Example panel was designed to interrogate Acute myeloid leukemia (AML) tumors. 47 genes were in the input to generate the panel. JAK2 was included as specified by the user. However, JAK2 was not mutated in the panel cohort.
The total number of kilo base pairs included in the panel was set by user to 20.
Example panel (only Tier 1 genes) would contain 0.26 DNA Kbps and include 6 genes/gene fragments; it would identify 50.0% of the 196 tumors in the cohort.
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AML
Cancer Types
196 Samples available for analysis
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Tier 1 genes/regions
number of genes/regions 6
maximum mutational coverage 50.0%
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Tier 2 genes/regions
number of genes/regions 20
maximum mutational coverage 72.0%
Gene/region | Panel tier | Bp length gene/region | Cumulative mutational coverage | Cumulative KBps in panel | Relevant mutations | AML coverage |
---|---|---|---|---|---|---|
NPM1 Ex11(aa:287-288) | Tier1 | 5 | 0.265 | 0.005 | Resp | 0.265 |
IDH2 Ex4(aa:140-172) | Tier1 | 97 | 0.347 | 0.102 | Resp | 0.102 |
IDH1 Ex4(aa:132) | Tier1 | 2 | 0.398 | 0.104 | Resp | 0.097 |
RUNX1 Ex5(aa:141-164) | Tier1 | 71 | 0.434 | 0.175 | 0.041 | |
DNMT3A Ex23(aa:882-909) | Tier1 | 83 | 0.469 | 0.258 | Resp | 0.153 |
NRAS Ex3(aa:61) | Tier1 | 3 | 0.5 | 0.261 | Resp Resis | 0.031 |
FLT3 Ex20(aa:835-839) | Tier2 | 14 | 0.526 | 0.275 | 0.087 | |
U2AF1 Ex2(aa:34) | Tier2 | 1 | 0.546 | 0.276 | 0.036 | |
FLT3 Ex14(aa:582-601) | Tier2 | 59 | 0.566 | 0.335 | 0.036 | |
TP53 Ex6(aa:193-223) | Tier2 | 91 | 0.587 | 0.426 | Resp Resis | 0.02 |
WT1 Ex7(aa:370-402) | Tier2 | 97 | 0.607 | 0.523 | 0.041 | |
KIT Ex17(aa:816) | Tier2 | 2 | 0.622 | 0.525 | 0.026 | |
TP53 Ex8(aa:273-286) | Tier2 | 41 | 0.638 | 0.566 | Resp Resis | 0.015 |
EZH2 Ex20(aa:744) | Tier2 | 2 | 0.643 | 0.568 | Resp | 0.01 |
TP53 Ex10(aa:337-342) | Tier2 | 16 | 0.653 | 0.584 | Resp Resis | 0.01 |
KRAS | Tier2 | 570 | 0.663 | 1.154 | Resp Resis | 0.041 |
PHF6 | Tier2 | 1098 | 0.673 | 2.252 | 0.026 | |
NRAS Ex2(aa:12-13) | Tier2 | 4 | 0.679 | 2.256 | Resp Resis | 0.041 |
KIT Ex8(aa:416-418) | Tier2 | 6 | 0.684 | 2.262 | 0.015 | |
RUNX1 Ex6(aa:198-201) | Tier2 | 11 | 0.689 | 2.273 | 0.031 | |
TET2 Ex11(aa:1863-1868) | Tier2 | 15 | 0.694 | 2.288 | 0.01 | |
TP53 Ex5(aa:172-179) | Tier2 | 21 | 0.699 | 2.309 | Resp Resis | 0.015 |
TET2 Ex7(aa:1307-1316) | Tier2 | 27 | 0.704 | 2.336 | 0.01 | |
PTPN11 Ex3(aa:60-72) | Tier2 | 37 | 0.709 | 2.373 | 0.02 | |
TET2 Ex10(aa:1422-1452) | Tier2 | 91 | 0.714 | 2.464 | 0.02 | |
TET2 Ex6(aa:1216) | Tier3 | 1 | 0.719 | 2.465 | 0.01 | |
TET2 Ex3(aa:916-947) | Tier3 | 94 | 0.719 | 2.559 | 0.01 | |
PTPN11 Ex13(aa:491-510) | Tier3 | 59 | 0.719 | 2.618 | 0.02 | |
DNMT3A Ex20(aa:781-792) | Tier3 | 34 | 0.719 | 2.652 | Resp | 0.01 |
DNMT3A Ex13(aa:497-515) | Tier3 | 54 | 0.719 | 2.706 | Resp | 0.015 |
RUNX1 Ex8(aa:314-320) | Tier3 | 18 | 0.719 | 2.724 | 0.01 | |
DNMT3A Ex15(aa:590-615) | Tier3 | 77 | 0.719 | 2.801 | Resp | 0.015 |
DNMT3A Ex19(aa:729-741) | Tier3 | 38 | 0.719 | 2.839 | Resp | 0.026 |
TET2 Ex9(aa:1352-1381) | Tier3 | 88 | 0.719 | 2.927 | 0.015 | |
ASXL1 | Tier2 | 4626 | 0.719 | 7.553 | 0.02 |
Onco Validated oncogenic Resp Drug responsive Resis Drug resistant
Gene/region | Panel tier | Cumulative coverage 1 gene | Cumulative coverage 2 genes | Cumulative coverage 3 genes |
---|---|---|---|---|
NPM1 Ex11(aa:287-288) | Tier1 | 0.265 | 0.0 | 0.0 |
IDH2 Ex4(aa:140-172) | Tier1 | 0.347 | 0.02 | 0.0 |
IDH1 Ex4(aa:132) | Tier1 | 0.398 | 0.066 | 0.0 |
RUNX1 Ex5(aa:141-164) | Tier1 | 0.434 | 0.071 | 0.0 |
DNMT3A Ex23(aa:882-909) | Tier1 | 0.469 | 0.173 | 0.015 |
NRAS Ex3(aa:61) | Tier1 | 0.5 | 0.173 | 0.015 |
FLT3 Ex20(aa:835-839) | Tier2 | 0.526 | 0.204 | 0.036 |
U2AF1 Ex2(aa:34) | Tier2 | 0.546 | 0.219 | 0.036 |
FLT3 Ex14(aa:582-601) | Tier2 | 0.566 | 0.23 | 0.041 |
TP53 Ex6(aa:193-223) | Tier2 | 0.587 | 0.23 | 0.041 |
WT1 Ex7(aa:370-402) | Tier2 | 0.607 | 0.25 | 0.041 |
KIT Ex17(aa:816) | Tier2 | 0.622 | 0.255 | 0.041 |
TP53 Ex8(aa:273-286) | Tier2 | 0.638 | 0.255 | 0.041 |
EZH2 Ex20(aa:744) | Tier2 | 0.643 | 0.255 | 0.041 |
TP53 Ex10(aa:337-342) | Tier2 | 0.653 | 0.255 | 0.041 |
KRAS | Tier2 | 0.663 | 0.265 | 0.061 |
PHF6 | Tier2 | 0.673 | 0.265 | 0.077 |
NRAS Ex2(aa:12-13) | Tier2 | 0.679 | 0.286 | 0.087 |
KIT Ex8(aa:416-418) | Tier2 | 0.684 | 0.291 | 0.087 |
RUNX1 Ex6(aa:198-201) | Tier2 | 0.689 | 0.306 | 0.097 |
TET2 Ex11(aa:1863-1868) | Tier2 | 0.694 | 0.311 | 0.097 |
TP53 Ex5(aa:172-179) | Tier2 | 0.699 | 0.321 | 0.097 |
TET2 Ex7(aa:1307-1316) | Tier2 | 0.704 | 0.321 | 0.102 |
PTPN11 Ex3(aa:60-72) | Tier2 | 0.709 | 0.327 | 0.107 |
TET2 Ex10(aa:1422-1452) | Tier2 | 0.714 | 0.332 | 0.107 |
TET2 Ex6(aa:1216) | Tier3 | 0.719 | 0.362 | 0.122 |
TET2 Ex3(aa:916-947) | Tier3 | 0.719 | 0.372 | 0.153 |
PTPN11 Ex13(aa:491-510) | Tier3 | 0.719 | 0.388 | 0.158 |
DNMT3A Ex20(aa:781-792) | Tier3 | 0.719 | 0.352 | 0.122 |
DNMT3A Ex13(aa:497-515) | Tier3 | 0.719 | 0.372 | 0.143 |
RUNX1 Ex8(aa:314-320) | Tier3 | 0.719 | 0.347 | 0.117 |
DNMT3A Ex15(aa:590-615) | Tier3 | 0.719 | 0.393 | 0.163 |
DNMT3A Ex19(aa:729-741) | Tier3 | 0.719 | 0.372 | 0.133 |
TET2 Ex9(aa:1352-1381) | Tier3 | 0.719 | 0.372 | 0.153 |
ASXL1 | Tier2 | 0.719 | 0.342 | 0.112 |
* Gene with high density mutation hotspots identified
Gene | Exon | Protein coords | Bp length | Mutations count | Mutations proportion | CDS proportion | Genomic coords |
---|---|---|---|---|---|---|---|
KIT | Ex17 | 816 | 2 | 5 | 0.714 | 0.001 | chr4:55599320 |
KIT | Ex8 | 416-418 | 6 | 3 | 0.429 | 0.002 | chr4:55589766-55589771 |
RUNX1 | Ex5 | 141-164 | 71 | 8 | 0.5 | 0.049 | chr21:36252870-36252940 |
RUNX1 | Ex6 | 198-201 | 11 | 6 | 0.375 | 0.008 | chr21:36231782-36231792 |
U2AF1 | Ex2 | 34 | 1 | 7 | 0.875 | 0.001 | chr21:44524456 |
EZH2 | Ex20 | 744 | 2 | 2 | 1.0 | 0.001 | chr7:148504763 |
IDH1 | Ex4 | 132 | 2 | 19 | 1.0 | 0.002 | chr2:209113112 |
PTPN11 | Ex3 | 60-72 | 37 | 4 | 0.444 | 0.021 | chr12:112888163-112888199 |
FLT3 | Ex20 | 835-839 | 14 | 17 | 0.68 | 0.005 | chr13:28592629-28592642 |
FLT3 | Ex14 | 582-601 | 59 | 7 | 0.28 | 0.02 | chr13:28608254-28608312 |
DNMT3A | Ex23 | 882-909 | 83 | 30 | 0.612 | 0.03 | chr2:25457161-25457243 |
NRAS | Ex2 | 12-13 | 4 | 8 | 0.533 | 0.007 | chr1:115258744-115258747 |
NRAS | Ex3 | 61 | 3 | 6 | 0.4 | 0.005 | chr1:115256528 |
IDH2 | Ex4 | 140-172 | 97 | 20 | 1.0 | 0.071 | chr15:90631838-90631934 |
TET2 | Ex10 | 1422-1452 | 91 | 4 | 0.235 | 0.015 | chr4:106193802-106193892 |
TET2 | Ex11 | 1863-1868 | 15 | 2 | 0.118 | 0.002 | chr4:106197255-106197269 |
TET2 | Ex7 | 1307-1316 | 27 | 2 | 0.118 | 0.004 | chr4:106180893-106180919 |
WT1 | Ex7 | 370-402 | 97 | 8 | 0.8 | 0.062 | chr11:32417846-32417942 |
TP53 | Ex6 | 193-223 | 91 | 4 | 0.308 | 0.077 | chr17:7578182-7578272 |
TP53 | Ex8 | 273-286 | 41 | 3 | 0.231 | 0.035 | chr17:7577081-7577121 |
TP53 | Ex5 | 172-179 | 21 | 3 | 0.231 | 0.018 | chr17:7578394-7578414 |
TP53 | Ex10 | 337-342 | 16 | 2 | 0.154 | 0.014 | chr17:7574003-7574018 |
NPM1 | Ex11 | 287-288 | 5 | 52 | 0.963 | 0.006 | chr5:170837544-170837548 |
* Gene with high density mutation regions identified
Gene | Exon | Protein coords | Bp length | Mutations count | Mutations proportion | CDS proportion | Genomic coords |
---|---|---|---|---|---|---|---|
KIT | Ex17 | 816 | 2 | 5 | 0.714 | 0.001 | chr4:55599320 |
KIT | Ex8 | 416-418 | 6 | 3 | 0.429 | 0.002 | chr4:55589766-55589771 |
RUNX1 | Ex5 | 141-164 | 71 | 8 | 0.5 | 0.049 | chr21:36252870-36252940 |
RUNX1 | Ex6 | 198-201 | 11 | 6 | 0.375 | 0.008 | chr21:36231782-36231792 |
U2AF1 | Ex2 | 34 | 1 | 7 | 0.875 | 0.001 | chr21:44524456 |
EZH2 | Ex20 | 744 | 2 | 2 | 1.0 | 0.001 | chr7:148504763 |
IDH1 | Ex4 | 132 | 2 | 19 | 1.0 | 0.002 | chr2:209113112 |
PTPN11 | Ex3 | 60-72 | 37 | 4 | 0.444 | 0.021 | chr12:112888163-112888199 |
FLT3 | Ex20 | 835-839 | 14 | 17 | 0.68 | 0.005 | chr13:28592629-28592642 |
FLT3 | Ex14 | 582-601 | 59 | 7 | 0.28 | 0.02 | chr13:28608254-28608312 |
DNMT3A | Ex23 | 882-909 | 83 | 30 | 0.612 | 0.03 | chr2:25457161-25457243 |
NRAS | Ex2 | 12-13 | 4 | 8 | 0.533 | 0.007 | chr1:115258744-115258747 |
NRAS | Ex3 | 61 | 3 | 6 | 0.4 | 0.005 | chr1:115256528 |
IDH2 | Ex4 | 140-172 | 97 | 20 | 1.0 | 0.071 | chr15:90631838-90631934 |
TET2 | Ex10 | 1422-1452 | 91 | 4 | 0.235 | 0.015 | chr4:106193802-106193892 |
TET2 | Ex11 | 1863-1868 | 15 | 2 | 0.118 | 0.002 | chr4:106197255-106197269 |
TET2 | Ex7 | 1307-1316 | 27 | 2 | 0.118 | 0.004 | chr4:106180893-106180919 |
WT1 | Ex7 | 370-402 | 97 | 8 | 0.8 | 0.062 | chr11:32417846-32417942 |
TP53 | Ex6 | 193-223 | 91 | 4 | 0.308 | 0.077 | chr17:7578182-7578272 |
TP53 | Ex8 | 273-286 | 41 | 3 | 0.231 | 0.035 | chr17:7577081-7577121 |
TP53 | Ex5 | 172-179 | 21 | 3 | 0.231 | 0.018 | chr17:7578394-7578414 |
TP53 | Ex10 | 337-342 | 16 | 2 | 0.154 | 0.014 | chr17:7574003-7574018 |
NPM1 | Ex11 | 287-288 | 5 | 52 | 0.963 | 0.006 | chr5:170837544-170837548 |
Gene | Panel tier | Driver mode of action | Driver source | Major driver |
---|---|---|---|---|
ASXL1 | Tier2 | Loss of function | Rubio-Perez&Tamborero(2015) | |
KRAS | Tier2 | Activating | Rubio-Perez&Tamborero(2015), CGC, Validated somatic mutation list | |
PHF6 | Tier2 | Loss of function | Rubio-Perez&Tamborero(2015) | |
DNMT3A | Tier1 | Loss of function | Validated somatic mutation list, Rubio-Perez&Tamborero(2015), CGC | |
EZH2 | Tier2 | Loss of function | Rubio-Perez&Tamborero(2015) | |
FLT3 | Tier2 | Activating | Validated somatic mutation list, Rubio-Perez&Tamborero(2015), CGC | |
IDH1 | Tier1 | Activating | Validated somatic mutation list, Rubio-Perez&Tamborero(2015) | |
IDH2 | Tier1 | Activating | Validated somatic mutation list, Rubio-Perez&Tamborero(2015) | |
KIT | Tier2 | Activating | Validated somatic mutation list, Rubio-Perez&Tamborero(2015), CGC | |
NPM1 | Tier1 | Loss of function | Validated somatic mutation list, Rubio-Perez&Tamborero(2015), CGC | |
NRAS | Tier1&Tier2 | Activating | Validated somatic mutation list, Rubio-Perez&Tamborero(2015), CGC | |
PTPN11 | Tier2 | Activating | Rubio-Perez&Tamborero(2015), CGC | |
RUNX1 | Tier1&Tier2 | Loss of function | Validated somatic mutation list, Rubio-Perez&Tamborero(2015) | |
TET2 | Tier2 | Loss of function | Rubio-Perez&Tamborero(2015) | |
TP53 | Tier2 | Loss of function | Validated somatic mutation list, Rubio-Perez&Tamborero(2015) | |
U2AF1 | Tier2 | Activating | Validated somatic mutation list, Rubio-Perez&Tamborero(2015) | |
WT1 | Tier2 | Loss of function | Validated somatic mutation list, Rubio-Perez&Tamborero(2015) |