Skip to main content

Table 3 Genomic regions associated with specific clinical features in HNSCC patients

From: Identification of genomic copy number variations associated with specific clinical features of head and neck cancer

Stage I&II vs III&IV
  Locus # OR (95% CI) p(Chi2)a Log2 ratio range CNV sizesc # of genes
gain 1 chr6:
38,729,522–41,698,277
3/11 vs. 0/50 0.084 0.54–0.62 18.6–19.5 Mb 35
gain 2 chr8:
46,942,986–54,391,986
4/10 vs, 2/48 0.104 (0.017–0.649) 0.0232 0.29–0.9 1.56–146 Mb 20
gain 3 chr8:
49,091,330–50,447,801
6/8 vs. 3/47 0.085 (0.018–0.411) 0.0021 0.29–0.9 1.56–146 Mb 5
Histological grade 1 vs. grade 2 & 3
  Locus # OR (95% CI) p(Chi2)a Log2 ratio range CNV sizesc # of genes
gain 4 chr8:
122,449,344–123,538,355
5/7 vs. 6/46 5.476 (1.312–22.851) 0.0385 0.28–0.58 1.0–145 Mb 2
loss 1b chr3:
93,979–80,817,252
5/7 vs. 2/50; 4/8 vs. 3/49 17.86 (2.891–110.3)
8.167 (1.532–43.52)
0.0011–0.024 −0.64 – −0.26 1.4–93 Mb 647
loss 2 chr6:
85,683,523–86,925,006
2/10 vs. 0/52 0.0384 −0.7 – −0.26 1.24–40 Mb 6
loss 3 chr8:
221,641–32,847,282
3/9 vs. 1/51 17 (1.587–182.1) 0.0205 −0.64 – −0.26 6.8–43 Mb 309
Node lymph involvement vs. cases without affected lymph nodes
  Locus # OR (95% CI) p(Chi2)a Log2 ratio range CNV sizesc # of genes
gain 5 chr3:
147,963,947–148,708,961
9/33 vs. 0/22 0.0495 0.28–0.96 5.6–109 Mb 3
gain 6 chr3:
178,764,078–179,689,394
14/28 vs. 1/21 9.414 (1.141–77.65) 0.0349 0.27–0.96 5–109 Mb 13
gain 7 chr8:
108,460,956–109,567,888
3/39 vs. 7/15 0.165 (0.038–0.723) 0.0264 0.28–0.8 0.2–146 Mb 4
Cases treated with surgery vs. cases without surgical treatment
  Locus # OR (95% CI) p(Chi2)a Log2 ratio range CNV sizesc # of genes
gain 8 chr7:
92,828,329–105,027,875
2/42 vs. 5/15 0.143 (0.025–0.816) 0.0457 0.35–0.83 21–78 Mb 196
gain 9 chr20:
33,690,620–34,021,768
0/44 vs. 3/17 0.0462 0.35–0.67 33-34 Mb 9
  1. adegree of freedom = 1
  2. bvalues in categories # and OR correspond to the p(Chi2) values which are the lower and upper boundary of observed statistical significance in this region; values in categories Locus, Log2 ratio range and CNV size are range boundaries that do not correspond to the displayed statistical data for the entry loss1
  3. ccolumn CNV sizes displayes the range of sizes of CNVs that include the region of each particular entry