Disease intelligence · mutation landscape
Head and neck cancer mutation landscape
How often each gene is altered in head and neck cancer, 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 Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas) (515 sequenced patients, exome or genome), the most frequently altered of the 46 genes shown are TP53 68.54%, CDKN2A 30.75% (deep deletion), CCND1 23.21% (amplification), FAT1 21.55%, PIK3CA 17.48%. Each figure divides by the patients on whom that gene could be called.
4 of 515 patients are hypermutated (more than 990 non-silent mutations, ten times the cohort median of 99); every gene's frequency without them is beside the headline.
Of the briefing's 12 curated targets, 1 are altered in under 2% of this cohort (PDCD1): 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 | hnsc_tcga_pan_can_atlas_2018 515 pts · exome or genome | hnc_mskcc_2016 151 pts · targeted panel |
|---|---|---|
| TP53 SNV / small indel | 68.54%353/515 | 40.4%61/151 |
| CDKN2A SNV / small indel | 20.39%105/515 | 14.57%22/151 |
| CDKN2A deep deletion | 30.75%159/517 | 6.62%10/151 |
| PIK3CA SNV / small indel | 17.48%90/515 | 12.58%19/151 |
| PIK3CA amplification | 15.67%81/517 | 2.65%4/151 |
| EGFR SNV / small indel | 2.52%13/515 | 2.65%4/151 |
| EGFR amplification | 10.44%54/517 | 4.64%7/151 |
| CD274 SNV / small indel | 0.39%2/515 | 0% |
| CD274 amplification | 4.45%23/517 | 2.65%4/151 |
| PDCD1 SNV / small indel | 0.39%2/515 | 0.66%1/151 |
| NOTCH1 SNV / small indel | 17.09%88/515 | 21.85%33/151 |
| FAT1 SNV / small indel | 21.55%111/515 | 14.57%22/151 |
| FAT1 deep deletion | 6.77%35/517 | 0.66%1/151 |
| CCND1 SNV / small indel | 0.39%2/515 | 0.66%1/151 |
| CCND1 amplification | 23.21%120/517 | 5.3%8/151 |
| HRAS SNV / small indel | 6.02%31/515 | 5.96%9/151 |
| NFE2L2 SNV / small indel | 5.44%28/515 | 5.3%8/151 |
| NFE2L2 amplification | 3.29%17/517 | 0% |
| TERT SNV / small indel | 0.58%3/515 | 1.32%2/151 |
| TERT amplification | 5.03%26/517 | 1.32%2/151 |
| KMT2D SNV / small indel | 14.95%77/515 | 16.56%25/151 |
| NSD1 SNV / small indel | 11.65%60/515 | 5.3%8/151 |
| CASP8 SNV / small indel | 10.68%55/515 | 3.97%6/151 |
| HUWE1 SNV / small indel | 9.71%50/515 | · |
| FAM135B SNV / small indel | 9.71%50/515 | · |
| FAM135B amplification | 7.16%37/517 | 0% |
| SI SNV / small indel | 9.51%49/515 | · |
| SI amplification | 9.67%50/517 | 0% |
| RELN SNV / small indel | 9.13%47/515 | · |
| RELN amplification | 3.09%16/517 | 0% |
| PCDH15 SNV / small indel | 8.54%44/515 | · |
| PCDH11X SNV / small indel | 7.57%39/515 | · |
| LAMA2 SNV / small indel | 7.57%39/515 | · |
| HERC2 SNV / small indel | 7.38%38/515 | · |
| NAV3 SNV / small indel | 7.18%37/515 | · |
| KMT2C SNV / small indel | 7.18%37/515 | 9.93%15/151 |
| EP300 SNV / small indel | 7.18%37/515 | 4.64%7/151 |
| UNC13C SNV / small indel | 6.99%36/515 | · |
| VPS13B SNV / small indel | 6.6%34/515 | · |
| VPS13B amplification | 4.06%21/517 | 0% |
| PRDM9 SNV / small indel | 6.6%34/515 | · |
| PRDM9 amplification | 2.9%15/517 | 0% |
| PKHD1 SNV / small indel | 6.41%33/515 | · |
| PEG3 SNV / small indel | 6.41%33/515 | · |
| NPAP1 SNV / small indel | 6.41%33/515 | · |
| FMN2 SNV / small indel | 6.41%33/515 | · |
| FBXW7 SNV / small indel | 6.41%33/515 | 2.65%4/151 |
| FAT2 SNV / small indel | 6.21%32/515 | · |
| AKAP9 SNV / small indel | 6.21%32/515 | · |
| AKAP9 amplification | 3.87%20/517 | 0% |
| THSD7A SNV / small indel | 6.02%31/515 | · |
| MROH2B SNV / small indel | 6.02%31/515 | · |
| MROH2B amplification | 3.87%20/517 | 0% |
| LRP1 SNV / small indel | 6.02%31/515 | · |
| CDH10 SNV / small indel | 6.02%31/515 | · |
| CDH10 amplification | 2.9%15/517 | 0% |
| ASPM SNV / small indel | 6.02%31/515 | · |
| SCN1A SNV / small indel | 5.83%30/515 | · |
| RNF213 SNV / small indel | 5.83%30/515 | · |
| MDN1 SNV / small indel | 5.83%30/515 | · |
| DCHS2 SNV / small indel | 5.83%30/515 | · |
| CREBBP SNV / small indel | 5.83%30/515 | 5.3%8/151 |
observed — shade scales with frequency, full at 30% assayed, none found not on this cohort's panel cohort not readable
Key findings
TP53 is mutated in 353 of 515 patients in Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas).
CDKN2A is deleted in 159 of 517 patients in Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas).
CCND1 is amplified in 120 of 517 patients in Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas).
Gene table — reference cohort
Headline values are from the reference cohort, hnsc_tcga_pan_can_atlas_2018; 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 |
|---|---|---|---|---|---|---|---|---|
| TP53 | curated target | SNV / small indel | 353 / 515 | 68.54% | 68.49% | 2 / 2 | 40.4–68.54% | R175H (n=12), R282W (n=11), R248Q (n=11), G245S (n=8), R273H (n=8) |
| CDKN2A | curated target | deep deletion | 159 / 517 | 30.75% mutation 20.39% | 20.16% | 2 / 2 | 14.57–20.39% | R80* (n=23), R58* (n=12), W110* (n=10), X153_splice (n=9), E120* (n=5) |
| PIK3CA | curated target | SNV / small indel | 90 / 515 | 17.48% | 17.42% | 2 / 2 | 12.58–17.48% | E545K (n=26), E542K (n=19), H1047R (n=13), E726K (n=2), Q546R (n=2) |
| EGFR | curated target | amplification | 54 / 517 | 10.44% mutation 2.52% | 2.54% | 2 / 2 | 2.52–2.65% | D191N (n=1), G503S (n=1), A419P (n=1), I475V (n=1), P373Q (n=1) |
| CD274 | curated target | amplification | 23 / 517 | 4.45% mutation 0.39% | 0.39% | 1 / 2 | 0.0–0.39% | F259L (n=1), E71K (n=1) |
| PDCD1 | curated target | deep deletion | 8 / 517 | 1.55% mutation 0.39% | 0.39% | 2 / 2 | 0.39–0.66% | R112M (n=1), V239Rfs*6 (n=1) |
| NOTCH1 | curated target | SNV / small indel | 88 / 515 | 17.09% | 17.03% | 2 / 2 | 17.09–21.85% | E455K (n=3), R353C (n=2), A465T (n=2), G481C (n=1), Q513Hfs*116 (n=1) |
| FAT1 | curated target | SNV / small indel | 111 / 515 | 21.55% | 21.72% | 2 / 2 | 14.57–21.55% | S3373* (n=3), R937* (n=2), S2838* (n=2), R3400* (n=2), Q1694* (n=2) |
| CCND1 | curated target | amplification | 120 / 517 | 23.21% mutation 0.39% | 0.39% | 2 / 2 | 0.39–0.66% | P287L (n=1), D282H (n=1) |
| HRAS | curated target | SNV / small indel | 31 / 515 | 6.02% | 5.87% | 2 / 2 | 5.96–6.02% | G13V (n=8), G12S (n=7), G13R (n=3), Q61L (n=3), G12D (n=3) |
| NFE2L2 | curated target | SNV / small indel | 28 / 515 | 5.44% | 5.48% | 2 / 2 | 5.3–5.44% | E79Q (n=3), D29H (n=3), E79K (n=3), D262E (n=1), R34P (n=1) |
| TERT | curated target | amplification | 26 / 517 | 5.03% mutation 0.58% | 0.59% | 2 / 2 | 0.58–1.32% | P771L (n=1), R248W (n=1), G915D (n=1) |
| KMT2D | by frequency | SNV / small indel | 77 / 515 | 14.95% | 14.68% | 2 / 2 | 14.95–16.56% | Q2380* (n=2), R1252* (n=2), H5114Y (n=1), S654Pfs*276 (n=1), S2483C (n=1) |
| NSD1 | by frequency | SNV / small indel | 60 / 515 | 11.65% | 11.55% | 2 / 2 | 5.3–11.65% | R788* (n=2), I1873Kfs*18 (n=2), S707* (n=1), P1665L (n=1), E1575* (n=1) |
| CASP8 | by frequency | SNV / small indel | 55 / 515 | 10.68% | 10.57% | 2 / 2 | 3.97–10.68% | Q524* (n=4), X243_splice (n=3), R494* (n=3), R472* (n=3), R127* (n=2) |
| HUWE1 | by frequency | SNV / small indel | 50 / 515 | 9.71% | 9.39% | 1 / 2 | 9.71–9.71% | E3771K (n=2), E4177K (n=2), K4204del (n=2), H4339Y (n=1), G4370D (n=1) |
| FAM135B | by frequency | SNV / small indel | 50 / 515 | 9.71% | 9.2% | 1 / 2 | 9.71–9.71% | A418E (n=1), E1105Q (n=1), P549L (n=1), E289K (n=1), H1337Y (n=1) |
| SI | by frequency | amplification | 50 / 517 | 9.67% mutation 9.51% | 9.39% | 1 / 2 | 9.51–9.51% | I1343L (n=1), Y1063C (n=1), Q175E (n=1), Q1463H (n=1), I1271Nfs*3 (n=1) |
| RELN | by frequency | SNV / small indel | 47 / 515 | 9.13% | 8.61% | 1 / 2 | 9.13–9.13% | M944K (n=1), V2679L (n=1), V2092M (n=1), G2273D (n=1), D2941V (n=1) |
| PCDH15 | by frequency | SNV / small indel | 44 / 515 | 8.54% | 8.41% | 1 / 2 | 8.54–8.54% | X198_splice (n=1), R1292L (n=1), G794A (n=1), R598T (n=1), I385Tfs*32 (n=1) |
| PCDH11X | by frequency | SNV / small indel | 39 / 515 | 7.57% | 6.85% | 1 / 2 | 7.57–7.57% | A23T (n=2), D458H (n=1), S630* (n=1), M34I (n=1), A942D (n=1) |
| LAMA2 | by frequency | SNV / small indel | 39 / 515 | 7.57% | 7.05% | 1 / 2 | 7.57–7.57% | R2231S (n=1), G542V (n=1), E1637Q (n=1), P63H (n=1), E640* (n=1) |
| HERC2 | by frequency | SNV / small indel | 38 / 515 | 7.38% | 7.05% | 1 / 2 | 7.38–7.38% | I4701T (n=1), R3836W (n=1), R3671* (n=1), G2229* (n=1), T3325P (n=1) |
| NAV3 | by frequency | SNV / small indel | 37 / 515 | 7.18% | 7.05% | 1 / 2 | 7.18–7.18% | K549E (n=1), R855Q (n=1), R832G (n=1), G1148C (n=1), R1529G (n=1) |
| KMT2C | by frequency | SNV / small indel | 37 / 515 | 7.18% | 6.85% | 2 / 2 | 7.18–9.93% | X395_splice (n=2), G1020V (n=1), R196Kfs*9 (n=1), S1867T (n=1), R1698S (n=1) |
| EP300 | by frequency | SNV / small indel | 37 / 515 | 7.18% | 7.05% | 2 / 2 | 4.64–7.18% | D1399N (n=5), C1164Y (n=2), X1224_splice (n=2), E1514K (n=2), N2379H (n=1) |
| UNC13C | by frequency | SNV / small indel | 36 / 515 | 6.99% | 6.85% | 1 / 2 | 6.99–6.99% | Q1248K (n=1), Q817K (n=1), R182Q (n=1), Q958* (n=1), K189N (n=1) |
| VPS13B | by frequency | SNV / small indel | 34 / 515 | 6.6% | 6.07% | 1 / 2 | 6.6–6.6% | X403_splice (n=1), E1879K (n=1), Q3213H (n=1), H1446L (n=1), T1561S (n=1) |
| PRDM9 | by frequency | SNV / small indel | 34 / 515 | 6.6% | 6.26% | 1 / 2 | 6.6–6.6% | R77Q (n=2), G588R (n=1), V889F (n=1), Q400E (n=1), E193* (n=1) |
| PKHD1 | by frequency | SNV / small indel | 33 / 515 | 6.41% | 6.07% | 1 / 2 | 6.41–6.41% | S3977F (n=1), I1120T (n=1), W1248* (n=1), T777M (n=1), D170N (n=1) |
| PEG3 | by frequency | SNV / small indel | 33 / 515 | 6.41% | 5.87% | 1 / 2 | 6.41–6.41% | S792R (n=1), R651G (n=1), D1069Y (n=1), R889S (n=1), G1424R (n=1) |
| NPAP1 | by frequency | SNV / small indel | 33 / 515 | 6.41% | 5.87% | 1 / 2 | 6.41–6.41% | S528F (n=1), L437I (n=1), A134V (n=1), P119L (n=1), V114L (n=1) |
| FMN2 | by frequency | SNV / small indel | 33 / 515 | 6.41% | 6.07% | 1 / 2 | 6.41–6.41% | M1488I (n=1), K1648N (n=1), R94C (n=1), N1505I (n=1), S428L (n=1) |
| FBXW7 | by frequency | SNV / small indel | 33 / 515 | 6.41% | 6.46% | 2 / 2 | 2.65–6.41% | R505G (n=6), R479Q (n=3), R543G (n=2), A502V (n=1), R465C (n=1) |
| FAT2 | by frequency | SNV / small indel | 32 / 515 | 6.21% | 5.87% | 1 / 2 | 6.21–6.21% | F1838L (n=1), Q3697* (n=1), P1884H (n=1), N2102Kfs*35 (n=1), D1272G (n=1) |
| AKAP9 | by frequency | SNV / small indel | 32 / 515 | 6.21% | 5.87% | 1 / 2 | 6.21–6.21% | D3631H (n=1), E1344Q (n=1), Q413R (n=1), R3787* (n=1), E2670Q (n=1) |
| THSD7A | by frequency | SNV / small indel | 31 / 515 | 6.02% | 5.68% | 1 / 2 | 6.02–6.02% | R1046C (n=2), C728F (n=2), X1306_splice (n=2), V1571A (n=1), D1654V (n=1) |
| MROH2B | by frequency | SNV / small indel | 31 / 515 | 6.02% | 5.48% | 1 / 2 | 6.02–6.02% | G532R (n=1), W896L (n=1), Q723E (n=1), T1173I (n=1), R223W (n=1) |
| LRP1 | by frequency | SNV / small indel | 31 / 515 | 6.02% | 5.87% | 1 / 2 | 6.02–6.02% | N615S (n=1), V268M (n=1), S3955L (n=1), V1959L (n=1), G1467D (n=1) |
| CDH10 | by frequency | SNV / small indel | 31 / 515 | 6.02% | 5.68% | 1 / 2 | 6.02–6.02% | D481V (n=1), T495N (n=1), R449L (n=1), P270A (n=1), T298A (n=1) |
| ASPM | by frequency | SNV / small indel | 31 / 515 | 6.02% | 6.07% | 1 / 2 | 6.02–6.02% | E17D (n=1), R1765T (n=1), Q1800H (n=1), V571L (n=1), R1405H (n=1) |
| SCN1A | by frequency | SNV / small indel | 30 / 515 | 5.83% | 5.68% | 1 / 2 | 5.83–5.83% | G1470V (n=1), V1582A (n=1), F1718L (n=1), T1247M (n=1), H698Q (n=1) |
| RNF213 | by frequency | SNV / small indel | 30 / 515 | 5.83% | 5.68% | 1 / 2 | 5.83–5.83% | E4152K (n=1), M2419I (n=1), Q2176K (n=1), Q5080E (n=1), E3844K (n=1) |
| MDN1 | by frequency | SNV / small indel | 30 / 515 | 5.83% | 5.48% | 1 / 2 | 5.83–5.83% | R2957S (n=1), E1802V (n=1), E1542K (n=1), K717T (n=1), V4171I (n=1) |
| DCHS2 | by frequency | SNV / small indel | 30 / 515 | 5.83% | 5.28% | 1 / 2 | 5.83–5.83% | A1138S (n=1), A2536S (n=1), I487L (n=1), Y2860Tfs*10 (n=1), K381* (n=1) |
| CREBBP | by frequency | SNV / small indel | 30 / 515 | 5.83% | 5.28% | 2 / 2 | 5.3–5.83% | R1446C (n=2), L1556V (n=1), Q355Tfs*12 (n=1), E1023K (n=1), L1251M (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 |
|---|---|---|---|---|---|---|---|---|---|
| Head and Neck Squamous Cell Carcinoma (TCGA, PanCancer Atlas) reference | hnsc_tcga_pan_can_atlas_2018 | 515 observed | 515 / 523 | exome or genome | WES (515) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 4 | 99 |
| Recurrent and Metastatic Head & Neck Cancer (MSK, JAMA Oncol 2016) | hnc_mskcc_2016 | 151 observed | 151 / 151 | targeted panel | IMPACT410 (151) | hg19 | SNV, small indel, amplification, deep deletion, structural variant (profile present, not read) | 1 | 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 |
|---|---|---|---|---|---|---|
| CDKN2A | deep deletion | 159 | 517 | 30.75% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| CCND1 | amplification | 120 | 517 | 23.21% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| PIK3CA | amplification | 81 | 517 | 15.67% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| EGFR | amplification | 54 | 517 | 10.44% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| SI | amplification | 50 | 517 | 9.67% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| FAM135B | amplification | 37 | 517 | 7.16% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| FAT1 | deep deletion | 35 | 517 | 6.77% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| CDKN2A | deep deletion | 10 | 151 | 6.62% | hnc_mskcc_2016 | hnc_mskcc_2016_gistic |
| CCND1 | amplification | 8 | 151 | 5.3% | hnc_mskcc_2016 | hnc_mskcc_2016_gistic |
| TERT | amplification | 26 | 517 | 5.03% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| EGFR | amplification | 7 | 151 | 4.64% | hnc_mskcc_2016 | hnc_mskcc_2016_gistic |
| CD274 | amplification | 23 | 517 | 4.45% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| VPS13B | amplification | 21 | 517 | 4.06% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| AKAP9 | amplification | 20 | 517 | 3.87% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| MROH2B | amplification | 20 | 517 | 3.87% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| NFE2L2 | amplification | 17 | 517 | 3.29% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| RELN | amplification | 16 | 517 | 3.09% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| PRDM9 | amplification | 15 | 517 | 2.9% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| CDH10 | amplification | 15 | 517 | 2.9% | hnsc_tcga_pan_can_atlas_2018 | hnsc_tcga_pan_can_atlas_2018_gistic |
| PIK3CA | amplification | 4 | 151 | 2.65% | hnc_mskcc_2016 | hnc_mskcc_2016_gistic |
| CD274 | amplification | 4 | 151 | 2.65% | hnc_mskcc_2016 | hnc_mskcc_2016_gistic |
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) |
|---|---|---|
| TP53 | 40.4–68.54% | hnsc_tcga_pan_can_atlas_2018: 353/515 (68.54%) · hnc_mskcc_2016: 61/151 (40.4%) |
| CDKN2A | 14.57–20.39% | hnsc_tcga_pan_can_atlas_2018: 105/515 (20.39%) · hnc_mskcc_2016: 22/151 (14.57%) |
| PIK3CA | 12.58–17.48% | hnsc_tcga_pan_can_atlas_2018: 90/515 (17.48%) · hnc_mskcc_2016: 19/151 (12.58%) |
| EGFR | 2.52–2.65% | hnsc_tcga_pan_can_atlas_2018: 13/515 (2.52%) · hnc_mskcc_2016: 4/151 (2.65%) |
| CD274 | 0.0–0.39% | hnsc_tcga_pan_can_atlas_2018: 2/515 (0.39%) · hnc_mskcc_2016: 0/151 (0.0%) |
| PDCD1 | 0.39–0.66% | hnsc_tcga_pan_can_atlas_2018: 2/515 (0.39%) · hnc_mskcc_2016: 1/151 (0.66%) |
| NOTCH1 | 17.09–21.85% | hnsc_tcga_pan_can_atlas_2018: 88/515 (17.09%) · hnc_mskcc_2016: 33/151 (21.85%) |
| FAT1 | 14.57–21.55% | hnsc_tcga_pan_can_atlas_2018: 111/515 (21.55%) · hnc_mskcc_2016: 22/151 (14.57%) |
| CCND1 | 0.39–0.66% | hnsc_tcga_pan_can_atlas_2018: 2/515 (0.39%) · hnc_mskcc_2016: 1/151 (0.66%) |
| HRAS | 5.96–6.02% | hnsc_tcga_pan_can_atlas_2018: 31/515 (6.02%) · hnc_mskcc_2016: 9/151 (5.96%) |
| NFE2L2 | 5.3–5.44% | hnsc_tcga_pan_can_atlas_2018: 28/515 (5.44%) · hnc_mskcc_2016: 8/151 (5.3%) |
| TERT | 0.58–1.32% | hnsc_tcga_pan_can_atlas_2018: 3/515 (0.58%) · hnc_mskcc_2016: 2/151 (1.32%) |
| KMT2D | 14.95–16.56% | hnsc_tcga_pan_can_atlas_2018: 77/515 (14.95%) · hnc_mskcc_2016: 25/151 (16.56%) |
| NSD1 | 5.3–11.65% | hnsc_tcga_pan_can_atlas_2018: 60/515 (11.65%) · hnc_mskcc_2016: 8/151 (5.3%) |
| CASP8 | 3.97–10.68% | hnsc_tcga_pan_can_atlas_2018: 55/515 (10.68%) · hnc_mskcc_2016: 6/151 (3.97%) |
| HUWE1 | 9.71–9.71% | hnsc_tcga_pan_can_atlas_2018: 50/515 (9.71%) · hnc_mskcc_2016: not assayed |
| FAM135B | 9.71–9.71% | hnsc_tcga_pan_can_atlas_2018: 50/515 (9.71%) · hnc_mskcc_2016: not assayed |
| SI | 9.51–9.51% | hnsc_tcga_pan_can_atlas_2018: 49/515 (9.51%) · hnc_mskcc_2016: not assayed |
| RELN | 9.13–9.13% | hnsc_tcga_pan_can_atlas_2018: 47/515 (9.13%) · hnc_mskcc_2016: not assayed |
| PCDH15 | 8.54–8.54% | hnsc_tcga_pan_can_atlas_2018: 44/515 (8.54%) · hnc_mskcc_2016: not assayed |
| PCDH11X | 7.57–7.57% | hnsc_tcga_pan_can_atlas_2018: 39/515 (7.57%) · hnc_mskcc_2016: not assayed |
| LAMA2 | 7.57–7.57% | hnsc_tcga_pan_can_atlas_2018: 39/515 (7.57%) · hnc_mskcc_2016: not assayed |
| HERC2 | 7.38–7.38% | hnsc_tcga_pan_can_atlas_2018: 38/515 (7.38%) · hnc_mskcc_2016: not assayed |
| NAV3 | 7.18–7.18% | hnsc_tcga_pan_can_atlas_2018: 37/515 (7.18%) · hnc_mskcc_2016: not assayed |
| KMT2C | 7.18–9.93% | hnsc_tcga_pan_can_atlas_2018: 37/515 (7.18%) · hnc_mskcc_2016: 15/151 (9.93%) |
| EP300 | 4.64–7.18% | hnsc_tcga_pan_can_atlas_2018: 37/515 (7.18%) · hnc_mskcc_2016: 7/151 (4.64%) |
| UNC13C | 6.99–6.99% | hnsc_tcga_pan_can_atlas_2018: 36/515 (6.99%) · hnc_mskcc_2016: not assayed |
| VPS13B | 6.6–6.6% | hnsc_tcga_pan_can_atlas_2018: 34/515 (6.6%) · hnc_mskcc_2016: not assayed |
| PRDM9 | 6.6–6.6% | hnsc_tcga_pan_can_atlas_2018: 34/515 (6.6%) · hnc_mskcc_2016: not assayed |
| PKHD1 | 6.41–6.41% | hnsc_tcga_pan_can_atlas_2018: 33/515 (6.41%) · hnc_mskcc_2016: not assayed |
| PEG3 | 6.41–6.41% | hnsc_tcga_pan_can_atlas_2018: 33/515 (6.41%) · hnc_mskcc_2016: not assayed |
| NPAP1 | 6.41–6.41% | hnsc_tcga_pan_can_atlas_2018: 33/515 (6.41%) · hnc_mskcc_2016: not assayed |
| FMN2 | 6.41–6.41% | hnsc_tcga_pan_can_atlas_2018: 33/515 (6.41%) · hnc_mskcc_2016: not assayed |
| FBXW7 | 2.65–6.41% | hnsc_tcga_pan_can_atlas_2018: 33/515 (6.41%) · hnc_mskcc_2016: 4/151 (2.65%) |
| FAT2 | 6.21–6.21% | hnsc_tcga_pan_can_atlas_2018: 32/515 (6.21%) · hnc_mskcc_2016: not assayed |
| AKAP9 | 6.21–6.21% | hnsc_tcga_pan_can_atlas_2018: 32/515 (6.21%) · hnc_mskcc_2016: not assayed |
| THSD7A | 6.02–6.02% | hnsc_tcga_pan_can_atlas_2018: 31/515 (6.02%) · hnc_mskcc_2016: not assayed |
| MROH2B | 6.02–6.02% | hnsc_tcga_pan_can_atlas_2018: 31/515 (6.02%) · hnc_mskcc_2016: not assayed |
| LRP1 | 6.02–6.02% | hnsc_tcga_pan_can_atlas_2018: 31/515 (6.02%) · hnc_mskcc_2016: not assayed |
| CDH10 | 6.02–6.02% | hnsc_tcga_pan_can_atlas_2018: 31/515 (6.02%) · hnc_mskcc_2016: not assayed |
| ASPM | 6.02–6.02% | hnsc_tcga_pan_can_atlas_2018: 31/515 (6.02%) · hnc_mskcc_2016: not assayed |
| SCN1A | 5.83–5.83% | hnsc_tcga_pan_can_atlas_2018: 30/515 (5.83%) · hnc_mskcc_2016: not assayed |
| RNF213 | 5.83–5.83% | hnsc_tcga_pan_can_atlas_2018: 30/515 (5.83%) · hnc_mskcc_2016: not assayed |
| MDN1 | 5.83–5.83% | hnsc_tcga_pan_can_atlas_2018: 30/515 (5.83%) · hnc_mskcc_2016: not assayed |
| DCHS2 | 5.83–5.83% | hnsc_tcga_pan_can_atlas_2018: 30/515 (5.83%) · hnc_mskcc_2016: not assayed |
| CREBBP | 5.3–5.83% | hnsc_tcga_pan_can_atlas_2018: 30/515 (5.83%) · hnc_mskcc_2016: 8/151 (5.3%) |
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/head-and-neck-cancer.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.