Disease intelligence · mutation landscape
Myelodysplastic syndromes mutation landscape
How often each gene is altered in myelodysplastic syndromes, 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 IWG-PM myelodysplastic syndromes (NEJM Evidence 2022) (3323 sequenced patients, targeted panel), the most frequently altered of the 41 genes shown are TET2 31.39%, ASXL1 28.41%, SF3B1 22.69%, SRSF2 17.39%, DNMT3A 16.04%. Each figure divides by the patients on whom that gene could be called.
Of the briefing's 12 curated targets, 1 are altered in under 2% of this cohort (BCL2): 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 | mds_iwg_2022 3323 pts · targeted panel | mds_mskcc_2020 4231 pts · mixed |
|---|---|---|
| SF3B1 SNV / small indel | 22.69%754/3323 | 8.93%378/4231 |
| TP53 SNV / small indel | 11.74%390/3323 | 9.41%398/4231 |
| TET2 SNV / small indel | 31.39%1043/3323 | 16.12%682/4231 |
| ASXL1 SNV / small indel | 28.41%944/3323 | 10.26%434/4231 |
| DNMT3A SNV / small indel | 16.04%533/3323 | 20.14%852/4231 |
| RUNX1 SNV / small indel | 13.99%465/3323 | 9.57%405/4231 |
| SRSF2 SNV / small indel | 17.39%578/3323 | 9.81%415/4231 |
| U2AF1 SNV / small indel | 8.7%289/3323 | 4.77%202/4231 |
| EZH2 SNV / small indel | 7.22%240/3323 | 3.99%169/4231 |
| STAG2 SNV / small indel | 9.3%309/3323 | 4.4%186/4231 |
| IDH2 SNV / small indel | 5.39%179/3323 | 8.48%359/4231 |
| BCL2 SNV / small indel | 0.06%2/3323 | 0% |
| KMT2D SNV / small indel | 6.68%222/3323 | 2.08%75/3601 |
| BCOR SNV / small indel | 6.62%220/3323 | 3.71%157/4231 |
| ZRSR2 SNV / small indel | 6.02%200/3323 | 2.15%91/4231 |
| CBL SNV / small indel | 5.99%199/3323 | 3.17%134/4231 |
| CUX1 SNV / small indel | 5.66%188/3323 | 1.2%43/3598 |
| NF1 SNV / small indel | 5.57%185/3323 | 2.67%96/3601 |
| SETBP1 SNV / small indel | 5.39%179/3323 | 2.25%51/2265 |
| NRAS SNV / small indel | 5.39%179/3323 | 11.63%492/4231 |
| KMT2C SNV / small indel | 5.03%167/3323 | 1.97%71/3601 |
| SRCAP SNV / small indel | 4.6%153/3323 | 0.58%6/1026 |
| NOTCH1 SNV / small indel | 4.06%135/3323 | 0.87%37/4231 |
| JAK2 SNV / small indel | 4.06%135/3323 | 7.94%336/4231 |
| EP300 SNV / small indel | 3.91%130/3323 | 2.47%89/3601 |
| MGA SNV / small indel | 3.88%129/3323 | 0.49%8/1638 |
| KRAS SNV / small indel | 3.76%125/3323 | 4.35%184/4231 |
| DDX41 SNV / small indel | 3.73%124/3323 | 0.78%8/1026 |
| YLPM1 SNV / small indel | 3.61%120/3323 | 0.29%3/1026 |
| PHF6 SNV / small indel | 3.46%115/3323 | 2.65%112/4228 |
| KMT2A SNV / small indel | 3.4%113/3323 | 0.99%42/4231 |
| CREBBP SNV / small indel | 3.31%110/3323 | 1.14%41/3601 |
| IDH1 SNV / small indel | 3.28%109/3323 | 6.22%263/4231 |
| SMG1 SNV / small indel | 3.16%105/3323 | 0.61%10/1635 |
| NOTCH2 SNV / small indel | 3.16%105/3323 | 0.67%11/1638 |
| SH2B3 SNV / small indel | 3.04%101/3323 | 0.53%19/3601 |
| ARID1A SNV / small indel | 3.01%100/3323 | 0.49%8/1638 |
| MPL SNV / small indel | 2.92%97/3323 | 1.11%47/4231 |
| SETD2 SNV / small indel | 2.89%96/3323 | 0.79%13/1638 |
| PHIP SNV / small indel | 2.86%95/3323 | 0.97%10/1026 |
| ETNK1 SNV / small indel | 2.74%91/3323 | 0.37%6/1635 |
observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable
Key findings
TET2 is mutated in 1043 of 3323 patients in IWG-PM myelodysplastic syndromes (NEJM Evidence 2022).
ASXL1 is mutated in 944 of 3323 patients in IWG-PM myelodysplastic syndromes (NEJM Evidence 2022).
SF3B1 is mutated in 754 of 3323 patients in IWG-PM myelodysplastic syndromes (NEJM Evidence 2022).
Gene table — reference cohort
Headline values are from the reference cohort, mds_iwg_2022; 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 |
|---|---|---|---|---|---|---|---|---|
| SF3B1 | curated target | SNV / small indel | 754 / 3323 | 22.69% | — | 2 / 2 | 8.93–22.69% | K700E (n=426), H662Q (n=55), K666N (n=41), R625C (n=38), E622D (n=30) |
| TP53 | curated target | SNV / small indel | 390 / 3323 | 11.74% | — | 2 / 2 | 9.41–11.74% | R273H (n=28), Y220C (n=17), R248Q (n=16), R175H (n=12), R248W (n=12) |
| TET2 | curated target | SNV / small indel | 1043 / 3323 | 31.39% | — | 2 / 2 | 16.12–31.39% | I1873T (n=25), R550* (n=21), R1516* (n=19), N275Ifs*18 (n=18), H1380Y (n=15) |
| ASXL1 | curated target | SNV / small indel | 944 / 3323 | 28.41% | — | 2 / 2 | 10.26–28.41% | G646Wfs*12 (n=371), E635Rfs*15 (n=114), R693* (n=40), Y591* (n=25), R1068* (n=12) |
| DNMT3A | curated target | SNV / small indel | 533 / 3323 | 16.04% | — | 2 / 2 | 16.04–20.14% | R882H (n=81), R882C (n=32), Y735C (n=10), R635Q (n=8), X866_splice (n=7) |
| RUNX1 | curated target | SNV / small indel | 465 / 3323 | 13.99% | — | 2 / 2 | 9.57–13.99% | R201Q (n=27), R201* (n=15), R320* (n=15), R166* (n=14), R107C (n=10) |
| SRSF2 | curated target | SNV / small indel | 578 / 3323 | 17.39% | — | 2 / 2 | 9.81–17.39% | P95H (n=246), P95L (n=147), P95R (n=84), P95_R102del (n=60), P95A (n=9) |
| U2AF1 | curated target | SNV / small indel | 289 / 3323 | 8.7% | — | 2 / 2 | 4.77–8.7% | Q157P (n=102), S34F (n=97), Q157R (n=38), S34Y (n=19), R156H (n=13) |
| EZH2 | curated target | SNV / small indel | 240 / 3323 | 7.22% | — | 2 / 2 | 3.99–7.22% | R690H (n=10), X732_splice (n=6), R690C (n=6), X243_splice (n=5), R207* (n=5) |
| STAG2 | curated target | SNV / small indel | 309 / 3323 | 9.3% | — | 2 / 2 | 4.4–9.3% | R259* (n=17), R614* (n=16), R216* (n=13), R1012* (n=10), R953* (n=8) |
| IDH2 | curated target | SNV / small indel | 179 / 3323 | 5.39% | — | 2 / 2 | 5.39–8.48% | R140Q (n=142), R172K (n=13), R140W (n=8), Y179D (n=1), V147I (n=1) |
| BCL2 | curated target | SNV / small indel | 2 / 3323 | 0.06% | — | 1 / 2 | 0.0–0.06% | R109C (n=1), P40S (n=1) |
| KMT2D | by frequency | SNV / small indel | 222 / 3323 | 6.68% | — | 2 / 2 | 2.08–6.68% | A2379V (n=4), L2610P (n=3), E749G (n=3), P2146L (n=3), Q3899K (n=2) |
| BCOR | by frequency | SNV / small indel | 220 / 3323 | 6.62% | — | 2 / 2 | 3.71–6.62% | X1476_splice (n=7), L1646Pfs*6 (n=5), N1495S (n=4), X1659_splice (n=4), R1547* (n=4) |
| ZRSR2 | by frequency | SNV / small indel | 200 / 3323 | 6.02% | — | 2 / 2 | 2.15–6.02% | X276_splice (n=20), X68_splice (n=9), R126* (n=8), R295* (n=6), R290* (n=5) |
| CBL | by frequency | SNV / small indel | 199 / 3323 | 5.99% | — | 2 / 2 | 3.17–5.99% | R420Q (n=24), C404Y (n=15), L380P (n=12), R149* (n=6), C384R (n=6) |
| CUX1 | by frequency | SNV / small indel | 188 / 3323 | 5.66% | — | 2 / 2 | 1.2–5.66% | P431Sfs*16 (n=7), R996* (n=5), R1261* (n=5), X688_splice (n=3), L784V (n=3) |
| NF1 | by frequency | SNV / small indel | 185 / 3323 | 5.57% | — | 2 / 2 | 2.67–5.57% | I679Dfs*21 (n=21), K2547Qfs*9 (n=13), R1276Q (n=6), Y2264* (n=4), L2690Cfs*28 (n=3) |
| SETBP1 | by frequency | SNV / small indel | 179 / 3323 | 5.39% | — | 2 / 2 | 2.25–5.39% | D868N (n=62), G870S (n=26), I871T (n=10), S869N (n=5), M1319T (n=5) |
| NRAS | by frequency | SNV / small indel | 179 / 3323 | 5.39% | — | 2 / 2 | 5.39–11.63% | G12D (n=67), G13D (n=25), G12S (n=21), G12V (n=20), G13V (n=12) |
| KMT2C | by frequency | SNV / small indel | 167 / 3323 | 5.03% | — | 2 / 2 | 1.97–5.03% | S321N (n=5), D372V (n=5), G824D (n=4), S784Y (n=4), N2830H (n=3) |
| SRCAP | by frequency | SNV / small indel | 153 / 3323 | 4.6% | — | 2 / 2 | 0.58–4.6% | D81H (n=2), R1025* (n=2), N1078S (n=2), P2217S (n=2), A1591V (n=2) |
| NOTCH1 | by frequency | SNV / small indel | 135 / 3323 | 4.06% | — | 2 / 2 | 0.87–4.06% | V2536I (n=3), V726I (n=3), R2313Q (n=3), L2457V (n=2), G2300R (n=2) |
| JAK2 | by frequency | SNV / small indel | 135 / 3323 | 4.06% | — | 2 / 2 | 4.06–7.94% | V617F (n=84), G571S (n=4), I899T (n=4), R564L (n=2), E543_D544del (n=2) |
| EP300 | by frequency | SNV / small indel | 130 / 3323 | 3.91% | — | 2 / 2 | 2.47–3.91% | Y638C (n=7), P784L (n=4), P747L (n=3), L1520V (n=3), L2393V (n=3) |
| MGA | by frequency | SNV / small indel | 129 / 3323 | 3.88% | — | 2 / 2 | 0.49–3.88% | V599L (n=5), H1325Q (n=3), S1629F (n=2), V2842I (n=2), N1279T (n=2) |
| KRAS | by frequency | SNV / small indel | 125 / 3323 | 3.76% | — | 2 / 2 | 3.76–4.35% | G12R (n=14), G12D (n=14), K117N (n=9), G13D (n=9), T58I (n=8) |
| DDX41 | by frequency | SNV / small indel | 124 / 3323 | 3.73% | — | 2 / 2 | 0.78–3.73% | R525H (n=34), M1? (n=18), D140Gfs*2 (n=9), G530D (n=7), P321L (n=6) |
| YLPM1 | by frequency | SNV / small indel | 120 / 3323 | 3.61% | — | 2 / 2 | 0.29–3.61% | G255Wfs*3 (n=8), R784C (n=3), R789C (n=2), P593Q (n=2), T1989A (n=2) |
| PHF6 | by frequency | SNV / small indel | 115 / 3323 | 3.46% | — | 2 / 2 | 2.65–3.46% | I314T (n=11), R274* (n=5), R319* (n=5), R225* (n=5), R274Q (n=5) |
| KMT2A | by frequency | SNV / small indel | 113 / 3323 | 3.4% | — | 2 / 2 | 0.99–3.4% | K895R (n=2), L1303V (n=2), R3564Q (n=2), G3439S (n=2), S1861R (n=2) |
| CREBBP | by frequency | SNV / small indel | 110 / 3323 | 3.31% | — | 2 / 2 | 1.14–3.31% | S1934P (n=6), W1745* (n=5), E1709* (n=4), W1718* (n=4), Y1204F (n=4) |
| IDH1 | by frequency | SNV / small indel | 109 / 3323 | 3.28% | — | 2 / 2 | 3.28–6.22% | R132C (n=38), R132H (n=36), R132G (n=7), R132L (n=4), R314H (n=3) |
| SMG1 | by frequency | SNV / small indel | 105 / 3323 | 3.16% | — | 2 / 2 | 0.61–3.16% | Y1547H (n=2), A3141V (n=2), P2247A (n=2), N1636S (n=2), A1331T (n=2) |
| NOTCH2 | by frequency | SNV / small indel | 105 / 3323 | 3.16% | — | 2 / 2 | 0.67–3.16% | P287A (n=2), Q1791H (n=2), V1666I (n=2), L775V (n=2), R285H (n=2) |
| SH2B3 | by frequency | SNV / small indel | 101 / 3323 | 3.04% | — | 2 / 2 | 0.53–3.04% | E208Q (n=12), E523Rfs*23 (n=11), R308* (n=2), D231Y (n=2), R392W (n=2) |
| ARID1A | by frequency | SNV / small indel | 100 / 3323 | 3.01% | — | 2 / 2 | 0.49–3.01% | P1560A (n=3), N2220S (n=3), A167dup (n=2), G127dup (n=2), V1982I (n=2) |
| MPL | by frequency | SNV / small indel | 97 / 3323 | 2.92% | — | 2 / 2 | 1.11–2.92% | W515L (n=12), Y591D (n=8), V556F (n=6), R592* (n=6), R592Q (n=5) |
| SETD2 | by frequency | SNV / small indel | 96 / 3323 | 2.89% | — | 2 / 2 | 0.79–2.89% | K629E (n=5), N1943K (n=2), P2057S (n=2), G1967D (n=2), G508V (n=2) |
| PHIP | by frequency | SNV / small indel | 95 / 3323 | 2.86% | — | 2 / 2 | 0.97–2.86% | R110C (n=2), X14_splice (n=2), I1622V (n=2), X509_splice (n=2), R797C (n=2) |
| ETNK1 | by frequency | SNV / small indel | 91 / 3323 | 2.74% | — | 2 / 2 | 0.37–2.74% | N244S (n=61), G245D (n=3), N244Y (n=2), S124R (n=2), P248R (n=2) |
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 |
|---|---|---|---|---|---|---|---|---|---|
| IWG-PM myelodysplastic syndromes (NEJM Evidence 2022) reference | mds_iwg_2022 | 3323 observed | 3323 / 3323 | targeted panel | MDSIWG152 (3323) | hg19 | SNV, small indel | 0 | 4 |
| MSK myelodysplastic syndromes (2020) | mds_mskcc_2020 | 4231 observed | 4231 / 4231 | mixed | Papaemmanuil_NEJM_2016_MDS_2013_panel (1963), WES (1026), RDTB49 (630), IMPACT-HEME-400 (609), IMPACT468 (2), IMPACT410 (1) | hg19 | SNV, small indel | 22 | 3 |
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 |
|---|---|---|---|---|---|---|
| No copy-number profile reached 2% for any listed gene, or no cohort carries one. | ||||||
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) |
|---|---|---|
| SF3B1 | 8.93–22.69% | mds_iwg_2022: 754/3323 (22.69%) · mds_mskcc_2020: 378/4231 (8.93%) |
| TP53 | 9.41–11.74% | mds_iwg_2022: 390/3323 (11.74%) · mds_mskcc_2020: 398/4231 (9.41%) |
| TET2 | 16.12–31.39% | mds_iwg_2022: 1043/3323 (31.39%) · mds_mskcc_2020: 682/4231 (16.12%) |
| ASXL1 | 10.26–28.41% | mds_iwg_2022: 944/3323 (28.41%) · mds_mskcc_2020: 434/4231 (10.26%) |
| DNMT3A | 16.04–20.14% | mds_iwg_2022: 533/3323 (16.04%) · mds_mskcc_2020: 852/4231 (20.14%) |
| RUNX1 | 9.57–13.99% | mds_iwg_2022: 465/3323 (13.99%) · mds_mskcc_2020: 405/4231 (9.57%) |
| SRSF2 | 9.81–17.39% | mds_iwg_2022: 578/3323 (17.39%) · mds_mskcc_2020: 415/4231 (9.81%) |
| U2AF1 | 4.77–8.7% | mds_iwg_2022: 289/3323 (8.7%) · mds_mskcc_2020: 202/4231 (4.77%) |
| EZH2 | 3.99–7.22% | mds_iwg_2022: 240/3323 (7.22%) · mds_mskcc_2020: 169/4231 (3.99%) |
| STAG2 | 4.4–9.3% | mds_iwg_2022: 309/3323 (9.3%) · mds_mskcc_2020: 186/4231 (4.4%) |
| IDH2 | 5.39–8.48% | mds_iwg_2022: 179/3323 (5.39%) · mds_mskcc_2020: 359/4231 (8.48%) |
| BCL2 | 0.0–0.06% | mds_iwg_2022: 2/3323 (0.06%) · mds_mskcc_2020: 0/1638 (0.0%) |
| KMT2D | 2.08–6.68% | mds_iwg_2022: 222/3323 (6.68%) · mds_mskcc_2020: 75/3601 (2.08%) |
| BCOR | 3.71–6.62% | mds_iwg_2022: 220/3323 (6.62%) · mds_mskcc_2020: 157/4231 (3.71%) |
| ZRSR2 | 2.15–6.02% | mds_iwg_2022: 200/3323 (6.02%) · mds_mskcc_2020: 91/4231 (2.15%) |
| CBL | 3.17–5.99% | mds_iwg_2022: 199/3323 (5.99%) · mds_mskcc_2020: 134/4231 (3.17%) |
| CUX1 | 1.2–5.66% | mds_iwg_2022: 188/3323 (5.66%) · mds_mskcc_2020: 43/3598 (1.2%) |
| NF1 | 2.67–5.57% | mds_iwg_2022: 185/3323 (5.57%) · mds_mskcc_2020: 96/3601 (2.67%) |
| SETBP1 | 2.25–5.39% | mds_iwg_2022: 179/3323 (5.39%) · mds_mskcc_2020: 51/2265 (2.25%) |
| NRAS | 5.39–11.63% | mds_iwg_2022: 179/3323 (5.39%) · mds_mskcc_2020: 492/4231 (11.63%) |
| KMT2C | 1.97–5.03% | mds_iwg_2022: 167/3323 (5.03%) · mds_mskcc_2020: 71/3601 (1.97%) |
| SRCAP | 0.58–4.6% | mds_iwg_2022: 153/3323 (4.6%) · mds_mskcc_2020: 6/1026 (0.58%) |
| NOTCH1 | 0.87–4.06% | mds_iwg_2022: 135/3323 (4.06%) · mds_mskcc_2020: 37/4231 (0.87%) |
| JAK2 | 4.06–7.94% | mds_iwg_2022: 135/3323 (4.06%) · mds_mskcc_2020: 336/4231 (7.94%) |
| EP300 | 2.47–3.91% | mds_iwg_2022: 130/3323 (3.91%) · mds_mskcc_2020: 89/3601 (2.47%) |
| MGA | 0.49–3.88% | mds_iwg_2022: 129/3323 (3.88%) · mds_mskcc_2020: 8/1638 (0.49%) |
| KRAS | 3.76–4.35% | mds_iwg_2022: 125/3323 (3.76%) · mds_mskcc_2020: 184/4231 (4.35%) |
| DDX41 | 0.78–3.73% | mds_iwg_2022: 124/3323 (3.73%) · mds_mskcc_2020: 8/1026 (0.78%) |
| YLPM1 | 0.29–3.61% | mds_iwg_2022: 120/3323 (3.61%) · mds_mskcc_2020: 3/1026 (0.29%) |
| PHF6 | 2.65–3.46% | mds_iwg_2022: 115/3323 (3.46%) · mds_mskcc_2020: 112/4228 (2.65%) |
| KMT2A | 0.99–3.4% | mds_iwg_2022: 113/3323 (3.4%) · mds_mskcc_2020: 42/4231 (0.99%) |
| CREBBP | 1.14–3.31% | mds_iwg_2022: 110/3323 (3.31%) · mds_mskcc_2020: 41/3601 (1.14%) |
| IDH1 | 3.28–6.22% | mds_iwg_2022: 109/3323 (3.28%) · mds_mskcc_2020: 263/4231 (6.22%) |
| SMG1 | 0.61–3.16% | mds_iwg_2022: 105/3323 (3.16%) · mds_mskcc_2020: 10/1635 (0.61%) |
| NOTCH2 | 0.67–3.16% | mds_iwg_2022: 105/3323 (3.16%) · mds_mskcc_2020: 11/1638 (0.67%) |
| SH2B3 | 0.53–3.04% | mds_iwg_2022: 101/3323 (3.04%) · mds_mskcc_2020: 19/3601 (0.53%) |
| ARID1A | 0.49–3.01% | mds_iwg_2022: 100/3323 (3.01%) · mds_mskcc_2020: 8/1638 (0.49%) |
| MPL | 1.11–2.92% | mds_iwg_2022: 97/3323 (2.92%) · mds_mskcc_2020: 47/4231 (1.11%) |
| SETD2 | 0.79–2.89% | mds_iwg_2022: 96/3323 (2.89%) · mds_mskcc_2020: 13/1638 (0.79%) |
| PHIP | 0.97–2.86% | mds_iwg_2022: 95/3323 (2.86%) · mds_mskcc_2020: 10/1026 (0.97%) |
| ETNK1 | 0.37–2.74% | mds_iwg_2022: 91/3323 (2.74%) · mds_mskcc_2020: 6/1635 (0.37%) |
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 2026-09-17; 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/myelodysplastic-syndromes.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.