Table 2 Peaks of homozygous deletions over established tumour suppressors and candidate tumour suppressors
From: Pan-cancer analysis of homozygous deletions in primary tumours uncovers rare tumour suppressors
Peak region | # of HDs | p-value (q-value) | Tumour suppressor |
|---|---|---|---|
Known tumour suppressors | |||
chr1:51.58–53.53 | 4 | 4.16 × 10−2 (7.42 × 10−2) | CDKN2C |
chr3:10.18–10.20 | 6 | 0.229 (0.293) | FANCD2/VHL |
chr4:187.75–187.90 | 4 | 2.57 × 10−5 (2.82 × 10−4) | FAT1 |
chr9:22.02–22.02 | 108 | 1.30 × 10−3 (4.38 × 10−3) | CDKN2A(/CDKN2B) a |
chr10:70.05–70.95 | 8 | 7.37 × 10−5 (6.09 × 10−4) | TET1 |
chr10:89.74–89.83 | 16 | 6.05 × 10−9 (5.51 × 10−7) | PTEN |
chr11:101.95–102.05 | 6 | 4.87 × 10−4 (1.85 × 10−3) | BIRC3(/BIRC2) a |
chr13:32.92–33.05 | 4 | 3.18 × 10−8 (1.45 × 10−6) | BRCA2 |
chr13:49.04–49.09 | 23 | 1.52 × 10−7 (4.61 × 10−6) | RB1 |
chr16:50.72–50.94 | 5 | 2.00 × 10−3 (6.11 × 10−3) | CYLD |
chr16:68.64–69.95 | 6 | 9.46 × 10−3 (2.39 × 10−2) | CDH1 |
chr17:7.58–7.58 | 4 | 2.08 × 10−2 (4.21 × 10−2) | TP53 |
chr17:11.96–12.09 | 6 | 3.78 × 10−3 (1.07 × 10−2) | MAP2K4 |
chr17:29.55–29.83 | 4 | 2.02 × 10−3 (6.11 × 10−3) | NF1 |
chr22:24.19–24.48 | 6 | 3.29 × 10−4 (1.50 × 10−3) | SMARCB1 |
Candidate tumour suppressors | |||
chr1:15.90–15.92 | 7 | 4.39 × 10−4 (1.74 × 10−3) | CASP9 |
chr1:17.58–17.63 | 4 | 1.99 × 10−4 (1.16 × 10−3) | ARHGEF10L |
chr3:185.44–185.53 | 4 | 1.85 × 10−6 (3.37 × 10−5) | IGF2BP2 |
chr4:39.08–39.15 | 12 | 8.87 × 10−4 (3.23 × 10−3) | N4BP2 |
chr4:83.68–83.68 | 4 | 1.04 × 10−6 (2.36 × 10−5) | HELQ/FAM175A |
chr4:185.60–185.65 | 4 | 2.43 × 10−4 (1.16 × 10−3) | CASP3 |
chr4:189.47–190.50 | 5 | 1.04 × 10−2 (2.56 × 10−2) | LINC01060 |
chr5:58.41–58.41 | 4 | 4.00 × 10−4 (1.66 × 10−3) | PDE4D b |
chr5:68.40–68.69 | 6 | 9.32 × 10−4 (3.26 × 10−3) | RAD17 |
chr8:1.77–1.94 | 8 | 4.68 × 10−6 (7.09 × 10−5) | ARHGEF10 |
chr8:29.97–29.98 | 4 | 1.63 × 10−2 (3.72 × 10−2) | LEPROTL1 |
chr9:9.42–9.64 | 5 | 7.36 × 10−3 (1.97 × 10−2) | PTPRD |
chr10:76.72–76.81 | 5 | 3.59 × 10−5 (3.27 × 10−4) | KAT6B |
chr10:93.99–94.03 | 5 | 1.91 × 10−4 (1.16 × 10−3) | CPEB3 |
chr10:131.42–131.49 | 5 | 1.74 × 10−4 (1.16 × 10−3) | MGMT |
chr12:32.15–32.24 | 5 | 1.29 × 10−2 (3.01 × 10−2) | KIAA1551 |
chr12:95.88–96.27 | 4 | 2.01 × 10−2 (4.16 × 10−2) | USP44 |
chr12:122.30–122.37 | 6 | 2.21 × 10−5 (2.82 × 10−4) | SETD1B |
chr13:85.51–85.66 | 4 | 1.81 × 10−2 (3.97 × 10−2) | LINC00375 |
chr13:92.45–92.45 | 10 | 2.16 × 10−4 (1.16 × 10−3) | GPC5 |
chr13:95.39–95.46 | 4 | 2.35 × 10−4 (1.16 × 10−3) | SOX21 |
chr14:35.09–35.32 | 6 | 1.94 × 10−2 (4.11 × 10−2) | BAZ1A |
chr14:74.07–74.55 | 4 | 2.55 × 10−2 (4.95 × 10−2) | MIDEAS |
chr16:74.65–74.69 | 5 | 4.65 × 10−3 (1.28 × 10−2) | RFWD3 |
chr16:79.80–79.80 | 4 | 7.58 × 10−3 (1.97 × 10−2) | MAFTRR |
chr19:28.14–28.15 | 6 | 1.18 × 10−2 (2.83 × 10−2) | LINC00662 |
