Disease intelligence · mutation landscape
Gastrointestinal stromal tumour mutation landscape
How often each gene is altered in gastrointestinal stromal tumour, in each sequenced cohort, over the patients on whom it could have been called. Copy number is its own row. Nothing is pooled.
Answer block
In Gastrointestinal Stromal Tumors (MSK, Clin Cancer Res 2023) (469 sequenced patients, targeted panel), the most frequently altered of the 47 genes shown are KIT 75.27%, CDKN2A 21.11% (deep deletion), PDGFRA 11.09%, NF1 4.48%, TP53 4.48%. Each figure divides by the patients on whom that gene could be called.
Of the briefing's 12 curated targets, 5 are altered in under 2% of this cohort (SDHB, SDHC, SDHD, BRAF, ETV1): targets by expression, dependency or drug label, not by mutation. Frequency is not targetability, in either direction.
2 cohorts are shown and none are pooled; overlap between them has not been checked and there is no disease-wide percentage.
Evidence boundary: frequency here is a count in a named cohort. Whether an alteration is a driver, is actionable, or has a drug is the briefing's question and is not inferred from these numbers.
What is altered, by cohort
One row per alteration, not per gene: a gene that is amplified and rarely mutated (ERBB2, MYCN, EGFR) gets a row for each. Every cell divides by its own denominator — the patients in that cohort on whom that gene could be called. Copy-number rows are shown only where at least one cohort reaches 2%.
| Alteration | gist_msk_2023 469 pts · targeted panel | gist_msk_2022 499 pts · targeted panel |
|---|---|---|
| KIT SNV / small indel | 75.27%353/469 | 76.95%384/499 |
| KIT amplification | 3.2%15/469 | 3.81%19/499 |
| PDGFRA SNV / small indel | 11.09%52/469 | 9.82%49/499 |
| PDGFRA amplification | 1.92%9/469 | 2.0%10/499 |
| SDHB SNV / small indel | 0.43%2/469 | 0.4%2/499 |
| SDHA SNV / small indel | 1.92%9/469 | 2.0%10/499 |
| SDHA amplification | 2.35%11/469 | 2.0%10/499 |
| SDHC SNV / small indel | 0% | 0% |
| SDHD SNV / small indel | 0% | 0% |
| NF1 SNV / small indel | 4.48%21/469 | 4.01%20/499 |
| BRAF SNV / small indel | 0.43%2/469 | 0.4%2/499 |
| ETV1 SNV / small indel | 0% | 0% |
| ANO1 SNV / small indel | · | · |
| CDKN2A SNV / small indel | 0% | 0.2%1/499 |
| CDKN2A deep deletion | 21.11%99/469 | 22.04%110/499 |
| TP53 SNV / small indel | 4.48%21/469 | 4.21%21/499 |
| SETD2 SNV / small indel | 4.05%19/469 | 4.01%20/499 |
| MGA SNV / small indel | 4.03%18/447 | 3.76%18/479 |
| MAX SNV / small indel | 3.84%18/469 | 3.41%17/499 |
| RB1 SNV / small indel | 3.62%17/469 | 3.01%15/499 |
| RB1 deep deletion | 3.2%15/469 | 2.81%14/499 |
| CSDE1 SNV / small indel | 3.22%11/342 | 3.21%12/374 |
| PTEN SNV / small indel | 2.13%10/469 | 2.61%13/499 |
| PIK3CA SNV / small indel | 1.92%9/469 | 1.8%9/499 |
| TSC1 SNV / small indel | 1.71%8/469 | 2.0%10/499 |
| ARID1A SNV / small indel | 1.71%8/469 | 1.4%7/499 |
| KMT2D SNV / small indel | 1.49%7/469 | 0.4%2/499 |
| CREBBP SNV / small indel | 1.49%7/469 | 1.0%5/499 |
| ROS1 SNV / small indel | 1.28%6/469 | 1.0%5/499 |
| MTOR SNV / small indel | 1.28%6/469 | 1.2%6/499 |
| ZFHX3 SNV / small indel | 1.12%5/447 | 0.63%3/479 |
| KMT2C SNV / small indel | 1.07%5/469 | 1.2%6/499 |
| KMT2A SNV / small indel | 1.07%5/469 | 0.6%3/499 |
| CBL SNV / small indel | 1.07%5/469 | 1.2%6/499 |
| ATM SNV / small indel | 1.07%5/469 | 1.4%7/499 |
| TET2 SNV / small indel | 0.85%4/469 | 0.6%3/499 |
| PIK3R1 SNV / small indel | 0.85%4/469 | 0.6%3/499 |
| PIK3C2G SNV / small indel | 0.85%4/469 | 0.6%3/499 |
| JAK1 SNV / small indel | 0.85%4/469 | 0.8%4/499 |
| IRS2 SNV / small indel | 0.85%4/469 | 0.8%4/499 |
| GRIN2A SNV / small indel | 0.85%4/469 | 0.8%4/499 |
| ATRX SNV / small indel | 0.85%4/469 | 0.8%4/499 |
| ARID2 SNV / small indel | 0.85%4/469 | 0.6%3/499 |
| TSC2 SNV / small indel | 0.64%3/469 | 0.4%2/499 |
| TRAF7 SNV / small indel | 0.64%3/469 | 0.6%3/499 |
| TP63 SNV / small indel | 0.64%3/469 | 0.6%3/499 |
| TGFBR2 SNV / small indel | 0.64%3/469 | 0.8%4/499 |
| RPTOR SNV / small indel | 0.64%3/469 | 0.2%1/499 |
| RET SNV / small indel | 0.64%3/469 | 0.6%3/499 |
| RBM10 SNV / small indel | 0.64%3/469 | 0.6%3/499 |
| RAD50 SNV / small indel | 0.64%3/469 | 0.6%3/499 |
| PTPRD SNV / small indel | 0.64%3/469 | 0.4%2/499 |
observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable
Key findings
KIT is mutated in 353 of 469 patients in Gastrointestinal Stromal Tumors (MSK, Clin Cancer Res 2023).
CDKN2A is deleted in 99 of 469 patients in Gastrointestinal Stromal Tumors (MSK, Clin Cancer Res 2023).
PDGFRA is mutated in 52 of 469 patients in Gastrointestinal Stromal Tumors (MSK, Clin Cancer Res 2023).
Gene table — reference cohort
Headline values are from the reference cohort, gist_msk_2023; the matrix above keeps every cohort separate. "Curated" marks a gene the disease briefing lists as a target; the rest are here because they are among the most frequently mutated genes in the reference cohort. Recurrent changes are the reference cohort's commonest protein changes.
| Gene | Why listed | Largest alteration | Altered / tested | Frequency | Without hypermutated | Cohorts observed | Range across cohorts | Recurrent changes |
|---|---|---|---|---|---|---|---|---|
| KIT | curated target | SNV / small indel | 353 / 469 | 75.27% | — | 2 / 2 | 75.27–76.95% | A502_Y503dup (n=34), W557_K558del (n=31), V559D (n=21), N822K (n=16), V654A (n=14) |
| PDGFRA | curated target | SNV / small indel | 52 / 469 | 11.09% | — | 2 / 2 | 9.82–11.09% | D842V (n=29), V561D (n=5), N659K (n=3), I843_D846del (n=3), D846Y (n=2) |
| SDHB | curated target | SNV / small indel | 2 / 469 | 0.43% | — | 2 / 2 | 0.4–0.43% | R46* (n=1), R230G (n=1) |
| SDHA | curated target | amplification | 11 / 469 | 2.35% mutation 1.92% | — | 2 / 2 | 1.92–2.0% | R31* (n=1), C311F (n=1), R512* (n=1), R188Q (n=1), S445L (n=1) |
| SDHC | curated target | SNV / small indel | 0 / 469 | 0.0% | — | 0 / 2 | 0.0–0.0% | none recurrent |
| SDHD | curated target | SNV / small indel | 0 / 469 | 0.0% | — | 0 / 2 | 0.0–0.0% | none recurrent |
| NF1 | curated target | SNV / small indel | 21 / 469 | 4.48% | — | 2 / 2 | 4.01–4.48% | F1275Pfs*8 (n=1), Q83Vfs*23 (n=1), R1241Qfs*25 (n=1), K111* (n=1), Q181* (n=1) |
| BRAF | curated target | SNV / small indel | 2 / 469 | 0.43% | — | 2 / 2 | 0.4–0.43% | V600E (n=2) |
| ETV1 | curated target | amplification | 4 / 469 | 0.85% mutation 0.0% | — | 0 / 2 | 0.0–0.0% | none recurrent |
| ANO1 | curated target | SNV / small indel | 0 / null | 0.0% | — | 0 / 2 | null–null% | none recurrent |
| CDKN2A | curated target | deep deletion | 99 / 469 | 21.11% mutation 0.0% | — | 1 / 2 | 0.0–0.2% | none recurrent |
| TP53 | curated target | SNV / small indel | 21 / 469 | 4.48% | — | 2 / 2 | 4.21–4.48% | V216M (n=1), M340Dfs*7 (n=1), C275Y (n=1), R248Q (n=1), P27S (n=1) |
| SETD2 | by frequency | SNV / small indel | 19 / 469 | 4.05% | — | 2 / 2 | 4.01–4.05% | S204* (n=1), K2001* (n=1), I277T (n=1), E750* (n=1), N1396Kfs*2 (n=1) |
| MGA | by frequency | SNV / small indel | 18 / 447 | 4.03% | — | 2 / 2 | 3.76–4.03% | H1803Y (n=1), I2540Nfs*17 (n=1), X698_splice (n=1), P1956Hfs*22 (n=1), T1197Mfs*2 (n=1) |
| MAX | by frequency | SNV / small indel | 18 / 469 | 3.84% | — | 2 / 2 | 3.41–3.84% | R33* (n=1), Q91Pfs*53 (n=1), R75* (n=1), R35L (n=1), Y70Ifs*100 (n=1) |
| RB1 | by frequency | SNV / small indel | 17 / 469 | 3.62% | — | 2 / 2 | 3.01–3.62% | C438Vfs*19 (n=1), X738_splice (n=1), E54* (n=1), X654_splice (n=1), L477R (n=1) |
| CSDE1 | by frequency | SNV / small indel | 11 / 342 | 3.22% | — | 2 / 2 | 3.21–3.22% | P487* (n=1), X396_splice (n=1), Y184Ifs*2 (n=1), R145* (n=1), X593_splice (n=1) |
| PTEN | by frequency | SNV / small indel | 10 / 469 | 2.13% | — | 2 / 2 | 2.13–2.61% | C105S (n=1), G129R (n=1), I28M (n=1), I33del (n=1), D324N (n=1) |
| PIK3CA | by frequency | SNV / small indel | 9 / 469 | 1.92% | — | 2 / 2 | 1.8–1.92% | H1047L (n=2), R88Q (n=1), V344M (n=1), H1047R (n=1), G106R (n=1) |
| TSC1 | by frequency | SNV / small indel | 8 / 469 | 1.71% | — | 2 / 2 | 1.71–2.0% | S276Lfs*42 (n=1), Q3Hfs*23 (n=1), E218* (n=1), Q830H (n=1), X246_splice (n=1) |
| ARID1A | by frequency | SNV / small indel | 8 / 469 | 1.71% | — | 2 / 2 | 1.4–1.71% | E1060del (n=1), R110Efs*3 (n=1), R1109W (n=1), Q2037Pfs*62 (n=1), Y500Ffs*120 (n=1) |
| KMT2D | by frequency | SNV / small indel | 7 / 469 | 1.49% | — | 2 / 2 | 0.4–1.49% | Q3601* (n=1), X1377_splice (n=1), L1271V (n=1), T4938Nfs*56 (n=1), L1721F (n=1) |
| CREBBP | by frequency | SNV / small indel | 7 / 469 | 1.49% | — | 2 / 2 | 1.0–1.49% | Q786P (n=1), P1647H (n=1), N374Y (n=1), R1140Q (n=1), Q1113* (n=1) |
| ROS1 | by frequency | SNV / small indel | 6 / 469 | 1.28% | — | 2 / 2 | 1.0–1.28% | R1467* (n=1), I1514V (n=1), S2297Y (n=1), W847C (n=1), G830V (n=1) |
| MTOR | by frequency | SNV / small indel | 6 / 469 | 1.28% | — | 2 / 2 | 1.2–1.28% | A1459D (n=1), X1871_splice (n=1), M2057I (n=1), T571R (n=1), K1465E (n=1) |
| ZFHX3 | by frequency | SNV / small indel | 5 / 447 | 1.12% | — | 2 / 2 | 0.63–1.12% | C2835S (n=1), A472E (n=1), R1119Q (n=1), K3239E (n=1), G3523_G3527del (n=1) |
| KMT2C | by frequency | SNV / small indel | 5 / 469 | 1.07% | — | 2 / 2 | 1.07–1.2% | P4310S (n=1), G3435V (n=1), Q587P (n=1), F4496Lfs*21 (n=1), T3504S (n=1) |
| KMT2A | by frequency | SNV / small indel | 5 / 469 | 1.07% | — | 2 / 2 | 0.6–1.07% | M1018I (n=1), R1249G (n=1), P193Rfs*10 (n=1), S1294* (n=1), K212R (n=1) |
| CBL | by frequency | SNV / small indel | 5 / 469 | 1.07% | — | 2 / 2 | 1.07–1.2% | C384R (n=1), X410_splice (n=1), Y368N (n=1), S667Pfs*35 (n=1), Y368C (n=1) |
| ATM | by frequency | SNV / small indel | 5 / 469 | 1.07% | — | 2 / 2 | 1.07–1.4% | K3004E (n=1), I2888T (n=1), G1746* (n=1), D203N (n=1), T909Nfs*11 (n=1) |
| TET2 | by frequency | SNV / small indel | 4 / 469 | 0.85% | — | 2 / 2 | 0.6–0.85% | L1514I (n=1), D299E (n=1), C1932F (n=1), G641E (n=1) |
| PIK3R1 | by frequency | SNV / small indel | 4 / 469 | 0.85% | — | 2 / 2 | 0.6–0.85% | K567_L570del (n=1), N564K (n=1), N564D (n=1), D168N (n=1) |
| PIK3C2G | by frequency | SNV / small indel | 4 / 469 | 0.85% | — | 2 / 2 | 0.6–0.85% | F171L (n=1), H99L (n=1), G564R (n=1), X731_splice (n=1) |
| JAK1 | by frequency | SNV / small indel | 4 / 469 | 0.85% | — | 2 / 2 | 0.8–0.85% | R997Q (n=1), V36M (n=1), R997W (n=1), I855T (n=1) |
| IRS2 | by frequency | SNV / small indel | 4 / 469 | 0.85% | — | 2 / 2 | 0.8–0.85% | G1188S (n=1), S555C (n=1), V1299I (n=1), C409Y (n=1) |
| GRIN2A | by frequency | SNV / small indel | 4 / 469 | 0.85% | — | 2 / 2 | 0.8–0.85% | F553L (n=1), T141K (n=1), R1288H (n=1), A818V (n=1) |
| ATRX | by frequency | SNV / small indel | 4 / 469 | 0.85% | — | 2 / 2 | 0.8–0.85% | G1945R (n=1), E822G (n=1), I2145M (n=1), T1529N (n=1) |
| ARID2 | by frequency | SNV / small indel | 4 / 469 | 0.85% | — | 2 / 2 | 0.6–0.85% | X1757_splice (n=1), K1791R (n=1), M667L (n=1), R143_L148del (n=1) |
| TSC2 | by frequency | SNV / small indel | 3 / 469 | 0.64% | — | 2 / 2 | 0.4–0.64% | K658del (n=1), W441R (n=1), L1423P (n=1) |
| TRAF7 | by frequency | SNV / small indel | 3 / 469 | 0.64% | — | 2 / 2 | 0.6–0.64% | C670W (n=1), N18Pfs*108 (n=1), S158A (n=1) |
| TP63 | by frequency | SNV / small indel | 3 / 469 | 0.64% | — | 2 / 2 | 0.6–0.64% | S471N (n=1), R647C (n=1), T434M (n=1) |
| TGFBR2 | by frequency | SNV / small indel | 3 / 469 | 0.64% | — | 2 / 2 | 0.64–0.8% | G549E (n=1), T309M (n=1), S353F (n=1) |
| RPTOR | by frequency | SNV / small indel | 3 / 469 | 0.64% | — | 2 / 2 | 0.2–0.64% | R583T (n=1), R788C (n=1), V327M (n=1) |
| RET | by frequency | deep deletion | 4 / 469 | 0.85% mutation 0.64% | — | 2 / 2 | 0.6–0.64% | C216Y (n=1), D267N (n=1), R833C (n=1) |
| RBM10 | by frequency | SNV / small indel | 3 / 469 | 0.64% | — | 2 / 2 | 0.6–0.64% | E219* (n=1), X622_splice (n=1), R739L (n=1) |
| RAD50 | by frequency | SNV / small indel | 3 / 469 | 0.64% | — | 2 / 2 | 0.6–0.64% | L1195F (n=1), -933fs (n=1), K574Nfs*24 (n=1) |
| PTPRD | by frequency | SNV / small indel | 3 / 469 | 0.64% | — | 2 / 2 | 0.4–0.64% | G855C (n=1), W630* (n=1), S1333N (n=1) |
Cohorts
Listed in the disease profile, not searched: a name search returns the same patients under several accessions. Patients are unique patient ids in the study's sequenced sample list. Hypermutated: more than ten times the cohort's median non-silent mutations per sample, and at least 100.
| Cohort | Accession | Patients | Samples sequenced / in study | Assay | Panels (samples) | Build | Profiles read | Hypermutated patients | Median mutations / sample |
|---|---|---|---|---|---|---|---|---|---|
| Gastrointestinal Stromal Tumors (MSK, Clin Cancer Res 2023) reference | gist_msk_2023 | 469 observed | 469 / 469 | targeted panel | IMPACT468 (281), IMPACT410 (105), IMPACT505 (61), IMPACT341 (22) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 0 | 2 |
| Gastrointestinal Stromal Tumor (MSK, NPJ Precis Oncol 2023) | gist_msk_2022 | 499 observed | 499 / 499 | targeted panel | IMPACT468 (308), IMPACT410 (105), IMPACT505 (66), IMPACT341 (20) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 0 | 2 |
Copy-number events
Discrete calls from each study's copy-number profile: 2 is high-level amplification, −2 deep deletion. Gains and shallow losses are not counted. Denominators are the cohort's copy-number sample list, which differs from its sequenced list. Rows at 2% or more.
| Gene | Event | Observed patients | Tested patients | Frequency | Cohort | Profile |
|---|---|---|---|---|---|---|
| CDKN2A | deep deletion | 110 | 499 | 22.04% | gist_msk_2022 | gist_msk_2022_cna |
| CDKN2A | deep deletion | 99 | 469 | 21.11% | gist_msk_2023 | gist_msk_2023_cna |
| KIT | amplification | 19 | 499 | 3.81% | gist_msk_2022 | gist_msk_2022_cna |
| KIT | amplification | 15 | 469 | 3.2% | gist_msk_2023 | gist_msk_2023_cna |
| RB1 | deep deletion | 15 | 469 | 3.2% | gist_msk_2023 | gist_msk_2023_cna |
| RB1 | deep deletion | 14 | 499 | 2.81% | gist_msk_2022 | gist_msk_2022_cna |
| SDHA | amplification | 11 | 469 | 2.35% | gist_msk_2023 | gist_msk_2023_cna |
| PDGFRA | amplification | 10 | 499 | 2.0% | gist_msk_2022 | gist_msk_2022_cna |
| SDHA | amplification | 10 | 499 | 2.0% | gist_msk_2022 | gist_msk_2022_cna |
Cohort-aware frequencies
Each row is calculated from unique patients in that study's sequenced sample list. The range is descriptive; no pooled estimate is shown because cross-study overlap and assay comparability have not been checked.
| Gene | Range | Per cohort (altered / tested) |
|---|---|---|
| KIT | 75.27–76.95% | gist_msk_2023: 353/469 (75.27%) · gist_msk_2022: 384/499 (76.95%) |
| PDGFRA | 9.82–11.09% | gist_msk_2023: 52/469 (11.09%) · gist_msk_2022: 49/499 (9.82%) |
| SDHB | 0.4–0.43% | gist_msk_2023: 2/469 (0.43%) · gist_msk_2022: 2/499 (0.4%) |
| SDHA | 1.92–2.0% | gist_msk_2023: 9/469 (1.92%) · gist_msk_2022: 10/499 (2.0%) |
| SDHC | 0.0–0.0% | gist_msk_2023: 0/469 (0.0%) · gist_msk_2022: 0/499 (0.0%) |
| SDHD | 0.0–0.0% | gist_msk_2023: 0/469 (0.0%) · gist_msk_2022: 0/499 (0.0%) |
| NF1 | 4.01–4.48% | gist_msk_2023: 21/469 (4.48%) · gist_msk_2022: 20/499 (4.01%) |
| BRAF | 0.4–0.43% | gist_msk_2023: 2/469 (0.43%) · gist_msk_2022: 2/499 (0.4%) |
| ETV1 | 0.0–0.0% | gist_msk_2023: 0/469 (0.0%) · gist_msk_2022: 0/499 (0.0%) |
| ANO1 | null–null% | gist_msk_2023: not assayed · gist_msk_2022: not assayed |
| CDKN2A | 0.0–0.2% | gist_msk_2023: 0/469 (0.0%) · gist_msk_2022: 1/499 (0.2%) |
| TP53 | 4.21–4.48% | gist_msk_2023: 21/469 (4.48%) · gist_msk_2022: 21/499 (4.21%) |
| SETD2 | 4.01–4.05% | gist_msk_2023: 19/469 (4.05%) · gist_msk_2022: 20/499 (4.01%) |
| MGA | 3.76–4.03% | gist_msk_2023: 18/447 (4.03%) · gist_msk_2022: 18/479 (3.76%) |
| MAX | 3.41–3.84% | gist_msk_2023: 18/469 (3.84%) · gist_msk_2022: 17/499 (3.41%) |
| RB1 | 3.01–3.62% | gist_msk_2023: 17/469 (3.62%) · gist_msk_2022: 15/499 (3.01%) |
| CSDE1 | 3.21–3.22% | gist_msk_2023: 11/342 (3.22%) · gist_msk_2022: 12/374 (3.21%) |
| PTEN | 2.13–2.61% | gist_msk_2023: 10/469 (2.13%) · gist_msk_2022: 13/499 (2.61%) |
| PIK3CA | 1.8–1.92% | gist_msk_2023: 9/469 (1.92%) · gist_msk_2022: 9/499 (1.8%) |
| TSC1 | 1.71–2.0% | gist_msk_2023: 8/469 (1.71%) · gist_msk_2022: 10/499 (2.0%) |
| ARID1A | 1.4–1.71% | gist_msk_2023: 8/469 (1.71%) · gist_msk_2022: 7/499 (1.4%) |
| KMT2D | 0.4–1.49% | gist_msk_2023: 7/469 (1.49%) · gist_msk_2022: 2/499 (0.4%) |
| CREBBP | 1.0–1.49% | gist_msk_2023: 7/469 (1.49%) · gist_msk_2022: 5/499 (1.0%) |
| ROS1 | 1.0–1.28% | gist_msk_2023: 6/469 (1.28%) · gist_msk_2022: 5/499 (1.0%) |
| MTOR | 1.2–1.28% | gist_msk_2023: 6/469 (1.28%) · gist_msk_2022: 6/499 (1.2%) |
| ZFHX3 | 0.63–1.12% | gist_msk_2023: 5/447 (1.12%) · gist_msk_2022: 3/479 (0.63%) |
| KMT2C | 1.07–1.2% | gist_msk_2023: 5/469 (1.07%) · gist_msk_2022: 6/499 (1.2%) |
| KMT2A | 0.6–1.07% | gist_msk_2023: 5/469 (1.07%) · gist_msk_2022: 3/499 (0.6%) |
| CBL | 1.07–1.2% | gist_msk_2023: 5/469 (1.07%) · gist_msk_2022: 6/499 (1.2%) |
| ATM | 1.07–1.4% | gist_msk_2023: 5/469 (1.07%) · gist_msk_2022: 7/499 (1.4%) |
| TET2 | 0.6–0.85% | gist_msk_2023: 4/469 (0.85%) · gist_msk_2022: 3/499 (0.6%) |
| PIK3R1 | 0.6–0.85% | gist_msk_2023: 4/469 (0.85%) · gist_msk_2022: 3/499 (0.6%) |
| PIK3C2G | 0.6–0.85% | gist_msk_2023: 4/469 (0.85%) · gist_msk_2022: 3/499 (0.6%) |
| JAK1 | 0.8–0.85% | gist_msk_2023: 4/469 (0.85%) · gist_msk_2022: 4/499 (0.8%) |
| IRS2 | 0.8–0.85% | gist_msk_2023: 4/469 (0.85%) · gist_msk_2022: 4/499 (0.8%) |
| GRIN2A | 0.8–0.85% | gist_msk_2023: 4/469 (0.85%) · gist_msk_2022: 4/499 (0.8%) |
| ATRX | 0.8–0.85% | gist_msk_2023: 4/469 (0.85%) · gist_msk_2022: 4/499 (0.8%) |
| ARID2 | 0.6–0.85% | gist_msk_2023: 4/469 (0.85%) · gist_msk_2022: 3/499 (0.6%) |
| TSC2 | 0.4–0.64% | gist_msk_2023: 3/469 (0.64%) · gist_msk_2022: 2/499 (0.4%) |
| TRAF7 | 0.6–0.64% | gist_msk_2023: 3/469 (0.64%) · gist_msk_2022: 3/499 (0.6%) |
| TP63 | 0.6–0.64% | gist_msk_2023: 3/469 (0.64%) · gist_msk_2022: 3/499 (0.6%) |
| TGFBR2 | 0.64–0.8% | gist_msk_2023: 3/469 (0.64%) · gist_msk_2022: 4/499 (0.8%) |
| RPTOR | 0.2–0.64% | gist_msk_2023: 3/469 (0.64%) · gist_msk_2022: 1/499 (0.2%) |
| RET | 0.6–0.64% | gist_msk_2023: 3/469 (0.64%) · gist_msk_2022: 3/499 (0.6%) |
| RBM10 | 0.6–0.64% | gist_msk_2023: 3/469 (0.64%) · gist_msk_2022: 3/499 (0.6%) |
| RAD50 | 0.6–0.64% | gist_msk_2023: 3/469 (0.64%) · gist_msk_2022: 3/499 (0.6%) |
| PTPRD | 0.4–0.64% | gist_msk_2023: 3/469 (0.64%) · gist_msk_2022: 2/499 (0.4%) |
What this page does not do
Structural variants
Read the structural-variant profiles the studies carry; fusions are the defining event in several of these diseases.
Context
Stage, subtype, age and treatment line are not attached to any count; the cohorts differ on all four.
Interpretation
Activating versus inactivating, actionable versus not, and evidence level are not inferred here; the briefing's target table carries the drug and trial facts.
Limitations
- A cBioPortal public-API snapshot retrieved 2026-09-18; the page does not refresh source data at request time.
- Counts are patients with at least one non-silent call in the study's sequenced sample list; silent, intronic and UTR calls are excluded.
- For targeted-panel cohorts each gene divides by the patients whose panel carried it; a gene absent from the panel is shown as not assayed, not as zero.
- Copy-number rows use discrete calls (2 = high-level amplification, −2 = deep deletion) against the cohort's copy-number sample list, which is a different roster from the sequenced one.
- Cohorts are not pooled. Cross-study patient overlap has not been checked and no disease-wide frequency is reported.
- Structural variants and fusions are not read in this snapshot even where the study carries a profile; germline variants, mutational signatures, TMB and MSI are not reported.
- The gene set is the briefing's curated targets plus the reference cohort's most frequently mutated genes; it is not genome-wide.
How a machine should read this page
- Denominators: every frequency divides by the patients in one named cohort on whom the gene could be called; there is no disease-wide figure.
- Missing values:
not_assayed(the panel did not carry the gene),not_observed(assayed, none found) andnot_evaluable(the cohort could not be read) are three different facts and are never converted to zero. - Counting: patients, not samples; several samples from one patient count once. Non-silent calls only.
- Copy number: a separate assay with a separate roster; discrete calls at ±2 only.
- Hypermutation: flagged per cohort; the headline keeps all patients and the frequency without them is reported beside it.
- Provenance: every value carries the study id, the retrieval date and the processing version; the source is the cBioPortal public API.
Machine endpoints: full landscape · genes · cohorts · the disease's own facts: /disease/gastrointestinal-stromal-tumor.json.
Built by the BioTransfer briefings pipeline from the cBioPortal public API. The neuroblastoma page was assembled by hand and set the rules this page follows; how these are built.