpress_001 |
| 50 | PIK3CA | c.C1616G | p.P539R | 0.075 | US | SC | IonXpress_001 |
| 51 | PIK3CA | c.G1624A | p.E542K | 0.074 | US | SC | IonXpress_001 |
| 52 | PIK3CA | c.G1633A | p.E545K | 0.076 | US | SC | IonXpress_001 |
| 53 | PIK3CA | c.A1640G | p.E547G | 0.078 | US | SC | IonXpress_001 |
| 54 | PIK3CA | c.A2102C | p.H701P | 0.088 | US | SC | IonXpress_001 |
| 55 | PIK3CA | c.G2702T | p.C901F | 0.085 | US | SC | IonXpress_001 |
| 56 | PIK3CA | c.T2725C | p.F909L | 0.084 | US | SC | IonXpress_001 |
| 57 | PIK3CA | c.A3110G | p.E1037G | 0.091 | US | SC | IonXpress_001 |
| 58 | PIK3CA | c.A3140G | p.H1047R | 0.090 | US | SC | IonXpress_001 |
| 59 | FGFR3 | c.C746G | p.S249C | 0.087 | US | SC | IonXpress_001 |
| 60 | FGFR3 | c.G1114T | p.G372C | 0.088 | US | SC | IonXpress_001 |
| 61 | FGFR3 | c.G1144A | p.G382R | 0.086 | US | SC | IonXpress_001 |
| 62 | FGFR3 | c.T1156C | p.F386L | 0.087 | US | SC | IonXpress_001 |
| 63 | FGFR3 | c.C1178A | p.A393E | 0.086 | US | SC | IonXpress_001 |
| 64 | FGFR3 | c.G2095T | p.G699C | 0.071 | US | SC | IonXpress_001 |
| 65 | PDGFRA | c.C1977A | p.N659K | 0.100 | US | SC | IonXpress_001 |
| 66 | PDGFRA | c.C2021T | p.T674I | 0.086 | US | SC | IonXpress_001 |
| 67 | PDGFRA | c.A2525T | p.D842V | 0.078 | US | SC | IonXpress_001 |
| 68 | PDGFRA | c.C2544A | p.N848K | 0.093 | US | SC | IonXpress_001 |
| 69 | KIT | c.C92T | p.P31L | 0.084 | KS | SC | IonXpress_001 |
| 70 | KIT | c.G154A | p.D52N | 0.094 | KS | SC | IonXpress_001 |
| 71 | KIT | c.T1516C | p.F506L | 0.088 | KS | SC | IonXpress_001 |
| 72 | KIT | c.A1526T | p.K509I | 0.100 | KS | SC | IonXpress_001 |
| 73 | KIT | c.A1535G | p.N512S | 0.096 | KS | SC | IonXpress_001 |
| 74 | KIT | c.G1588A | p.V530I | 0.077 | KS | SC | IonXpress_001 |
| 75 | KIT | c.T1727C | p.L576P | 0.089 | KS | SC | IonXpress_001 |
| 76 | KIT | c.A1924G | p.K642E | 0.089 | KS | SC | IonXpress_001 |
| 77 | KIT | c.T1961C | p.V654A | 0.091 | KS | SC | IonXpress_001 |
| 78 | KIT | c.C2410T | p.R804W | 0.071 | KS | SC | IonXpress_001 |
| 79 | KIT | c.G2558A | p.W853X | 0.163 | KS | SC | IonXpress_001 |
| 80 | KDR | c.G3433A | p.G1145R | 0.075 | US | SC | IonXpress_001 |
| 81 | KDR | c.G2917T | p.A973S | 0.095 | US | SC | IonXpress_001 |
| 82 | KDR | c.G824T | p.R275L | 0.094 | US | SC | IonXpress_001 |
| 83 | FBXW7 | c.G1451T | p.R484M | 0.090 | US | SC | IonXpress_001 |
| 84 | FBXW7 | c.G1436A | p.R479Q | 0.087 | US | SC | IonXpress_001 |
| 85 | FBXW7 | c.G1394A | p.R465H | 0.083 | US | SC | IonXpress_001 |
| 86 | FBXW7 | c.G1338A | p.W446X | 0.096 | US | SC | IonXpress_001 |
| 87 | FBXW7 | c.G1322T | p.R441L | 0.086 | US | SC | IonXpress_001 |
| 88 | FBXW7 | c.C1177T | p.R393X | 0.086 | US | SC | IonXpress_001 |
| 89 | FBXW7 | c.C832T | p.R278X | 0.088 | US | SC | IonXpress_001 |
| 90 | APC | c.C2626T | p.R876X | 0.214 | US | SC | IonXpress_001 |
| 91 | APC | c.T2639C | p.I880T | 0.208 | US | SC | IonXpress_001 |
| 92 | APC | c.C2656T | p.Q886X | 0.209 | US | SC | IonXpress_001 |
| 93 | APC | c.C3286T | p.Q1096X | 0.212 | US | SC | IonXpress_001 |
| 94 | APC | c.A3305G | p.Y1102C | 0.216 | US | SC | IonXpress_001 |
| 95 | APC | c.C3871T | p.Q1291X | 0.207 | US | SC | IonXpress_001 |
| 96 | APC | c.C3880T | p.Q1294X | 0.206 | US | SC | IonXpress_001 |
| 97 | APC | c.3921dupA | p.I1307fs | 0.196 | US | SC | IonXpress_001 |
| 98 | APC | c.G3964T | p.E1322X | 0.199 | US | SC | IonXpress_001 |
| 99 | APC | c.G4057T | p.E1353X | 0.242 | US | SC | IonXpress_001 |
| 100 | APC | c.T4063C | p.S1355P | 0.258 | US | SC | IonXpress_001 |
| 101 | APC | c.C4132T | p.Q1378X | 0.237 | US | SC | IonXpress_001 |
| 102 | APC | c.C4141T | p.P1381S | 0.245 | US | SC | IonXpress_001 |
| 103 | APC | c.C4285T | p.Q1429X | 0.238 | US | SC | IonXpress_001 |
| 104 | APC | c.4385_4386del | p.K1462fs | 0.210 | US | SC | IonXpress_001 |
| 105 | APC | c.4540delC | p.P1514fs | 0.237 | US | SC | IonXpress_001 |
| 106 | APC | c.G4561T | p.E1521X | 0.220 | US | SC | IonXpress_001 |
| 107 | APC | c.G4639T | p.E1547X | 0.186 | US | SC | IonXpress_001 |
| 108 | APC | c.G4654T | p.E1552X | 0.173 | US | SC | IonXpress_001 |
| 109 | APC | c.4661dupA | p.E1554fs | 0.110 | US | SC | IonXpress_001 |
| 110 | CSF1R | c.A2906G | p.Y969C | 0.210 | US | SC | IonXpress_001 |
| 111 | CSF1R | c.G2878A | p.A960T | 0.216 | US | SC | IonXpress_001 |
| 112 | NPM1 | c.859_860insTCTG | p.L287fs | 0.225 | KS | SC | IonXpress_001 |
| 113 | EGFR | c.G323A | p.R108K | 0.218 | KS | SC | IonXpress_001 |
| 114 | EGFR | c.G340A | p.E114K | 0.212 | KS | SC | IonXpress_001 |
| 115 | EGFR | c.C866T | p.A289V | 0.218 | KS | SC | IonXpress_001 |
| 116 | EGFR | c.G874T | p.V292L | 0.217 | KS | SC | IonXpress_001 |
| 117 | EGFR | c.G1793T | p.G598V | 0.212 | KS | SC | IonXpress_001 |
| 118 | EGFR | c.G2092A | p.A698T | 0.259 | KS | SC | IonXpress_001 |
| 119 | EGFR | c.G2156C | p.G719A | 0.246 | KS | SC | IonXpress_001 |
| 120 | EGFR | c.G2170A | p.G724S | 0.254 | KS | SC | IonXpress_001 |
| 121 | EGFR | c.C2197T | p.P733S | 0.232 | KS | SC | IonXpress_001 |
| 122 | EGFR | c.G2203A | p.G735S | 0.233 | KS | SC | IonXpress_001 |
| 123 | EGFR | c.C2222T | p.P741L | 0.232 | KS | SC | IonXpress_001 |
| 124 | EGFR | c.2235_2249del | p.745_750del | 0.239 | KS | SC | IonXpress_001 |
| 125 | EGFR | c.G2293A | p.V765M | 0.226 | KS | SC | IonXpress_001 |
| 126 | EGFR | c.T2375C | p.L792P | 0.228 | KS | SC | IonXpress_001 |
| 127 | EGFR | c.T2573G | p.L858R | 0.200 | KS | SC | IonXpress_001 |
| 128 | EGFR | c.T2582A | p.L861Q | 0.201 | KS | SC | IonXpress_001 |
| 129 | EGFR | c.G2588A | p.G863D | 0.196 | KS | SC | IonXpress_001 |
| 130 | EGFR | c.C2612G | p.A871G | 0.197 | KS | SC | IonXpress_001 |
| 131 | MET | c.G504T | p.E168D | 0.242 | US | SC | IonXpress_001 |
| 132 | MET | c.C3370G | p.H1124D | 0.227 | US | SC | IonXpress_001 |
| 133 | MET | c.T3757G | p.Y1253D | 0.213 | US | SC | IonXpress_001 |
| 134 | MET | c.G3778T | p.G1260C | 0.221 | US | SC | IonXpress_001 |
| 135 | MET | c.A3785G | p.K1262R | 0.217 | US | SC | IonXpress_001 |
| 136 | MET | c.T3803C | p.M1268T | 0.221 | US | SC | IonXpress_001 |
| 137 | SMO | c.C595T | p.R199W | 0.204 | US | SC | IonXpress_001 |
| 138 | SMO | c.G970A | p.A324T | 0.206 | US | SC | IonXpress_001 |
| 139 | SMO | c.C1234T | p.L412F | 0.240 | US | SC | IonXpress_001 |
| 140 | SMO | c.G1604T | p.W535L | 0.238 | US | SC | IonXpress_001 |
| 141 | SMO | c.A1918G | p.T640A | 0.203 | US | SC | IonXpress_001 |
| 142 | BRAF | c.T1799A | p.V600E | 0.230 | KS | SC | IonXpress_001 |
| 143 | BRAF | c.T1790G | p.L597R | 0.224 | KS | SC | IonXpress_001 |
| 144 | BRAF | c.A1781G | p.D594G | 0.222 | KS | SC | IonXpress_001 |
| 145 | BRAF | c.A1742G | p.N581S | 0.231 | KS | SC | IonXpress_001 |
| 146 | BRAF | c.G1391T | p.G464V | 0.214 | KS | SC | IonXpress_001 |
| 147 | BRAF | c.C1330T | p.R444W | 0.218 | KS | SC | IonXpress_001 |
| 148 | EZH2 | c.A1937T | p.Y646F | 0.245 | US | SC | IonXpress_001 |
| 149 | FGFR1 | c.A520G | p.T174A | 0.303 | US | SC | IonXpress_001 |
| 150 | FGFR1 | c.C473T | p.S158L | 0.206 | US | SC | IonXpress_001 |
| 151 | JAK2 | c.G1849T | p.V617F | 0.211 | KS | SC | IonXpress_001 |
| 152 | JAK2 | c.C1860A | p.D620E | 0.210 | KS | SC | IonXpress_001 |
| 153 | CDKN2A | c.G358T | p.E120X | 0.278 | US | SC | IonXpress_001 |
| 154 | CDKN2A | c.C341T | p.P114L | 0.274 | US | SC | IonXpress_001 |
| 155 | CDKN2A | c.G330A | p.W110X | 0.274 | US | SC | IonXpress_001 |
| 156 | CDKN2A | c.G322T | p.D108Y | 0.276 | US | SC | IonXpress_001 |
| 157 | CDKN2A | c.G365T | p.R122L | 0.276 | US | SC | IonXpress_001 |
| 158 | CDKN2A | c.C247T | p.H83Y | 0.241 | US | SC | IonXpress_001 |
| 159 | CDKN2A | c.C290T | p.A97V | 0.241 | US | SC | IonXpress_001 |
| 160 | CDKN2A | c.C238T | p.R80X | 0.241 | US | SC | IonXpress_001 |
| 161 | CDKN2A | c.G205T | p.E69X | 0.246 | US | SC | IonXpress_001 |
| 162 | CDKN2A | c.C172T | p.R58X | 0.259 | US | SC | IonXpress_001 |
| 163 | GNAQ | c.680_682GCA | 0.193 | US | SC | IonXpress_001 | |
| 164 | ABL1 | c.C799G | p.L267V | 0.194 | US | SC | IonXpress_001 |
| 165 | ABL1 | c.G806A | p.G269E | 0.190 | US | SC | IonXpress_001 |
| 166 | ABL1 | c.T814C | p.Y272H | 0.192 | US | SC | IonXpress_001 |
| 167 | ABL1 | c.G820A | p.E274K | 0.194 | US | SC | IonXpress_001 |
| 168 | ABL1 | c.A884G | p.D295G | 0.185 | US | SC | IonXpress_001 |
| 169 | ABL1 | c.T1109C | p.M370T | 0.166 | US | SC | IonXpress_001 |
| 170 | ABL1 | c.A1121G | p.E374G | 0.150 | US | SC | IonXpress_001 |
| 171 | ABL1 | c.T1132G | p.F378V | 0.152 | US | SC | IonXpress_001 |
| 172 | ABL1 | c.C1207A | p.L403M | 0.183 | US | SC | IonXpress_001 |
| 173 | ABL1 | c.A1244G | p.H415R | 0.180 | US | SC | IonXpress_001 |
| 174 | NOTCH1 | c.C7412A | p.S2471X | 0.167 | US | SC | IonXpress_001 |
| 175 | NOTCH1 | c.C7375T | p.Q2459X | 0.196 | US | SC | IonXpress_001 |
| 176 | NOTCH1 | c.C7318T | p.Q2440X | 0.202 | US | SC | IonXpress_001 |
| 177 | NOTCH1 | c.T5033C | p.L1678P | 0.174 | US | SC | IonXpress_001 |
| 178 | NOTCH1 | c.T4799C | p.L1600P | 0.111 | US | SC | IonXpress_001 |
| 179 | NOTCH1 | c.G4793C | p.R1598P | 0.107 | US | SC | IonXpress_001 |
| 180 | NOTCH1 | c.T4778C | p.L1593P | 0.108 | US | SC | IonXpress_001 |
| 181 | NOTCH1 | c.T4721C | p.L1574P | 0.111 | US | SC | IonXpress_001 |
| 182 | RET | c.T1852C | p.C618R | 0.180 | US | SC | IonXpress_001 |
| 183 | RET | c.T1858C | p.C620R | 0.172 | US | SC | IonXpress_001 |
| 184 | RET | c.1894delG | p.E632fs | 0.150 | US | SC | IonXpress_001 |
| 185 | RET | c.1899_1906del | p.L633fs | 0.151 | US | SC | IonXpress_001 |
| 186 | RET | c.G2304C | p.E768D | 0.187 | US | SC | IonXpress_001 |
| 187 | RET | c.2647_2648TT | 0.151 | US | SC | IonXpress_001 | |
| 188 | RET | c.G2701A | p.E901K | 0.162 | US | SC | IonXpress_001 |
| 189 | RET | c.T2753C | p.M918T | 0.176 | US | SC | IonXpress_001 |
| 190 | PTEN | c.G19T | p.E7X | 0.177 | US | SC | IonXpress_001 |
| 191 | PTEN | c.A40G | p.R14G | 0.190 | US | SC | IonXpress_001 |
| 192 | PTEN | c.C49T | p.Q17X | 0.183 | US | SC | IonXpress_001 |
| 193 | PTEN | c.A71G | p.D24G | 0.202 | US | SC | IonXpress_001 |
| 194 | PTEN | c.T166G | p.F56V | 0.208 | US | SC | IonXpress_001 |
| 195 | PTEN | c.T202C | p.Y68H | 0.220 | US | SC | IonXpress_001 |
| 196 | PTEN | c.T302C | p.I101T | 0.190 | US | SC | IonXpress_001 |
| 197 | PTEN | c.G314T | p.C105F | 0.188 | US | SC | IonXpress_001 |
| 198 | PTEN | c.C334G | p.L112V | 0.191 | US | SC | IonXpress_001 |
| 199 | PTEN | c.G395A | p.G132D | 0.196 | US | SC | IonXpress_001 |
| 200 | PTEN | c.C697T | p.R233X | 0.227 | US | SC | IonXpress_001 |
| 201 | PTEN | c.G703T | p.E235X | 0.226 | US | SC | IonXpress_001 |
| 202 | PTEN | c.T721C | p.F241L | 0.229 | US | SC | IonXpress_001 |
| 203 | PTEN | c.A787T | p.K263X | 0.233 | US | SC | IonXpress_001 |
| 204 | PTEN | c.795delA | p.L265fs | 0.186 | US | SC | IonXpress_001 |
| 205 | PTEN | c.G895T | p.E299X | 0.173 | US | SC | IonXpress_001 |
| 206 | PTEN | c.950_953del | p.V317fs | 0.207 | US | SC | IonXpress_001 |
| 207 | PTEN | c.A1025G | p.K342R | 0.212 | US | SC | IonXpress_001 |
| 208 | FGFR2 | c.T1650A | p.N550K | 0.095 | US | SC | IonXpress_001 |
| 209 | FGFR2 | c.T1147C | p.C383R | 0.114 | US | SC | IonXpress_001 |
| 210 | FGFR2 | c.A1127G | p.Y376C | 0.114 | US | SC | IonXpress_001 |
| 211 | FGFR2 | c.A1111G | p.T371A | 0.111 | US | SC | IonXpress_001 |
| 212 | FGFR2 | c.A929G | p.K310R | 0.078 | US | SC | IonXpress_001 |
| 213 | FGFR2 | c.G913A | p.G305R | 0.086 | US | SC | IonXpress_001 |
| 214 | FGFR2 | c.C755G | p.S252W | 0.096 | US | SC | IonXpress_001 |
| 215 | HRAS | c.A182G | p.Q61R | 0.080 | US | SC | IonXpress_001 |
| 216 | HRAS | c.G175A | p.A59T | 0.080 | US | SC | IonXpress_001 |
| 217 | HRAS | c.G35T | p.G12V | 0.086 | US | SC | IonXpress_001 |
| 218 | ATM | c.C1009T | p.R337C | 0.077 | US | SC | IonXpress_001 |
| 219 | ATM | c.T1229C | p.V410A | 0.111 | US | SC | IonXpress_001 |
| 220 | ATM | c.C1810T | p.P604S | 0.100 | US | SC | IonXpress_001 |
| 221 | ATM | c.T2572C | p.F858L | 0.093 | US | SC | IonXpress_001 |
| 222 | ATM | c.G3925A | p.A1309T | 0.095 | US | SC | IonXpress_001 |
| 223 | ATM | c.G5044T | p.D1682Y | 0.089 | US | SC | IonXpress_001 |
| 224 | ATM | c.C5188T | p.R1730X | 0.104 | US | SC | IonXpress_001 |
| 225 | ATM | c.G5224C | p.A1742P | 0.098 | US | SC | IonXpress_001 |
| 226 | ATM | c.G5821C | p.V1941L | 0.095 | US | SC | IonXpress_001 |
| 227 | ATM | c.A7325C | p.Q2442P | 0.086 | US | SC | IonXpress_001 |
| 228 | ATM | c.A7996G | p.T2666A | 0.190 | US | SC | IonXpress_001 |
| 229 | ATM | c.G8084C | p.G2695A | 0.082 | US | SC | IonXpress_001 |
| 230 | ATM | c.C8095A | p.P2699T | 0.085 | US | SC | IonXpress_001 |
| 231 | ATM | c.A8174T | p.D2725V | 0.105 | US | SC | IonXpress_001 |
| 232 | ATM | c.A8624G | p.N2875S | 0.104 | US | SC | IonXpress_001 |
| 233 | ATM | c.C8668G | p.L2890V | 0.106 | US | SC | IonXpress_001 |
| 234 | ATM | c.A8839T | p.T2947S | 0.115 | US | SC | IonXpress_001 |
| 235 | ATM | c.G9023A | p.R3008H | 0.098 | US | SC | IonXpress_001 |
| 236 | ATM | c.C9139T | p.R3047X | 0.110 | US | SC | IonXpress_001 |
| 237 | KRAS | c.A351C | p.K117N | 0.096 | KS | SC | IonXpress_001 |
| 238 | KRAS | c.A183C | p.Q61H | 0.092 | KS | SC | IonXpress_001 |
| 239 | KRAS | c.G175A | p.A59T | 0.096 | KS | SC | IonXpress_001 |
| 240 | KRAS | c.C104T | p.T35I | 0.097 | KS | SC | IonXpress_001 |
| 241 | KRAS | c.G35A | p.G12D | 0.099 | KS | SC | IonXpress_001 |
| 242 | PTPN11 | c.G181T | p.D61Y | 0.100 | US | SC | IonXpress_001 |
| 243 | PTPN11 | c.G205A | p.E69K | 0.096 | US | SC | IonXpress_001 |
| 244 | PTPN11 | c.C215T | p.A72V | 0.101 | US | SC | IonXpress_001 |
| 245 | PTPN11 | c.G226A | p.E76K | 0.100 | US | SC | IonXpress_001 |
| 246 | PTPN11 | c.C1472T | p.P491L | 0.106 | US | SC | IonXpress_001 |
| 247 | PTPN11 | c.G1508C | p.G503A | 0.104 | US | SC | IonXpress_001 |
| 248 | PTPN11 | c.A1519G | p.T507A | 0.107 | US | SC | IonXpress_001 |
| 249 | PTPN11 | c.C1528A | p.Q510K | 0.106 | US | SC | IonXpress_001 |
| 250 | HNF1A | c.G617T | p.W206L | 0.094 | US | SC | IonXpress_001 |
| 251 | HNF1A | c.A632C | p.Q211P | 0.099 | US | SC | IonXpress_001 |
| 252 | HNF1A | c.C779T | p.T260M | 0.097 | US | SC | IonXpress_001 |
| 253 | HNF1A | c.C787T | p.R263C | 0.087 | US | SC | IonXpress_001 |
| 254 | FLT3 | c.A2516G | p.D839G | 0.071 | KS | SC | IonXpress_001 |
| 255 | FLT3 | c.G2503T | p.D835Y | 0.063 | KS | SC | IonXpress_001 |
| 256 | FLT3 | c.G2492A | p.G831E | 0.063 | KS | SC | IonXpress_001 |
| 257 | FLT3 | c.C2039T | p.A680V | 0.070 | KS | SC | IonXpress_001 |
| 258 | FLT3 | c.T1775C | p.V592A | 0.055 | KS | SC | IonXpress_001 |
| 259 | RB1 | c.T596A | p.L199X | 0.052 | US | SC | IonXpress_001 |
| 260 | RB1 | c.C958T | p.R320X | 0.056 | US | SC | IonXpress_001 |
| 261 | RB1 | c.A968G | p.E323G | 0.052 | US | SC | IonXpress_001 |
| 262 | RB1 | c.A982G | p.N328D | 0.057 | US | SC | IonXpress_001 |
| 263 | RB1 | c.C1072T | p.R358X | 0.051 | US | SC | IonXpress_001 |
| 264 | RB1 | c.C1363T | p.R455X | 0.064 | US | SC | IonXpress_001 |
| 265 | RB1 | c.C1654T | p.R552X | 0.066 | US | SC | IonXpress_001 |
| 266 | RB1 | c.C1666T | p.R556X | 0.066 | US | SC | IonXpress_001 |
| 267 | RB1 | c.T1687C | p.W563R | 0.067 | US | SC | IonXpress_001 |
| 268 | RB1 | c.C1735T | p.R579X | 0.058 | US | SC | IonXpress_001 |
| 269 | RB1 | c.G2117T | p.C706F | 0.096 | US | SC | IonXpress_001 |
| 270 | RB1 | c.A2143T | p.K715X | 0.094 | US | SC | IonXpress_001 |
| 271 | RB1 | c.A2153G | p.D718G | 0.093 | US | SC | IonXpress_001 |
| 272 | RB1 | c.G2242T | p.E748X | 0.073 | US | SC | IonXpress_001 |
| 273 | RB1 | c.T2261G | p.V754G | 0.077 | US | SC | IonXpress_001 |
| 274 | RB1 | c.A2267G | p.Y756C | 0.075 | US | SC | IonXpress_001 |
| 275 | RB1 | c.A2293T | p.K765X | 0.074 | US | SC | IonXpress_001 |
| 276 | IDH2 | c.G515A | p.R172K | 0.064 | KS | SC | IonXpress_001 |
| 277 | IDH2 | c.G419A | p.R140Q | 0.068 | KS | SC | IonXpress_001 |
| 278 | CDH1 | c.G1204A | p.D402N | 0.056 | US | SC | IonXpress_001 |
| 279 | TP53 | c.G1015T | p.E339X | 0.052 | US | SC | IonXpress_001 |
| 280 | TP53 | c.C916T | p.R306X | 0.057 | US | SC | IonXpress_001 |
| 281 | TP53 | c.G892T | p.E298X | 0.058 | US | SC | IonXpress_001 |
| 282 | TP53 | c.C833T | p.P278L | 0.056 | US | SC | IonXpress_001 |
| 283 | TP53 | c.G818A | p.R273H | 0.056 | US | SC | IonXpress_001 |
| 284 | TP53 | c.G743A | p.R248Q | 0.065 | US | SC | IonXpress_001 |
| 285 | TP53 | c.G733A | p.G245S | 0.058 | US | SC | IonXpress_001 |
| 286 | TP53 | c.C722T | p.S241F | 0.059 | US | SC | IonXpress_001 |
| 287 | TP53 | c.A701G | p.Y234C | 0.066 | US | SC | IonXpress_001 |
| 288 | TP53 | c.A659G | p.Y220C | 0.059 | US | SC | IonXpress_001 |
| 289 | TP53 | c.T653A | p.V218E | 0.059 | US | SC | IonXpress_001 |
| 290 | TP53 | c.G646A | p.V216M | 0.054 | US | SC | IonXpress_001 |
| 291 | TP53 | c.A614G | p.Y205C | 0.051 | US | SC | IonXpress_001 |
| 292 | TP53 | c.G542A | p.R181H | 0.066 | US | SC | IonXpress_001 |
| 293 | TP53 | c.A488G | p.Y163C | 0.060 | US | SC | IonXpress_001 |
| 294 | TP53 | c.G481A | p.A161T | 0.059 | US | SC | IonXpress_001 |
| 295 | TP53 | c.G469T | p.V157F | 0.065 | US | SC | IonXpress_001 |
| 296 | TP53 | c.G404A | p.C135Y | 0.060 | US | SC | IonXpress_001 |
| 297 | TP53 | c.A395G | p.K132R | 0.062 | US | SC | IonXpress_001 |
| 298 | TP53 | c.C388G | p.L130V | 0.062 | US | SC | IonXpress_001 |
| 299 | TP53 | c.C380T | p.S127F | 0.059 | US | SC | IonXpress_001 |
| 300 | TP53 | c.G273A | p.W91X | 0.056 | US | SC | IonXpress_001 |
| 301 | TP53 | c.C245T | p.P82L | 0.072 | US | SC | IonXpress_001 |
| 302 | ERBB2 | c.T2264C | p.L755S | 0.057 | US | SC | IonXpress_001 |
| 303 | ERBB2 | c.G2305T | p.D769Y | 0.056 | US | SC | IonXpress_001 |
| 304 | ERBB2 | c.G2524A | p.V842I | 0.056 | US | SC | IonXpress_001 |
| 305 | ERBB2 | c.A2570G | p.N857S | 0.058 | US | SC | IonXpress_001 |
| 306 | ERBB2 | c.C2632T | p.H878Y | 0.062 | US | SC | IonXpress_001 |
| 307 | SMAD4 | c.T377C | p.V126A | 0.083 | US | SC | IonXpress_001 |
| 308 | SMAD4 | c.C389T | p.P130L | 0.091 | US | SC | IonXpress_001 |
| 309 | SMAD4 | c.C403T | p.R135X | 0.097 | US | SC | IonXpress_001 |
| 310 | SMAD4 | c.C431G | p.S144X | 0.104 | US | SC | IonXpress_001 |
| 311 | SMAD4 | c.G502T | p.G168X | 0.084 | US | SC | IonXpress_001 |
| 312 | SMAD4 | c.C533A | p.S178X | 0.080 | US | SC | IonXpress_001 |
| 313 | SMAD4 | c.C547T | p.Q183X | 0.089 | US | SC | IonXpress_001 |
| 314 | SMAD4 | c.C733T | p.Q245X | 0.084 | US | SC | IonXpress_001 |
| 315 | SMAD4 | c.C766T | p.Q256X | 0.073 | US | SC | IonXpress_001 |
| 316 | SMAD4 | c.C931T | p.Q311X | 0.072 | US | SC | IonXpress_001 |
| 317 | SMAD4 | c.A1001G | p.Q334R | 0.085 | US | SC | IonXpress_001 |
| 318 | SMAD4 | c.A1010G | p.E337G | 0.080 | US | SC | IonXpress_001 |
| 319 | SMAD4 | c.A1018G | p.K340E | 0.085 | US | SC | IonXpress_001 |
| 320 | SMAD4 | c.C1028G | p.S343X | 0.076 | US | SC | IonXpress_001 |
| 321 | SMAD4 | c.G1156C | p.G386R | 0.082 | US | SC | IonXpress_001 |
| 322 | SMAD4 | c.G1216A | p.A406T | 0.082 | US | SC | IonXpress_001 |
| 323 | SMAD4 | c.A1246G | p.R416G | 0.081 | US | SC | IonXpress_001 |
| 324 | SMAD4 | c.C1333T | p.R445X | 0.072 | US | SC | IonXpress_001 |
| 325 | SMAD4 | c.A1504G | p.R502G | 0.082 | US | SC | IonXpress_001 |
| 326 | SMAD4 | c.A1519G | p.K507E | 0.083 | US | SC | IonXpress_001 |
| 327 | SMAD4 | c.G1576T | p.E526X | 0.079 | US | SC | IonXpress_001 |
| 328 | STK11 | c.C475T | p.Q159X | 0.107 | US | SC | IonXpress_001 |
| 329 | STK11 | c.C842T | p.P281L | 0.107 | US | SC | IonXpress_001 |
| 330 | JAK3 | c.G2164A | p.V722I | 0.071 | US | SC | IonXpress_001 |
| 331 | JAK3 | c.C1715T | p.A572V | 0.075 | US | SC | IonXpress_001 |
| 332 | GNAS | c.C2530T | p.R844C | 0.077 | US | SC | IonXpress_001 |
| 333 | GNAS | c.A2609T | p.Q870L | 0.095 | US | SC | IonXpress_001 |
| 334 | SMARCB1 | c.C118T | p.R40X | 0.083 | US | SC | IonXpress_001 |
| 335 | SMARCB1 | c.C141A | p.Y47X | 0.089 | US | SC | IonXpress_001 |
| 336 | SMARCB1 | c.C157T | p.R53X | 0.088 | US | SC | IonXpress_001 |
| 337 | SMARCB1 | c.C472T | p.R158X | 0.067 | US | SC | IonXpress_001 |
| 338 | SMARCB1 | c.C601T | p.R201X | 0.058 | US | SC | IonXpress_001 |
| 339 | SMARCB1 | c.G607A | p.A203T | 0.059 | US | SC | IonXpress_001 |
3 IGV Snapshots
3.1 KRAS c.G34T IonXpress_002
Variant ID:
ExampleIonTorrentRun123.IonXpress_002.KRAS.chr12.25398285.c.G34T
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| KRAS | c.G34T | p.G12C | 0.342 | KS | Sample2 | IonXpress_002 |
3.2 PIK3CA c.A3140G IonXpress_002
3.2.1 Short View
Variant ID:
ExampleIonTorrentRun123.IonXpress_002.PIK3CA.chr3.178952085.c.A3140G
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| PIK3CA | c.A3140G | p.H1047R | 0.176 | US | Sample2 | IonXpress_002 |
3.2.2 Long View
Variant ID:
ExampleIonTorrentRun123.IonXpress_002.PIK3CA.chr3.178952085.c.A3140G
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| PIK3CA | c.A3140G | p.H1047R | 0.176 | US | Sample2 | IonXpress_002 |
3.3 TP53 c.G1015T IonXpress_002
3.3.1 Short View
Variant ID:
ExampleIonTorrentRun123.IonXpress_002.TP53.chr17.7574012.c.G1015T
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| TP53 | c.G1015T | p.E339X | 0.165 | US | Sample2 | IonXpress_002 |
3.3.2 Long View
Variant ID:
ExampleIonTorrentRun123.IonXpress_002.TP53.chr17.7574012.c.G1015T
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| TP53 | c.G1015T | p.E339X | 0.165 | US | Sample2 | IonXpress_002 |
3.4 CTNNB1 c.T97C IonXpress_003
3.4.1 Short View
Variant ID:
ExampleIonTorrentRun123.IonXpress_003.CTNNB1.chr3.41266100.c.T97C
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| CTNNB1 | c.T97C | p.S33P | 0.214 | US | Sample3 | IonXpress_003 |
3.4.2 Long View
Variant ID:
ExampleIonTorrentRun123.IonXpress_003.CTNNB1.chr3.41266100.c.T97C
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| CTNNB1 | c.T97C | p.S33P | 0.214 | US | Sample3 | IonXpress_003 |
3.5 BRAF c.T1799A IonXpress_004
3.5.1 Short View
Variant ID:
ExampleIonTorrentRun123.IonXpress_004.BRAF.chr7.140453136.c.T1799A
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| BRAF | c.T1799A | p.V600E | 0.168 | KS | Sample4 | IonXpress_004 |
3.5.2 Long View
Variant ID:
ExampleIonTorrentRun123.IonXpress_004.BRAF.chr7.140453136.c.T1799A
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| BRAF | c.T1799A | p.V600E | 0.168 | KS | Sample4 | IonXpress_004 |
3.6 APC c.3932dupT IonXpress_005
3.6.1 Short View
Variant ID:
ExampleIonTorrentRun123.IonXpress_005.APC.chr5.112175222.c.3932dupT
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| APC | c.3932dupT | p.I1311fs | 0.151 | US | Sample5 | IonXpress_005 |
3.6.2 Long View
Variant ID:
ExampleIonTorrentRun123.IonXpress_005.APC.chr5.112175222.c.3932dupT
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| APC | c.3932dupT | p.I1311fs | 0.151 | US | Sample5 | IonXpress_005 |
3.7 JAK3 c.G2164A IonXpress_005
Variant ID:
ExampleIonTorrentRun123.IonXpress_005.JAK3.chr19.17945696.c.G2164A
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| JAK3 | c.G2164A | p.V722I | 0.556 | US | Sample5 | IonXpress_005 |
3.8 TP53 c.C742T IonXpress_006
Variant ID:
ExampleIonTorrentRun123.IonXpress_006.TP53.chr17.7577539.c.C742T
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| TP53 | c.C742T | p.R248W | 0.56 | US | Sample1 | IonXpress_006 |
3.9 PTEN c.A43T IonXpress_007
Variant ID:
ExampleIonTorrentRun123.IonXpress_007.PTEN.chr10.89624269.c.A43T
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| PTEN | c.A43T | p.R15X | 0.34 | US | Sample6 | IonXpress_007 |
3.10 TP53 c.C586T IonXpress_007
Variant ID:
ExampleIonTorrentRun123.IonXpress_007.TP53.chr17.7578263.c.C586T
| Gene | Coding | Amino.Acid.Change | Frequency | Review | Sample.Name | Barcode |
|---|---|---|---|---|---|---|
| TP53 | c.C586T | p.R196X | 0.303 | US | Sample6 | IonXpress_007 |
4 System Information
4.1 Hide
4.2 Show
## [1] "Linux 2.6.32-573.3.1.el6.x86_64 #1 SMP Thu Aug 13 22:55:16 UTC 2015"## [1] "/ifs/home/kellys04/projects/clinical_genomic_reporting/reporter_files/test_output2/ExampleIonTorrentRun123/reports/analysis_overview_report"## [1] "Fri Mar 17 14:34:05 EDT 2017"## R version 3.3.0 (2016-05-03)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: CentOS release 6.8 (Final)
##
## locale:
## [1] C
##
## attached base packages:
## [1] stats graphics grDevices utils datasets base
##
## other attached packages:
## [1] knitr_1.15.1
##
## loaded via a namespace (and not attached):
## [1] backports_1.0.4 magrittr_1.5 rprojroot_1.1 tools_3.3.0
## [5] htmltools_0.3.5 yaml_2.1.14 Rcpp_0.12.8 stringi_1.1.2
## [9] rmarkdown_1.3 highr_0.6 methods_3.3.0 stringr_1.1.0
## [13] digest_0.6.11 evaluate_0.10