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

Locus

#

OR (95% CI)

p(Chi2)^a

Log2 ratio range

CNV sizes^c

# 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

Locus

#

OR (95% CI)

p(Chi2)^a

Log2 ratio range

CNV sizes^c

# 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 1^b

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

Locus

#

OR (95% CI)

p(Chi2)^a

Log2 ratio range

CNV sizes^c

# 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

Locus

#

OR (95% CI)

p(Chi2)^a

Log2 ratio range

CNV sizes^c

# 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