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Table 1 Statistically significant hits from NGS of examined NMSC patients (n = 33)

From: Coordinated expression and genetic polymorphisms in Grainyhead-like genes in human non-melanoma skin cancers

Chr: Gene

dbSNP ID location

allele

AF_OBS

AF_EUR

(1000G)

p-value*

OR, (95%CI), p-value**

Chr1: GRHL3

rs55927162

intergenic

(dist = 4635)***

T/A

0.6667

0.21

P < 0.00001

(χ2)

(A) OR = 7.53

(95%CI:4.38–12.94)

P < 0.0001

rs56256719

intergenic

(dist = 4627)***

T/A

0.697

0.24

P < 0.00001

(χ2)

(A) OR = 7.15

(95%CI:4.14–12.44)

P < 0.0001

rs151171718

intronic

A/T

0.0455

0.0013

P < 0.05

(F)

(T) OR = 36.05

(95%CI:3.69–351.64)

P = 0.0020

rs141193530

exon 11 (P455A)

C/G

0.0758

0.004

P < 0.00001

(χ2)

(G) OR = 20.63

(95%CI:4.81–88.38)

P < 0.0001

rs151326764

exon 16 (R573H)

G/A

0.0303

0.0026

P < 0.01

(F)

(A) OR = 11.81

(95%CI:1.63–85.26)

P = 0.0143

Chr8: GRHL2

rs548650

intronic

G/A

0.0909

0.02

P = 0.000039

(χ2)

(A) OR = 5.73

(95%CI:2.10–15.62)

P = 0.0006

  1. AF_OBS observed allele frequency, AF_EUR expected allele frequency for general European population (1000Genomes)
  2. *p-value of association calculated with χ2-test (χ2) or Fisher’s exact test (F) for less frequent alleles
  3. **OR odds ratio for haplotype, 95%CI 95% confidence interval, calculated according to [25]
  4. ***distance upstream from transcription start site
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BMC Cancer

ISSN: 1471-2407

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